404
+ +Page not found
+ + +
'+ escapeHtml(title) + '
' + escapeHtml(summary) +'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ developers guide coming soon ...
+Code structure:
+Modules:
+-
+
- ClayCode.builder +
- ClayCode.siminp +
- ClayCode.config +
- ClayCode.data +
- ClayCode.tests +
Environemnt set up files:
+-
+
- setup.py +
- ... +
The code structure is as follows:
+ClayCode
+│
+├── builder
+│ ├── config
+│ └── tests
+│ └── data
+├── config
+├── core
+├── data
+│ ├── FF
+│ │ ├── ClayFF_Fe.ff
+│ ├── MDP
+│ ├── UCS
+│ │ ├── D11
+│ │ ├── D21
+│ │ └── LDH31
+│ └── user
+└── siminp
+
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/img/favicon.ico b/img/favicon.ico
new file mode 100644
index 00000000..e85006a3
Binary files /dev/null and b/img/favicon.ico differ
diff --git a/imt/index.html b/imt/index.html
new file mode 100644
index 00000000..ace4f0ef
--- /dev/null
+++ b/imt/index.html
@@ -0,0 +1,190 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ imt.md
+Illite IMt-1 and IMt-2
+ORIGIN: Silver Hill, Montana, USA +CHEMICAL COMPOSITION (%): SiO2: 49.3 Al2O3: 24.25, TiO2: 0.55, Fe2O3:7.32, FeO: 0.55, MnO: 0.03, MgO: 2.56, CaO: 0.43, Na2O: 0, K2O: 7.83, P2O5: 0.08, LOI: 8.02
+STRUCTURE: (Mg.09 Ca.06 K1.37)[Al2.69 Fe(III).76 Fe(II).06 Mntr Mg.43 Ti.06][Si6.77 Al1.23]O20(OH)4, Octahedral charge:-.44, Tetrahedral charge:-1.23, Interlayer charge:-1.68, Unbalanced charge:0.00
+The supplied exp_clay.csv file and contains clay structures corresponding to the Source Clays listed under "Physical and Chemical Data of Source Clays" clays.org.
NO interlayer water
+ClayCode builder -f path/to/input_Clay.yaml
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/index.html b/index.html
new file mode 100644
index 00000000..5255775b
--- /dev/null
+++ b/index.html
@@ -0,0 +1,210 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/js/html5shiv.min.js b/js/html5shiv.min.js
new file mode 100644
index 00000000..1a01c94b
--- /dev/null
+++ b/js/html5shiv.min.js
@@ -0,0 +1,4 @@
+/**
+* @preserve HTML5 Shiv 3.7.3 | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
+*/
+!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=t.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=t.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),t.elements=c+" "+a,j(b)}function f(a){var b=s[a[q]];return b||(b={},r++,a[q]=r,s[r]=b),b}function g(a,c,d){if(c||(c=b),l)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():p.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||o.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),l)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return t.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(t,b.frag)}function j(a){a||(a=b);var d=f(a);return!t.shivCSS||k||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),l||i(a,d),a}var k,l,m="3.7.3",n=a.html5||{},o=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,p=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,q="_html5shiv",r=0,s={};!function(){try{var a=b.createElement("a");a.innerHTML="
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 
ClayCode generates clay mineral structures based upon their natural partially ocupied unit cell compositions and assigns ClayFF forecefield parameters, generating all the input files ready for simulation with Gromacs software.
+Here
+ + + ++
On GitHub
+ + + +
+
Report bugs and give sugestions for future improvements and new features via issues
Contribute via branches and pull requests 
+
Claycode is published under the MIT License 
ClayCode is developed by Hannah Pollak, Matteo Degiacomi and Valentina Erastova, University of Edinburgh, 2023
+Please CITE us: HP, MTD, VE "ClayCode: setting up clay structures from simulation in Gromacs", DOI: XXX
+ +
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Kaolinite
+NOTE treatment of the Ti in the structure and what is the origin of the Ti, why to ignore
+Kaolin KGa-1(KGa-1b), (low-defect)
+ORIGIN: Tuscaloosa formation? (Cretaceous?) (stratigraphy uncertain) +County of Washington, State of Georgia, USA +LOCATION: 32°58′ N-82°53′ W approximately, topographic map Tabernacle, Georgia N 3252.5-W 8252.5/7.5, Collected from face of Coss-Hodges pit, October 3,1972. +CHEMICAL COMPOSITION (%): SiO2: 44.2, Al2O3: 39.7, TiO2: 1.39, Fe2O3: 0.13,FeO: 0.08, MnO: 0.002, MgO: 0.03, CaO: n.d., Na2O: 0.013, K2O: 0.05, F:0.013,P2O5: 0.034, Loss on heating: -550°C: 12.6; 550-1000°C: 1.18. +CATION EXCHANGE CAPACITY (CEC): 2.0 meq/100g +SURFACE AREA: N2 area: 10.05 +/- 0.02 m2 /g +THERMAL ANALYSIS: DTA: endotherm at 630oC, exotherm at 1015oC, TG: dehydroxylation weight loss 13.11% (theory 14%) indicating less than 7% impurities. +INFRARED SPECTROSCOPY: Typical spectrum for well crystallized kaolinite,however not as well crystallized as a typical China clay from Cornwall,as judged from the intensity of the 3669 cm-1 band. Splitting of the 1100cm- 1 band is due to the presence of coarse crystals.
+STRUCTURE:(Mg.02 Ca.01 Na.01 K.01)[Al3.86 Fe(III).02 Mntr Ti.11][Si3.83Al.17] O10(OH)8, Octahedral charge:.11, Tetrahedral charge:-.17,Interlayer charge:-.06, Unbalanced charge:0.00
+The supplied exp_clay.csv file and contains clay structures corresponding to the Source Clays listed under "Physical and Chemical Data of Source Clays" clays.org.
Removing invalid atom types:
+
+ sheet - at-type: occupancy
+ O - Mn : 0.00, O - Ti : 0.11
+
+Could not guess Ti charge.
+Enter Ti charge value: (or exit with 'e')
+
+++4
+
Assuming Ti charge of 4.
+
+Getting sheet occupancies:
+ Found 'O' sheet occupancies of 3.8800/4.0000 (-0.1200)
+ Found 'T' sheet occupancies of 4.0000/4.0000 (+0.0000)
+
+Adjusting values to match expected occupancies:
+ old occupancies -> new occupancies per unit cell:
+ sheet - atom type : occupancies (difference)
+ 'O' - 'ao' : 3.8600 -> 3.9800 (+0.1200)
+
+Splitting total iron content (0.0200) to match charge.
+
+ Will use the following target composition:
+ 'T' - 'at' : 0.1700
+ 'T' - 'st' : 3.8300
+ 'O' - 'ao' : 3.9800
+ 'O' - 'feo' : 0.0200
+
+Writing new target clay composition to 'KGa-1_exp_df.csv'
+
+ClayCode builder -f path/to/input_Clay.yaml
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/ldh/index.html b/ldh/index.html
new file mode 100644
index 00000000..d01c6f2f
--- /dev/null
+++ b/ldh/index.html
@@ -0,0 +1,185 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ldh example
+3:1 Al-Mg LDH
+ClayCode builder -f path/to/input_Clay.yaml
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/mmt/index.html b/mmt/index.html
new file mode 100644
index 00000000..55c3ccc1
--- /dev/null
+++ b/mmt/index.html
@@ -0,0 +1,357 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Montmorillonite
+Clay composition
+Wyoming montmorillonite is widely studied and used smectite. It is available for purchase from Source Clays of The Clay Minerals Society, and is identified as SWy-1, SWy-2 or SWy-3, depending on the batch.
+This is a well-characterised clay with the structure listed under "Physical and Chemical Data of Source Clays" at the clays.org, as:
+Swy-1: ,
with unbalanced charge of 0.05.
Ti is often identified during clay analysis, but is attributed to the TiO inclusions, therefore, we will omit it in the input. Meanwhile, ClayFF force field does not have parameters for Mn, which is shown at the level of detection and so we will also omit this entry.
+The provided clay_comp.csv file contains an entry SWy-1 which corresponds to this Wyoming montmorillonite clay.
Construction of the model
+Let's examine the Swy1.yaml, which is provided in the Tutorial directory. This file contains all of the information necessary to build the clay model.
Please consult YAML for the parameter description
+Required parameters
+
+# =============================================================================
+# General specifications for clay model construction
+# =============================================================================
+
+# =============================================================================
+# Required Parameters
+# =============================================================================
+
+OUTPATH: .
+
+# name of system to call according to CLAY_COMP (exp_clay.csv)
+# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'LDH31' 'IMt-1' 'KGa-1'
+SYSNAME: SWy-1
+
+# specify whether new clay model should be constructed:
+# new - a new clay model is constructed
+# load - sheet coordinates or unit cell sequences are loaded from existent .gro or .npy files
+# load: [X, Y]
+# with X - 'np' or 'gro', Y - '.npy' or '.gro' filename
+# False - no clay model is constructed
+BUILD: new
+
+# name of .csv file with target stoichiometry
+CLAY_COMP: exp_clay.csv
+
+# clay type available options in 'clay_units' directory:
+# Dioctahedral 2:1 - D21
+# Trioctahedral 2:1 - T21
+# Dioctahedral 1:1 - D11
+# Trioctahedral 1:1 - T11
+# layered double hydroxide 3:1 - L31
+# layered double hydroxide 2:1 - L21
+# Sepiolite - SEP
+
+CLAY_TYPE: D21
+
+
+# =============================================================================
+# Optional: Clay Sheet and Interlayer Specifications
+# =============================================================================
+
+# number of unit cells in x direction (Default 7)
+X_CELLS: 7
+
+# number of unit cells in y direction (Default 5)
+Y_CELLS: 5
+
+# number of unit cells in z direction (Default 3)
+N_SHEETS: 3
+
+# ----------------------------------------------------------------------------
+# Optional: Unit Cell Composition and Ratios input
+# if not given, these will be calculated from data in the CLAY_COMP .csv file
+# (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: [])
+# -----------------------------------------------------------------------------
+
+# required UCs to builder system as list
+# UC_INDEX_LIST: [1]
+
+# probability list of unit cells in system
+# p(tot): 1.00
+# UC_RATIOS_LIST: [1]
+
+# -----------------------------------------------------------------------------
+
+# interlayer solvent present or not (Default True)
+IL_SOLV: True
+
+# -----------------------------------------------------------------------------
+# Optional: Interlayer Ion Specification Options (comment the other options!)
+# (Default UC_WATERS: 20)
+# -----------------------------------------------------------------------------
+
+# 1. Number of water molecules that should be added per ion (ION_WATERS)
+# a. as ion species dictionary for hydration number
+# ION_WATERS: {'Ca': 12,
+# 'Na': 12
+# }
+
+# b. as ion species int for hydration number
+# ION_WATERS : 12
+
+# 3. OR per unit cell
+#UC_WATERS: 25
+
+# 4. OR for a target d-spacing value in A
+SPACING_WATERS: 20
+
+# =============================================================================
+# Optional: Simulation Box Specifications
+# =============================================================================
+
+# full simulation box height in A (Default 150.0)
+BOX_HEIGHT: 150.0
+
+# =============================================================================
+# Optional: Solvation and Bulk Ions Specifications
+# =============================================================================
+
+# Bulk solvent added or not (Default: True)
+BULK_SOLV: True
+
+# Ion species and concentration in mol/L name to add in bulk solvent
+# (Default: BULK_IONS:
+# Na: 0.1)
+
+BULK_IONS:
+ Na: 0.1
+ Cl: 0.05
+
+# =============================================================================
+# Optional: Simulation Runs Specifications
+# =============================================================================
+
+# Generate scripts and '.mdp' files for simulation runs.
+# Available options:
+# EM - energy minimisation
+# EQ - equilibration
+# D-SPACE - d-spacing equilibration
+# P - production
+# SIMINP: [EM, D-SPACE]
+
+# select where EM and EQ should be run (Default: False)
+# MDRUNS_REMOTE: False
+
+# -----------------------------------------------------------------------------
+# d-spacing equilibration options
+# -----------------------------------------------------------------------------
+
+# Target d-spacing in A
+# D_SPACE: 19.5
+
+# Water molecules to be removed at a time during d-spacing equilibration runs
+# REMOVE_STEPS: 1000
+
+# Absolute number of water molecules per interlayer space
+# SHEET_WAT: 2
+
+# Number of water molecules per unit cell
+# UC_WAT: 0.1
+
+# Percentage of water molecules from interlayer
+# PERCENT_WAT: 5
+
+# -----------------------------------------------------------------------------
+# bash alias for used GROMACS version
+# -----------------------------------------------------------------------------
+
+GMX: gmx
+
+run as
+ClayCode builder -f path/to/input_Clay.yaml
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/nont/index.html b/nont/index.html
new file mode 100644
index 00000000..ffc311ab
--- /dev/null
+++ b/nont/index.html
@@ -0,0 +1,433 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Nontronites
+In this Tutorial we look at the two South Australian nontronite clays, part of the Source Clays of The Clay Minerals Society. These are commonly known as NAu-1 or the Uley green nontronite and NAu-2 or Uley brown nontronite.
+Their structures are listed under "Physical and Chemical Data of Source Clays" at the clays.org, as:
+NAu-1:
+NAu-2: ,
+where indicates interlayer counter-balancing cationic charge.
Assigning iron distribution and valence
+Iron can be present as either Fe(II) or Fe(III) and found in both, the tetrahedral and the octahedral sheets, as well as a charge compensating cation in the interlayer space space. +Furthermore, in many samples, such as NAu-2, ferrihydrydes are adsorbed to clay surfaces.1 +While methods such as near-infrared (NIR), extended X-ray adsorption fine structures (EXAFS), Moessbauer spectroscopy, X-ray diffraction (XRD) and thermogravimetric analysis (TGA) have been used to determine the charge distributions of Fe in the sample,234 the exact composition of these nontronites remains matter of debate.
+Conventionally, when Al and Fe(III), are present in a structure, because of their larger ionic radius, Fe(III) is assigned complitely to the octahedral sheet. Only once all octahedral spaces are occupied by Fe(III), the structure is assumed to also have Fe(III) in tetrahedral positions. +However, this assignment is not necessarily correct and due to the detection limits of commonly used spectroscopic or chemical analysis techniques tetrahedral Fe(III) contents below 5% often remain undetected.3
+To this end, after a review of the literature, we use the structures identified by Gates et al2. We note that the octahedral occupancy fro NAu-2 is 3.93 instead of full 4. ClayCode will address this when generating the structure. Furthermore, we assign as counterbalancing ion to all the systems. Resulting structures are, therefore, as follows:
+NAu-1: +
+NAu-2: +
+Tutorial directory provides the clay_comp.csv file which contains the above clay structures.
+See CSV for details on this file.
| sheet | +element | +NAu-1-fe | +NAu-2-fe | +
|---|---|---|---|
| T | +Si | +6.98 | +7.55 | +
| T | +Al | +0.95 | +0.16 | +
| T | +Fe | +0.07 | +0.29 | +
| O | +Fe | +3.61 | +3.54 | +
| O | +Al | +0.36 | +0.34 | +
| O | +Mg | +0.04 | +0.05 | +
| I | +Ca | +0.525 | +0.36 | +
| I | +Na | +0 | +0 | +
| I | +Mg | +0 | +0 | +
| I | +K | +0 | +0 | +
| I | +Cl | +0 | +0 | +
| C | +T | +-1.02 | +-0.45 | +
| C | +O | +-0.03 | +-0.27 | +
| C | +tot | +-1.05 | +-0.72 | +
System specification
+We now create the system specification YAML file, which will contain the information necessary to build the clay structures of or interest.
+The files NAu-1.yaml and NAu-2.yaml are provided.
The first section contains general parameters that are required for the model construction.
+If the directives in the optional section are not given by the user, ClayCode will use default values.
# =============================================================================
+# General specifications for clay model construction
+# =============================================================================
+
+# =============================================================================
+# Required Parameters
+# =============================================================================
+
+OUTPATH: /path/to/output/directory
+# name of system
+SYSNAME: NAu-1-fe
+
+# name of CSV file with target stoichiometry
+CLAY_COMP: /path/to/clay_comp.csv
+
+# clay type available options in 'clay_units' directory:
+# Dioctahedral 2:1 - D21
+# Trioctahedral 2:1 - T21
+# Dioctahedral 1:1 - D11
+# Trioctahedral 1:1 - T11
+# layered double hydroxide 3:1 - L31
+# layered double hydroxide 2:1 - L21
+# Sepiolite - SEP
+
+CLAY_TYPE: D21
+
+
+# =============================================================================
+# Optional: Clay Sheet and Interlayer Specifications
+# =============================================================================
+
+# number of unit cells in x direction (Default 7)
+X_CELLS: 7
+
+# number of unit cells in y direction (Default 5)
+Y_CELLS: 5
+
+# number of unit cells in z direction (Default 3)
+N_SHEETS: 3
+
+# ----------------------------------------------------------------------------
+# Optional: Unit Cell Composition and Ratios input
+# if not given, these will be calculated from data in the CLAY_COMP CSV file
+# (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: [])
+# -----------------------------------------------------------------------------
+
+# required UCs to builder system as list
+# UC_INDEX_LIST: [1]
+
+# probability list of unit cells in system
+# p(tot) = 1.00
+# UC_RATIOS_LIST: [1]
+
+# -----------------------------------------------------------------------------
+
+# interlayer solvent present or not (Default True)
+IL_SOLV: True
+
+# -----------------------------------------------------------------------------
+# Optional: Interlayer Ion Specification Options (comment the other options!)
+# (Default UC_WATERS: 20)
+# -----------------------------------------------------------------------------
+
+# 1. Number of water molecules that should be added per ion (ION_WATERS)
+# a. as ion species dictionary for hydration number
+# ION_WATERS = {'Ca': 12,
+# 'Na': 12
+# }
+
+# b. as ion species int for hydration number
+# ION_WATERS = 12
+
+# 3. OR per unit cell
+UC_WATERS: 20
+
+# 4. OR for a target d-spacing value in A
+# SPACING_WATERS = 10.0
+
+# =============================================================================
+# Optional: Simulation Box Specifications
+# =============================================================================
+
+# full simulation box height in A (Default 150.0)
+BOX_HEIGHT: 150.0
+
+# =============================================================================
+# Optional: Solvation and Bulk Ions Specifications
+# =============================================================================
+
+# Bulk solvent added or not (Default: True)
+BULK_SOLV: True
+
+# Ion species and concentration in mol/L name to add in bulk solvent
+# (Default: BULK_IONS:
+# Na: 0.1
+# Cl: 0.1)
+
+BULK_IONS:
+ Na: 0.1
+ Cl: 0.1
+
+# -----------------------------------------------------------------------------
+# bash alias for used GROMACS version
+# -----------------------------------------------------------------------------
+
+GMX: gmx_mpi
+ClayCode builder -f path/to/input_Clay.yaml
+
+
+
+
+ +
-
+
-
+
Ray L. Frost, J. Theo Kloprogge, and Zhe Ding. The Garfield and Uley nontronites - An infrared spectroscopic comparison. Spectrochimica Acta - Part A Molecular and Biomolecular Spectroscopy, 58(9):1881–1894, 7 2002. doi:10.1016/S1386-1425(01)00638-2. ↩
+
+ -
+
W. P. Gates, P. G. Slade, A. Manceau, and B. Lanson. Site Occupancies by Iron in Nontronites. Clays and Clay Minerals, 50(2):223–239, 4 2002. doi:10.1346/000986002760832829. ↩↩
+
+ -
+
Fabien Baron, Sabine Petit, Martin Pentrák, Alain Decarreau, and Joseph W. Stucki. Revisiting the nontronite Mössbauer spectra. American Mineralogist, 102(7):1501–1515, 7 2017. doi:10.2138/am-2017-1501x. ↩↩
+
+ -
+
A. Decarreau and S. Petit. Fe 3+ /Al 3+ partitioning between tetrahedral and octahedral sites in dioctahedral smectites. Clay Minerals, 49(5):657–665, 12 2014. doi:10.1180/claymin.2014.049.5.03. ↩
+
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/output/index.html b/output/index.html
new file mode 100644
index 00000000..5c01b9fe
--- /dev/null
+++ b/output/index.html
@@ -0,0 +1,249 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The OUTPUT directory:
+The <OUTPATH> directory is specified in the YAML file
Output files inside <OUTPATH> directory:
-
+
-
+
Sheet coordinates
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>.gro
+ -
+
Interlayer coordinates and topology (with solvent and/or ions) (if interlayer is solvated and/or clay has non-zero charge)
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_interlayer.groand<SYSNAME>_<X_CELLS>_<Y_CELLS>_interlayer.top
+ -
+
(Solvated) clay sheet stack coordinates and topology
+<SYSNAME>_<X_CELLS>_<Y_CELLS>.groand<SYSNAME>_<X_CELLS>_<Y_CELLS>.top
+ -
+
Sheet stack coordinates and topology in extended box (if specfied box height > height of clay sheet stack)
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_ext.groand<SYSNAME>_<X_CELLS>_<Y_CELLS>_ext.top
+ -
+
Sheet stack coordinates and topology in extended and solvated box (if bulk solvation is specified and specfied box height > height of clay sheet stack)
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv.groand<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv.top
+ -
+
Sheet stack coordinates and topology in extended and solvated box with ions (if bulk solvation is specified and specified box height > height of clay sheet stack)
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions.groand<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions.top
+ -
+
Sheet stack coordinates and topology in box after energy minimisation
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.groand<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.top
+ -
+
Sheet stack energy minimisation parameter file and log
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.mdpand<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.log
+ -
+
Setup log file
+<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>.log
+
Example:
+The output generated in the nontronite tutorial executing command:
+ClayCode builder -f Tutorial/NAu1.yaml
+asking to generate clay named NAu-1-fe using 7 x 5 x 3 unit cells, featuring adding interlayer water and ions and solvated.
+The output files are as follows:
+CWD
+│
+│
+└───Tutorials
+│ NAu1.yaml
+│ clay_conf.csv
+│ ...
+│
+└─── NAu-1-fe
+
+ │ NAu-1-fe_exp_df.csv
+ │ NAu-1-fe_match_df.csv
+ │ NAu-1-fe_7_5_0.gro
+ │ NAu-1-fe_7_5_1.gro
+ │ NAu-1-fe_7_5_2.gro
+ │ NAu-1-fe_7_5_interlayer.gro
+ │ NAu-1-fe_7_5_interlayer.top
+ │ NAu-1-fe_7_5.gro
+ │ NAu-1-fe_7_5.top
+ │ NAu-1-fe_7_5_ext.gro
+ │ NAu-1-fe_7_5_ext.top
+ │ NAu-1-fe_7_5_solv.gro
+ │ NAu-1-fe_7_5_solv.top
+ │ NAu-1-fe_7_5_solv_ions.mdp
+ │ NAu-1-fe_7_5_solv_ions.log
+ │ NAu-1-fe_7_5_solv_ions.gro
+ │ NAu-1-fe_7_5_solv_ions.top
+ │ NAu-1-fe_7_5_2307041912.log
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/pyr/index.html b/pyr/index.html
new file mode 100644
index 00000000..9c7e546e
--- /dev/null
+++ b/pyr/index.html
@@ -0,0 +1,205 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Pyrophyllite is a phyllosilicate mineral composed of aluminium silicate hydroxide: Al2Si4O10(OH)2.
+non-charged
+can be with Fe-incorporated, example: +https://hal.science/insu-00160523/
+or
+Pütürge pyrophyllite with small iron and chromium contents has a bright white colour after firing, and it is has been used in white cement production, where it is known to produce the whitest cement in Europe (Uygun & Solakoğlu, Reference Uygun and Solakoğlu2002).
+https://www.cambridge.org/core/journals/clay-minerals/article/beneficiation-of-the-puturge-pyrophyllite-ore-by-flotation-mineralogical-and-chemical-evaluation/2E4E88D5CF9A97EAFCE9E6997E2AB1DA
+There is no .CSV file, as quite simple set up, using 1 (or 2 if incl. some Fe) UCs:
+from the D21_UCs_infor.csv
+
+UC,st,at,fet,ao,feo,fe2,mgo,cao,lio,mgh,cah,C_Td,C_Oct,Comments
+D221,8,0,0,4,0,0,0,0,0,0,0,0,0,Smectite UC neutral
+D228,8,0,0,3,1,0,0,0,0,0,0,0,0,Smectite UC neutral Oct Fe3
+
+The .yaml file can set up with something like this:
+# required UCs to builder system as list
+UC_INDEX_LIST: [D221 D228]
+
+# probability list of unit cells in system
+UC_RATIOS_LIST: [0.9 0.1]
+ClayCode builder -f Tutorial/Pyr.yaml
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/references.bib b/references.bib
new file mode 100644
index 00000000..e09f21c7
--- /dev/null
+++ b/references.bib
@@ -0,0 +1,16085 @@
+@article{Sugisaki2019,
+ title = {{ Quantum chemistry on quantum computers: quantum simulations of the time evolution of wave functions under the S 2 operator and determination of the spin quantum number S }},
+ year = {2019},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Sugisaki, Kenji and Nakazawa, Shigeaki and Toyota, Kazuo and Sato, Kazunobu and Shiomi, Daisuke and Takui, Takeji},
+ number = {28},
+ pages = {15356--15361},
+ volume = {21},
+ url = {http://xlink.rsc.org/?DOI=C9CP02546D},
+ doi = {10.1039/c9cp02546d},
+ issn = {1463-9076}
+}
+
+@article{JGarlickGASteigmannELamb1972,
+ title = {{"' {\~{}} Structure of the F e-S Complex in a Bacterial F erredoxin}},
+ year = {1972},
+ journal = {Proc. Intern. Space Sci. Symp},
+ author = {J Garlick G A Steigmann E Lamb, G F},
+ number = {1},
+ pages = {929},
+ volume = {235},
+ publisher = {Pergamon}
+}
+
+@article{Ilgen2019a,
+ title = {{"Switching on" iron in clay minerals}},
+ year = {2019},
+ journal = {Environmental Science: Nano},
+ author = {Ilgen, A. G. and Kukkadapu, R. K. and Leung, K. and Washington, R. E.},
+ number = {6},
+ pages = {1704--1715},
+ volume = {6},
+ publisher = {Royal Society of Chemistry},
+ doi = {10.1039/C9EN00228F},
+ issn = {20518161}
+}
+
+@article{Veryazov2004,
+ title = {{2MOLCAS as a development platform for quantum chemistry software}},
+ year = {2004},
+ journal = {International Journal of Quantum Chemistry},
+ author = {Veryazov, Valera and Widmark, Per-Olof and Serrano-Andr{\'{e}}s, Luis and Lindh, Roland and Roos, Björn O.},
+ number = {4},
+ pages = {626--635},
+ volume = {100},
+ url = {http://doi.wiley.com/10.1002/qua.20166},
+ doi = {10.1002/qua.20166},
+ issn = {00207608}
+}
+
+@article{Dippy1959,
+ title = {{498. The dissociation constants of some symmetrically disubstituted succinic acids}},
+ year = {1959},
+ journal = {Journal of the Chemical Society (Resumed)},
+ author = {Dippy, J. F. J. and Hughes, S. R. C. and Rozanski, A.},
+ number = {0},
+ pages = {2492--2498},
+ publisher = {The Royal Society of Chemistry},
+ url = {http://xlink.rsc.org/?DOI=jr9590002492 http://dx.doi.org/10.1039/JR9590002492},
+ doi = {10.1039/jr9590002492},
+ issn = {0368-1769}
+}
+
+@article{DeCastroSilva2020,
+ title = {{A comparative study of alanine adsorption and condensation to peptides in two clay minerals}},
+ year = {2020},
+ journal = {Applied Clay Science},
+ author = {de Castro Silva, Fabrícia and Lima, Luciano Clécio Brandão and Silva-Filho, Edson C. and Fonseca, Maria Gardênnia and Lambert, Jean-François and Jaber, Maguy},
+ month = {7},
+ pages = {105617},
+ volume = {192},
+ publisher = {Elsevier Ltd},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0169131720301824},
+ doi = {10.1016/j.clay.2020.105617},
+ issn = {01691317},
+ keywords = {Alanine, Hectorite, Kaolinitte, Peptide bond, Prebiotic chemistry}
+}
+
+@article{Wolters2009,
+ title = {{A Comprehensive Characterization of Dioctahedral Smectites}},
+ year = {2009},
+ journal = {Clays and Clay Minerals},
+ author = {Wolters, Felicitas and Lagaly, Gerhard and Kahr, Guenter and Nueeshch, Rolf and Emmerich, Katja},
+ number = {1},
+ month = {2},
+ pages = {115--133},
+ volume = {57},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1346/CCMN.2009.0570111 http://link.springer.com/10.1346/CCMN.2009.0570111},
+ doi = {10.1346/CCMN.2009.0570111},
+ issn = {00098604},
+ keywords = {Biogeosciences, CEC, Chemical Composition, Cis-vacant, Dehydroxylation, Fe content, Geochemistry, Layer Charge, Medicinal Chemistry, Mineralogy, Montmorillonite, Nanoscale Science and Technology, Octahedral Charge, Simultaneous Thermal Analysis, Soil Science {\&} Conservation, Structural Formula, Tetra-hedral Charge, Trans-vacant}
+}
+
+@article{Palin2004,
+ title = {{A computational investigation of the Al/Fe/Mg order-disorder behavior in the dioctahedral sheet of phyllosilicates}},
+ year = {2004},
+ journal = {American Mineralogist},
+ author = {Palin, Erika J. and Dove, Martin T. and Hern{\'{a}}ndez-Laguna, Alfonso and Sainz-D{\'{i}}az, C. Ignacio},
+ number = {1},
+ month = {1},
+ pages = {164--175},
+ volume = {89},
+ publisher = {De Gruyter},
+ url = {https://www.degruyter.com/document/doi/10.2138/am-2004-0119/html},
+ doi = {10.2138/am-2004-0119},
+ issn = {0003-004X}
+}
+
+@article{Escamilla-Roa2017,
+ title = {{A DFT study of the adsorption of glycine in the interlayer space of montmorillonite}},
+ year = {2017},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Escamilla-Roa, Elizabeth and Huertas, F. Javier and Hern{\'{a}}ndez-Laguna, Alfonso and Sainz-D{\'{i}}az, C. Ignacio},
+ number = {23},
+ month = {6},
+ pages = {14961--14971},
+ volume = {19},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2017/cp/c7cp02300f https://pubs.rsc.org/en/content/articlelanding/2017/cp/c7cp02300f},
+ doi = {10.1039/C7CP02300F},
+ issn = {1463-9084}
+}
+
+@article{Preiner2020,
+ title = {{A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism}},
+ year = {2020},
+ journal = {Nature Ecology {\&} Evolution 2020 4:4},
+ author = {Preiner, Martina and Igarashi, Kensuke and Muchowska, Kamila B. and Yu, Mingquan and Varma, Sreejith J. and Kleinermanns, Karl and Nobu, Masaru K. and Kamagata, Yoichi and T{\"{u}}ys{\"{u}}z, Harun and Moran, Joseph and Martin, William F.},
+ number = {4},
+ month = {3},
+ pages = {534--542},
+ volume = {4},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s41559-020-1125-6},
+ doi = {10.1038/s41559-020-1125-6},
+ issn = {2397-334X},
+ pmid = {32123322},
+ keywords = {Biogeochemistry, Chemical origin of life}
+}
+
+@article{Barth_1972,
+ title = {{A local exchange-correlation potential for the spin polarized case. I}},
+ year = {1972},
+ journal = {Journal of Physics C: Solid State Physics},
+ author = {Von Barth, U. and Hedin, L.},
+ number = {13},
+ month = {7},
+ pages = {1629--1642},
+ volume = {5},
+ publisher = {{\{}IOP{\}} Publishing},
+ url = {https://doi.org/10.1088%2F0022-3719%2F5%2F13%2F012},
+ doi = {10.1088/0022-3719/5/13/012},
+ issn = {00223719}
+}
+
+@article{Lee2003,
+ title = {{A Major Outbreak of Severe Acute Respiratory Syndrome in Hong Kong}},
+ year = {2003},
+ journal = {New England Journal of Medicine},
+ author = {Lee, Nelson and Hui, David and Wu, Alan and Chan, Paul and Cameron, Peter and Joynt, Gavin M. and Ahuja, Anil and Yung, Man Yee and Leung, C.B. and To, K.F. and Lui, S.F. and Szeto, C.C. and Chung, Sydney and Sung, Joseph J.Y.},
+ number = {20},
+ month = {5},
+ pages = {1986--1994},
+ volume = {348},
+ url = {http://www.nejm.org/doi/abs/10.1056/NEJMoa030685},
+ doi = {10.1056/NEJMoa030685},
+ issn = {0028-4793}
+}
+
+@article{Leroy2009,
+ title = {{A mechanistic model for the spectral induced polarization of clay materials}},
+ year = {2009},
+ journal = {Journal of Geophysical Research},
+ author = {Leroy, P. and Revil, A.},
+ number = {B10},
+ month = {10},
+ pages = {B10202},
+ volume = {114},
+ publisher = {Blackwell Publishing Ltd},
+ url = {http://doi.wiley.com/10.1029/2008JB006114},
+ doi = {10.1029/2008JB006114},
+ issn = {0148-0227},
+ keywords = {clay, complex conductivity, doi:10.1029/2008JB006114, double layer, http://dx.doi.org/10.1029/2008JB006114, induced polarization, particle size distribution, porous media, spectral impedance}
+}
+
+@article{MDjalili-Moghaddam2005,
+ title = {{A model for short-range interactions in fiber suspensions}},
+ year = {2005},
+ journal = {Journal of Non-Newtonian Mechanics},
+ author = {M Djalili-Moghaddam, S Toll},
+ pages = {73--83},
+ volume = {132}
+}
+
+@article{Bertagnolli1976,
+ title = {{A neutron-diffraction study of liquid acetonitrile}},
+ year = {1976},
+ journal = {Molecular Physics},
+ author = {Bertagnolli, H and Chieux, P and Zeidler, M D},
+ number = {3},
+ month = {9},
+ pages = {759--773},
+ volume = {32},
+ publisher = {Taylor {\&} Francis},
+ url = {https://doi.org/10.1080/00268977600102201},
+ doi = {10.1080/00268977600102201},
+ issn = {0026-8976}
+}
+
+@article{EGalan1999,
+ title = {{A new approach to compositional limits for sepiolite and palygorskite}},
+ year = {1999},
+ journal = {Clays and Clay Minerals},
+ author = {E Galan, MI Carretero},
+ pages = {399--409},
+ volume = {47}
+}
+
+@article{Burgess1975,
+ title = {{A new approach to empirical intermolecular and conformational potential energy functions. II. Applications to crystal packing, rotational barriers, and conformational analysis}},
+ year = {1975},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Burgess, A. W. and Shipman, L. L. and Scheraga, H. A.},
+ number = {3},
+ pages = {854--858},
+ volume = {72},
+ doi = {10.1073/pnas.72.3.854},
+ issn = {00278424}
+}
+
+@article{Cabaleiro-Lago1997,
+ title = {{A Potential Function for Intermolecular Interaction in the Acetonitrile Dimer Constructed from ab Initio Data}},
+ year = {1997},
+ journal = {The Journal of Physical Chemistry A},
+ author = {Cabaleiro-Lago, Enrique M and R{\'{i}}os, Miguel A},
+ number = {44},
+ month = {10},
+ pages = {8327--8334},
+ volume = {101},
+ publisher = {American Chemical Society},
+ url = {https://doi.org/10.1021/jp971084+},
+ doi = {10.1021/jp971084+},
+ issn = {1089-5639}
+}
+
+@book{Fiolhais2003,
+ title = {{A Primer in Density Functional Theory}},
+ year = {2003},
+ booktitle = {Materials Today},
+ editor = {Fiolhais, Carlos and Nogueira, Fernando and Marques, Miguel A. L.},
+ number = {12},
+ pages = {59},
+ series = {Lecture Notes in Physics},
+ volume = {6},
+ publisher = {Springer Berlin Heidelberg},
+ url = {http://link.springer.com/10.1007/3-540-37072-2},
+ address = {Berlin, Heidelberg},
+ isbn = {978-3-540-03083-6},
+ doi = {10.1016/s1369-7021(03)01229-x},
+ issn = {13697021}
+}
+
+@article{Wu2011,
+ title = {{A Primer on High-Throughput Computing for Genomic Selection}},
+ year = {2011},
+ journal = {Frontiers in Genetics},
+ author = {Wu, Xiao-Lin and Beissinger, Timothy M. and Bauck, Stewart and Woodward, Brent and Rosa, Guilherme J. M. and Weigel, Kent A. and Gatti, Natalia de Leon and Gianola, Daniel},
+ volume = {2},
+ url = {http://journal.frontiersin.org/article/10.3389/fgene.2011.00004/abstract},
+ doi = {10.3389/fgene.2011.00004},
+ issn = {1664-8021}
+}
+
+@article{Marty2020,
+ title = {{A quantitative and mechanistic model for the coupling between chemistry and clay hydration}},
+ year = {2020},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Marty, Nicolas C.M. and Grangeon, Sylvain and Lassin, Arnault and Mad{\'{e}}, Benoit and Blanc, Philippe and Lanson, Bruno},
+ month = {8},
+ pages = {124--135},
+ volume = {283},
+ publisher = {Elsevier Ltd},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0016703720303483},
+ doi = {10.1016/j.gca.2020.05.029},
+ issn = {00167037},
+ keywords = {Clay composition, Exchange reaction, Gapon, Hydration model, Ionic strength, Rothmund-Kornfeld}
+}
+
+@article{Grabe2004,
+ title = {{A quantitative assesment of models for voltage-dependent gating of ion channels}},
+ year = {2004},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Grabe, Michael and Lecar, Harold and Jan, Yuh Nung and Jan, Lily Yeh},
+ number = {51},
+ month = {12},
+ pages = {17640--17645},
+ volume = {101},
+ doi = {10.1073/pnas.0408116101},
+ issn = {00278424},
+ keywords = {Electrostatics, Poisson-Boltzmann equation, Potassium channel, Voltage gating}
+}
+
+@article{Hodgkin1952,
+ title = {{A quantitative description of membrane current and its application to conduction and excitation in nerve}},
+ year = {1952},
+ journal = {The Journal of Physiology},
+ author = {Hodgkin, A. L. and Huxley, A. F.},
+ number = {4},
+ month = {8},
+ pages = {500--544},
+ volume = {117},
+ publisher = {Wiley-Blackwell},
+ url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1392413/ https://onlinelibrary.wiley.com/doi/abs/10.1113/jphysiol.1952.sp004764},
+ doi = {10.1113/jphysiol.1952.sp004764},
+ issn = {0022-3751},
+ pmid = {12991237}
+}
+
+@article{Garcia-Risueno2012a,
+ title = {{A review of high performance computing foundations for scientists}},
+ year = {2012},
+ journal = {International Journal of Modern Physics C},
+ author = {Garcia-Risue{\~{n}}o, Pablo and Ib{\'{a}}{\~{n}}ez, PABLO E. and GARC{\'{I}}A-RISUE{\~{N}}O, PABLO and Ib{\'{a}}{\~{n}}ez, PABLO E.},
+ number = {7},
+ month = {7},
+ pages = {1230001},
+ volume = {23},
+ url = {https://www.worldscientific.com/doi/abs/10.1142/S0129183112300011},
+ doi = {10.1142/S0129183112300011},
+ issn = {01291831},
+ arxivId = {1205.5177},
+ keywords = {High performance computing, computer architecture, distributed computing, parallel calculations, scientific supercomputing, simulation}
+}
+
+@article{Ketterings2014,
+ title = {{A Simple Method for Estimating Effective Cation Exchange Capacity, Cation Saturation Ratios, and Sulfur Across a Wide Range of Soils}},
+ year = {2014},
+ journal = {Soil Science},
+ author = {Ketterings, Quirine M. and Gami, Sanjay K. and Mathur, Renuka R. and Woods, Micah},
+ number = {5},
+ month = {5},
+ pages = {230--236},
+ volume = {179},
+ publisher = {Lippincott Williams and Wilkins},
+ url = {https://journals.lww.com/00010694-201405000-00002},
+ doi = {10.1097/SS.0000000000000062},
+ issn = {0038-075X},
+ keywords = {Cation exchange capacity, compulsive exchange, strontium chloride, sulfur}
+}
+
+@article{Mahler2012,
+ title = {{A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution}},
+ year = {2012},
+ journal = {Inorganic Chemistry},
+ author = {M{\"{a}}hler, Johan and Persson, Ingmar},
+ number = {1},
+ month = {1},
+ pages = {425--438},
+ volume = {51},
+ publisher = {American Chemical Society},
+ url = {/pmc/articles/PMC3250073/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250073/ https://pubs.acs.org/doi/10.1021/ic2018693},
+ doi = {10.1021/ic2018693},
+ issn = {0020-1669}
+}
+
+@article{Benson1982,
+ title = {{A tabulation and evaluation of ion exchange data on smectites}},
+ year = {1982},
+ journal = {Environmental Geology},
+ author = {Benson, L. V.},
+ number = {1},
+ month = {3},
+ pages = {23--29},
+ volume = {4},
+ publisher = {Springer-Verlag},
+ url = {http://link.springer.com/10.1007/BF02380496},
+ doi = {10.1007/BF02380496},
+ issn = {0943-0105}
+}
+
+@article{Liu2006a,
+ title = {{A thermodynamic understanding of clay-swelling inhibition by potassium ions}},
+ year = {2006},
+ journal = {Angewandte Chemie - International Edition},
+ author = {Liu, Xian Dong and Lu, Xian Cai},
+ number = {38},
+ month = {9},
+ pages = {6300--6303},
+ volume = {45},
+ doi = {10.1002/ANIE.200601740},
+ keywords = {Clays, Mobility, Molecular dynamics, Potassium, Thermodynamics}
+}
+
+@article{Liu2006,
+ title = {{A thermodynamic understanding of clay-swelling inhibition by potassium ions}},
+ year = {2006},
+ journal = {Angewandte Chemie - International Edition},
+ author = {Liu, Xian Dong and Lu, Xian Cai},
+ number = {38},
+ month = {9},
+ pages = {6300--6303},
+ volume = {45},
+ doi = {10.1002/ANIE.200601740},
+ issn = {14337851},
+ keywords = {Clays, Mobility, Molecular dynamics, Potassium, Thermodynamics}
+}
+
+@article{Tazi2012a,
+ title = {{A transferable ab initio based force field for aqueous ions}},
+ year = {2012},
+ journal = {Journal of Chemical Physics},
+ author = {Tazi, Sami and Molina, John J. and Rotenberg, Benjamin and Turq, Pierre and Vuilleumier, Rodolphe and Salanne, Mathieu},
+ number = {11},
+ month = {3},
+ volume = {136},
+ doi = {10.1063/1.3692965},
+ issn = {00219606},
+ pmid = {22443777},
+ arxivId = {1204.2084}
+}
+
+@article{Ickmore,
+ title = {{AB INITIO DETERMINATION OF EDGE SURFACE STRUCTURES FOR DIOCTAHEDRAL 2:1 PHYLLOSILICATES: IMPLICATIONS FOR ACID-BASE REACTIVITY}},
+ author = {Ickmore, Arry R B and Osso, Vin M R and Nagy, Kathryn L and Yga N, Randall T C and Hristophe, C and Tadanier, R J},
+ doi = {10.1346/CCMN.2003.0510401},
+ keywords = {Ab Initio, Clay Edge Surfaces, Density Functional Theory, Dissolution Kinetics, MUSIC, Pyrophyllite, Surface Structure}
+}
+
+@article{Boek2003,
+ title = {{Ab Initio Molecular Dynamics Study of the Hydration of a Sodium Smectite Clay}},
+ year = {2003},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Boek, E. S. and Sprik, M.},
+ number = {14},
+ month = {4},
+ pages = {3251--3256},
+ volume = {107},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/abs/10.1021/jp0262564 https://pubs.acs.org/doi/10.1021/jp0262564},
+ doi = {10.1021/jp0262564},
+ issn = {1520-6106}
+}
+
+@article{Mignon2010,
+ title = {{Ab initio molecular dynamics study of the hydration of Li+, Na+ and K+ in a montmorillonite model. Influence of isomorphic substitution}},
+ year = {2010},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Mignon, Pierre and Ugliengo, Piero and Sodupe, Mariona and Hernandez, Eduardo R.},
+ number = {3},
+ month = {12},
+ pages = {688--697},
+ volume = {12},
+ publisher = {The Royal Society of Chemistry},
+ url = {www.rsc.org/pccp},
+ doi = {10.1039/b915689e},
+ issn = {14639076}
+}
+
+@article{Wang2019,
+ title = {{Abiotic reduction of uranium(VI) with humic acid at mineral surfaces: Competing mechanisms, ligand and substituent effects, and electronic structure and vibrational properties}},
+ year = {2019},
+ journal = {Environmental Pollution},
+ author = {Wang, Qian and Zhu, Chang and Huang, Xiaoxiao and Yang, Gang},
+ month = {11},
+ pages = {113110},
+ volume = {254},
+ publisher = {Elsevier Ltd},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749119324984},
+ doi = {10.1016/j.envpol.2019.113110},
+ issn = {02697491},
+ pmid = {31479808},
+ keywords = {Abiotic reduction, Humic substances, Ligand effect, Substituent effect, Uranium contamination}
+}
+
+@article{Tazi2012,
+ title = {{Absolute acidity of clay edge sites from ab-initio simulations}},
+ year = {2012},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Tazi, Sami and Rotenberg, Benjamin and Salanne, Mathieu and Sprik, Michiel and Sulpizi, Marialore},
+ month = {10},
+ pages = {1--11},
+ volume = {94},
+ publisher = {Pergamon},
+ doi = {10.1016/j.gca.2012.07.010}
+}
+
+@article{Engkvist2000,
+ title = {{Accurate intermolecular potentials obtained from molecular wave functions: bridging the gap between quantum chemistry and molecular simulations}},
+ year = {2000},
+ journal = {Chemical Reviews},
+ author = {Engkvist, Ola and {\AA}strand, Per Olof and Karlstr{\"{o}}m, Gunnar},
+ number = {11},
+ month = {11},
+ pages = {4087--4108},
+ volume = {100},
+ publisher = {ACS},
+ url = {https://pubs.acs.org/doi/pdf/10.1021/cr9900477},
+ doi = {10.1021/cr9900477},
+ issn = {00092665},
+ pmid = {11749341}
+}
+
+@article{Tafipolsky2011,
+ title = {{Accurate Intermolecular Potentials with Physically Grounded Electrostatics}},
+ year = {2011},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Tafipolsky, Maxim and Engels, Bernd},
+ number = {6},
+ month = {6},
+ pages = {1791--1803},
+ volume = {7},
+ url = {https://pubs.acs.org/doi/10.1021/ct200185h},
+ doi = {10.1021/ct200185h},
+ issn = {1549-9618}
+}
+
+@article{Harvey2009,
+ title = {{ACEMD: Accelerating biomolecular dynamics in the microsecond time scale}},
+ year = {2009},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Harvey, M. J. and Giupponi, G. and De Fabritiis, G.},
+ number = {6},
+ month = {6},
+ pages = {1632--1639},
+ volume = {5},
+ publisher = {American Chemical Society},
+ url = {https://doi.org/10.1021/ct9000685},
+ doi = {10.1021/ct9000685},
+ issn = {15499618},
+ arxivId = {0902.0827}
+}
+
+@incollection{Komadel2013,
+ title = {{Acid activation of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Komadel, P. and Madejov{\'{a}}, J.},
+ pages = {385--409},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00013-4},
+ issn = {15724352},
+ keywords = {Acid sites, Acid treatment, FTIR spectroscopy, Structural modification, Surface area}
+}
+
+@incollection{Bergaya2013k,
+ title = {{Acknowledgements}},
+ year = {2013},
+ booktitle = {Journal of Chemical Information and Modeling},
+ author = {Bergaya, Faïza and Lagaly, Gerhard},
+ number = {9},
+ pages = {vii-viii},
+ volume = {53},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/B9780080982588099934 https://linkinghub.elsevier.com/retrieve/pii/B9780080982595099923},
+ isbn = {9788578110796},
+ doi = {10.1016/B978-0-08-098259-5.09992-3},
+ issn = {1098-6596},
+ pmid = {25246403},
+ arxivId = {arXiv:1011.1669v3},
+ keywords = {icle}
+}
+
+@unpublished{coen,
+ title = {{Acrolein}},
+ year = {2019},
+ author = {de Graaf, Coen},
+ institution = {IIC2019},
+ address = {Madrid}
+}
+
+@article{Zhu2016,
+ title = {{Adsorbents based on montmorillonite for contaminant removal from water: A review}},
+ year = {2016},
+ journal = {Applied Clay Science},
+ author = {Zhu, Runliang and Chen, Qingze and Zhou, Qing and Xi, Yunfei and Zhu, Jianxi and He, Hongping},
+ pages = {239--258},
+ volume = {123},
+ publisher = {Elsevier B.V.},
+ url = {http://dx.doi.org/10.1016/j.clay.2015.12.024},
+ doi = {10.1016/j.clay.2015.12.024},
+ issn = {01691317},
+ keywords = {Adsorption, Contaminant, Environmental remediation, Montmorillonite}
+}
+
+@misc{Lambert2008,
+ title = {{Adsorption and polymerization of amino acids on mineral surfaces: A review}},
+ year = {2008},
+ booktitle = {Origins of Life and Evolution of Biospheres},
+ author = {Lambert, Jean François},
+ number = {3},
+ pages = {211--242},
+ volume = {38},
+ doi = {10.1007/s11084-008-9128-3},
+ issn = {01696149},
+ pmid = {18344011},
+ keywords = {Adsorption, Amino acids, Bernal's hypothesis, Oxide minerals, Surface polymerization}
+}
+
+@misc{Bhattacharyya2008,
+ title = {{Adsorption of a few heavy metals on natural and modified kaolinite and montmorillonite: A review}},
+ year = {2008},
+ booktitle = {Advances in Colloid and Interface Science},
+ author = {Bhattacharyya, Krishna Gopal and Gupta, Susmita Sen},
+ number = {2},
+ month = {8},
+ pages = {114--131},
+ volume = {140},
+ doi = {10.1016/j.cis.2007.12.008},
+ issn = {00018686},
+ keywords = {Adsorption, Heavy metals, Kaolinite, Modified clay, Montmorillonite}
+}
+
+@article{Zhu2019,
+ title = {{Adsorption of amino acids at clay surfaces and implication for biochemical reactions: Role and impact of surface charges}},
+ year = {2019},
+ journal = {Colloids and Surfaces B: Biointerfaces},
+ author = {Zhu, Chang and Wang, Qian and Huang, Xiaoxiao and Yun, Jiena and Hu, Qiaoli and Yang, Gang},
+ month = {11},
+ pages = {110458},
+ volume = {183},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0927776519306022},
+ doi = {10.1016/j.colsurfb.2019.110458},
+ issn = {09277765},
+ pmid = {31472392},
+ keywords = {Binding affinity, Biochemical reactions, Clay minerals, Origin of life, Surface charges}
+}
+
+@incollection{Jia2016,
+ title = {{Adsorption of Ions at the Interface of Clay Minerals and Aqueous Solutions}},
+ year = {2016},
+ booktitle = {Advances in Colloid Science},
+ author = {Jia, Zengqiang and Wang, Qian and Zhu, Chang and Yang, Gang},
+ month = {11},
+ publisher = {IntechOpen},
+ url = {http://dx.doi.org/10.5772/65529},
+ doi = {10.5772/65529},
+ keywords = {clay mineral, interfacial adsorption, ion-specific effects, molecular dynamics, quantum me-chanics}
+}
+
+@article{Li2020,
+ title = {{Adsorption of metal ions at kaolinite surfaces: Ion-specific effects, and impacts of charge source and hydroxide formation}},
+ year = {2020},
+ journal = {Applied Clay Science},
+ author = {Li, Tingting and Huang, Xiaoxiao and Wang, Qian and Yang, Gang},
+ month = {9},
+ pages = {105706},
+ volume = {194},
+ publisher = {Elsevier Ltd},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0169131720302714},
+ doi = {10.1016/j.clay.2020.105706},
+ issn = {01691317},
+ keywords = {Adsorption, Charge source, Hydroxide, Ion-specific effects, Soil acidification}
+}
+
+@article{SenGupta2014,
+ title = {{Adsorption of metal ions by clays and inorganic solids}},
+ year = {2014},
+ journal = {RSC Adv.},
+ author = {Sen Gupta, Susmita and Bhattacharyya, Krishna G.},
+ number = {54},
+ month = {6},
+ pages = {28537--28586},
+ volume = {4},
+ publisher = {Royal Society of Chemistry},
+ url = {www.rsc.org/advances http://xlink.rsc.org/?DOI=C4RA03673E},
+ doi = {10.1039/C4RA03673E},
+ issn = {2046-2069}
+}
+
+@article{Mignon2020,
+ title = {{Adsorption of nucleotides on clay surfaces: Effects of mineral composition, pH and solution salts}},
+ year = {2020},
+ journal = {Applied Clay Science},
+ author = {Mignon, Pierre and Corbin, Gwenaëlle and Le Crom, Sébastien and Marry, Virginie and Hao, Jihua and Daniel, Isabelle},
+ month = {6},
+ pages = {105544},
+ volume = {190},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.clay.2020.105544},
+ issn = {01691317}
+}
+
+@article{Feuillie2013,
+ title = {{Adsorption of nucleotides onto Fe–Mg–Al rich swelling clays}},
+ year = {2013},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Feuillie, Cécile and Daniel, Isabelle and Michot, Laurent J. and Pedreira-Segade, Ulysse},
+ month = {11},
+ pages = {97--108},
+ volume = {120},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0016703713003554},
+ doi = {10.1016/j.gca.2013.06.021},
+ issn = {00167037}
+}
+
+@article{Blachier2009,
+ title = {{Adsorption of polyamine on clay minerals}},
+ year = {2009},
+ journal = {Journal of Colloid and Interface Science},
+ author = {Blachier, C. and Michot, L. and Bihannic, I. and Barr{\`{e}}s, O. and Jacquet, A. and Mosquet, M.},
+ number = {2},
+ month = {8},
+ pages = {599--606},
+ volume = {336},
+ keywords = {Adsorption, Clay, Flocculation, Infrared spectroscopy, Polycation, SAXS-WAXS, Zeta potential}
+}
+
+@article{Lipson1983,
+ title = {{Adsorption of reovirus to clay minerals: Effects of cation-exchange capacity, cation saturation, and surface area}},
+ year = {1983},
+ journal = {Applied and Environmental Microbiology},
+ author = {Lipson, S. M. and Stotzky, G.},
+ number = {3},
+ pages = {673--682},
+ volume = {46},
+ publisher = {American Society for Microbiology (ASM)},
+ url = {/pmc/articles/PMC239333/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC239333/},
+ doi = {10.1128/aem.46.3.673-682.1983},
+ issn = {00992240},
+ pmid = {6639022}
+}
+
+@book{Xu2010b,
+ title = {{Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units}},
+ year = {2010},
+ booktitle = {Annual Reports in Computational Chemistry},
+ author = {Xu, Dong and Williamson, Mark J. and Walker, Ross C.},
+ number = {C},
+ pages = {2--19},
+ volume = {6},
+ publisher = {Elsevier B.V.},
+ url = {http://dx.doi.org/10.1016/S1574-1400(10)06001-9 https://linkinghub.elsevier.com/retrieve/pii/S1574140010060019},
+ doi = {10.1016/S1574-1400(10)06001-9},
+ issn = {15741400},
+ keywords = {ACEMD, AMBER, ATI, Accelerator, CUDA, GPU, Molecular dynamics, NAMD, NVIDIA, OpenMM, Stream}
+}
+
+@article{Geysermans2009,
+ title = {{Advances in atomistic simulations of mineral surfaces}},
+ year = {2009},
+ journal = {Journal of Materials Chemistry},
+ author = {Geysermans, P and Noguera, C},
+ number = {42},
+ pages = {7807},
+ volume = {19},
+ url = {www.rsc.org/materials http://xlink.rsc.org/?DOI=b903642c},
+ doi = {10.1039/b903642c},
+ issn = {0959-9428}
+}
+
+@article{Cygan2021,
+ title = {{Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces}},
+ year = {2021},
+ journal = {Journal of Physical Chemistry C},
+ author = {Cygan, Randall T. and Greathouse, Jeffery A. and Kalinichev, Andrey G.},
+ number = {32},
+ month = {8},
+ pages = {17573--17589},
+ volume = {125},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/acs.jpcc.1c04600},
+ doi = {10.1021/ACS.JPCC.1C04600/SUPPL{\_}FILE/JP1C04600{\_}SI{\_}001.PDF},
+ issn = {19327455}
+}
+
+@article{WZChang2014,
+ title = {{Ageing and collapse of bentonite gels—effects of Li, Na, K and Cs ions}},
+ year = {2014},
+ journal = {Rheologica Acta},
+ author = {WZ Chang, YK Leong},
+ pages = {109--122},
+ volume = {53}
+}
+
+@incollection{BoettcherCh30,
+ title = {{Alteration of Substrate Specificity and Stereoselectivity of Lipases and Esterases}},
+ year = {2011},
+ booktitle = {Protein Engineering Handbook},
+ author = {B{\"{o}}ttcher, Dominique and Schmidt, Marlen and Bornscheuer, Uwe T.},
+ chapter = {30},
+ month = {3},
+ pages = {753--775},
+ volume = {2},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/9783527634026.ch30},
+ address = {Weinheim, Germany},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch30},
+ keywords = {Directed evolution, Enantioselectivity, Esterase, High-throughput screening, Lipase, Rational protein design, Substrate specificity}
+}
+
+@incollection{DeSienoChap31,
+ title = {{Altering Enzyme Substrate and Cofactor Specificity via Protein Engineering}},
+ year = {2011},
+ booktitle = {Protein Engineering Handbook},
+ author = {DeSieno, Matthew and Du, Jing and Zhao, Huimin},
+ chapter = {31},
+ month = {3},
+ pages = {777--796},
+ volume = {2},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/9783527634026.ch31},
+ address = {Weinheim, Germany},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch31},
+ keywords = {Biosynthesis, Cofactor specificity, Directed evolution, Enzyme engineering, Gene therapy, Rational design, Substrate specificity}
+}
+
+@article{Reid2021,
+ title = {{An algorithm to calculate the cationic composition of soil solutions. 1. Theory and structure.}},
+ year = {2021},
+ journal = {Soil Research},
+ author = {Reid, Jeff B.},
+ number = {2},
+ month = {2},
+ pages = {179--194},
+ volume = {59},
+ publisher = {CSIRO Publishing},
+ url = {https://go-gale-com.ezproxy.is.ed.ac.uk/ps/i.do?p=AONE&sw=w&issn=1838675X&v=2.1&it=r&id=GALE%7CA672247663&sid=googleScholar&linkaccess=fulltext https://go-gale-com.ezproxy.is.ed.ac.uk/ps/i.do?p=AONE&sw=w&issn=1838675X&v=2.1&it=r&id=GALE%7CA672247663&sid=g},
+ doi = {10.1071/SR20226},
+ issn = {1838675X},
+ keywords = {Algorithms, Cations, Soil acidity}
+}
+
+@article{Porte2008,
+ title = {{An introduction to diffusion maps}},
+ year = {2008},
+ journal = {{\ldots} Sciences, University of {\ldots}},
+ author = {Porte, J De La and Herbst, Bm},
+ number = {November},
+ pages = {11},
+ url = {http://dip.sun.ac.za/~herbst/research/publications/diff_maps_prasa2008.pdf}
+}
+
+@book{Shen2015,
+ title = {{An Introduction to Numerical Computation}},
+ year = {2015},
+ author = {Shen, Wen},
+ month = {12},
+ publisher = {WORLD SCIENTIFIC},
+ url = {https://www.worldscientific.com/worldscibooks/10.1142/9844},
+ isbn = {978-981-4730-06-8},
+ doi = {10.1142/9844},
+ keywords = {numcomp}
+}
+
+@book{Kaye2006,
+ title = {{An introduction to quantum computing for non-physicists}},
+ year = {2000},
+ booktitle = {ACM Computing Surveys},
+ author = {Rieffel, Eleanor and Polak, Wolfgang},
+ number = {3},
+ pages = {300--335},
+ volume = {32},
+ publisher = {OUP Oxford},
+ url = {https://books.google.es/books?id=-sHS-sE0w0MC},
+ isbn = {9780198570004},
+ doi = {10.1145/367701.367709},
+ issn = {03600300},
+ arxivId = {quant-ph/9809016},
+ keywords = {Complexity, Parallelism, Quantum computing}
+}
+
+@article{Pillaiyar2016,
+ title = {{An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy}},
+ year = {2016},
+ journal = {Journal of Medicinal Chemistry},
+ author = {Pillaiyar, Thanigaimalai and Manickam, Manoj and Namasivayam, Vigneshwaran and Hayashi, Yoshio and Jung, Sang-Hun},
+ number = {14},
+ month = {7},
+ pages = {6595--6628},
+ volume = {59},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jmedchem.5b01461},
+ doi = {10.1021/acs.jmedchem.5b01461},
+ issn = {0022-2623},
+ pmid = {26878082}
+}
+
+@article{White1988,
+ title = {{ANALYSIS AND IMPLICATIONS OF THE EDGE STRUCTURE OF DIOCTAHEDRAL PHYLLOSILICATES.}},
+ year = {1988},
+ journal = {Clays and Clay Minerals},
+ author = {White, G. Norman and Zelazny, L. W.},
+ number = {2},
+ month = {4},
+ pages = {141--146},
+ volume = {36},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1346/CCMN.1988.0360207},
+ doi = {10.1346/CCMN.1988.0360207},
+ issn = {00098604},
+ keywords = {Biogeosciences, Geochemistry, Medicinal Chemistry, Mineralogy, Nanoscale Science and Technology, Soil Science {\&} Conservation}
+}
+
+@article{Giorgino2019,
+ title = {{Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis}},
+ year = {2019},
+ journal = {Methods in Molecular Biology},
+ author = {Giorgino, Toni},
+ pages = {503--527},
+ volume = {2022},
+ publisher = {Humana, New York, NY},
+ url = {https://link.springer.com/protocol/10.1007/978-1-4939-9608-7_20},
+ doi = {10.1007/978-1-4939-9608-7{\_}20},
+ issn = {19406029},
+ pmid = {31396916},
+ keywords = {Bio3D, HTMD, MDAnalysis, MDTraj, Molecular dynamics, Scripting languages, Trajectory analysis, VMD}
+}
+
+@article{Pedersen2010,
+ title = {{Analysis of copper corrosion in compacted bentonite clay as a function of clay density and growth conditions for sulfate-reducing bacteria}},
+ year = {2010},
+ journal = {Journal of Applied Microbiology},
+ author = {Pedersen, K.},
+ number = {3},
+ month = {3},
+ pages = {1094--1104},
+ volume = {108},
+ doi = {10.1111/j.1365-2672.2009.04629.x},
+ issn = {13645072},
+ pmid = {20015208},
+ keywords = {Activity, Biocorrosion, Clay, Hazardous waste, Subsurface}
+}
+
+@article{Hodges1998,
+ title = {{Analytical potentials for HF dimer and larger HF clusters from ab initio calculations}},
+ year = {1998},
+ journal = {Journal of Physical Chemistry A},
+ author = {Hodges, Matthew P. and Stone, Anthony J. and Lago, Enrique Cabaleiro},
+ number = {14},
+ pages = {2455--2465},
+ volume = {102},
+ doi = {10.1021/jp972148j},
+ issn = {10895639}
+}
+
+@article{Stone1994,
+ title = {{Anisotropy of Atom-Atom Repulsions}},
+ year = {1994},
+ author = {Stone, A J and Tong, C and Road, Lensfield and W, Cambridge C B E},
+ number = {12},
+ pages = {1377--1392},
+ volume = {15}
+}
+
+@article{Marry2013,
+ title = {{Anisotropy of water dynamics in clays: Insights from molecular simulations for experimental QENS analysis}},
+ year = {2013},
+ journal = {Journal of Physical Chemistry C},
+ author = {Marry, V. and Dubois, E. and Malikova, N. and Breu, J. and Haussler, W.},
+ number = {29},
+ month = {7},
+ pages = {15106--15115},
+ volume = {117},
+ doi = {10.1021/jp403501h},
+ issn = {19327447}
+}
+
+@article{Murray2006a,
+ title = {{Appendix A Commonly used Tests and Procedures for Evaluating Kaolin Samples}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {147--160},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02009-5},
+ issn = {15724352}
+}
+
+@article{Murray2006,
+ title = {{Appendix B Common Tests for Evaluation of Ball Clay Samples}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {161--168},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02010-1},
+ issn = {15724352}
+}
+
+@article{Murray2006j,
+ title = {{Appendix C Commonly used Tests to Evaluate Bentonite Samples}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {169--170},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02011-3},
+ issn = {15724352}
+}
+
+@article{Murray2006d,
+ title = {{Appendix D Palygorskite-Sepiolite Laboratory Tests}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {171--178},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02012-5},
+ issn = {15724352}
+}
+
+@incollection{Yun2018,
+ title = {{Application of Density Functional Theory in Soil Science}},
+ year = {2018},
+ booktitle = {Density Functional Calculations - Recent Progresses of Theory and Application},
+ author = {Yun, Jiena and Wang, Qian and Zhu, Chang and Yang, Gang},
+ month = {5},
+ publisher = {InTech},
+ url = {http://www.intechopen.com/books/density-functional-calculations-recent-progresses-of-theory-and-application/application-of-density-functional-theory-in-soil-science},
+ doi = {10.5772/intechopen.74079}
+}
+
+@article{doi:10.1063/1.477941,
+ title = {{Application of spin-restricted open-shell Kohn-Sham method to atomic and molecular multiplet states}},
+ year = {1999},
+ journal = {Journal of Chemical Physics},
+ author = {Filatov, Michael and Shaik, Sason},
+ number = {1},
+ pages = {116--125},
+ volume = {110},
+ url = {https://doi.org/10.1063/1.477941},
+ doi = {10.1063/1.477941},
+ issn = {00219606}
+}
+
+@incollection{Galimberti2013,
+ title = {{Applications of Clay–Polymer Nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Galimberti, M. and Cipolletti, V. R. and Coombs, M.},
+ number = {C},
+ month = {1},
+ pages = {539--586},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00020-2},
+ issn = {15724352},
+ keywords = {Applications, Automotive, Barrier properties, Biomedicine, Cables, Clay polymer nanocomposites, Coatings, Degradation properties, Fuel cells, Mechanical properties, Packaging, Rheological properties, Sporting goods, Thermal properties, Tyres, Wire}
+}
+
+@incollection{Gates2017,
+ title = {{Applications of NIR/MIR to Determine Site Occupancy in Smectites}},
+ year = {2017},
+ booktitle = {Developments in Clay Science},
+ author = {Gates, W.P. and Petit, S. and Madejov{\'{a}}, J.},
+ month = {1},
+ pages = {200--221},
+ volume = {8},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780081003558000072},
+ doi = {10.1016/B978-0-08-100355-8.00007-2},
+ keywords = {Bond strength, Bond valence, Chemical composition, Clay mineral, Dioctahedral array, IR, IR spectroscopy, Ionic size, Nearest neighbour, Octahedral sites, Raman, Raman Spectroscopy, Reduced mass, Structure types, Trioctahedral array}
+}
+
+@incollection{Bommarius11,
+ title = {{Applications of Recombinant DNA Technology: Directed Evolution}},
+ year = {2004},
+ booktitle = {Biocatalysis},
+ author = {Bommarius, Andreas Sebastian and Riebel, Bettina R.},
+ chapter = {11},
+ month = {1},
+ pages = {309--338},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://onlinelibrary.wiley.com/doi/10.1002/3527602364.ch11/pdf http://doi.wiley.com/10.1002/3527602364.ch11},
+ address = {Weinheim, FRG},
+ isbn = {9783527602360},
+ doi = {10.1002/3527602364.ch11}
+}
+
+@article{Murray2007,
+ title = {{Applied clay mineralogy : occurrences, processing, and application of kaolins, bentonites, palygorskite-sepiolite, and common clays}},
+ year = {2007},
+ author = {Murray, Haydn H. (Haydn Herbert)},
+ pages = {180},
+ publisher = {Elsevier},
+ isbn = {978-0-444-51701-2}
+}
+
+@article{DeClercq2016,
+ title = {{Approved antiviral drugs over the past 50 years}},
+ year = {2016},
+ journal = {Clinical Microbiology Reviews},
+ author = {De Clercq, Erik and Li, Guangdi},
+ number = {3},
+ month = {7},
+ pages = {695--747},
+ volume = {29},
+ publisher = {American Society for Microbiology},
+ doi = {10.1128/CMR.00102-15},
+ issn = {10986618}
+}
+
+@incollection{Christidis2013,
+ title = {{Assessment of Industrial Clays}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Christidis, G. E.},
+ number = {C},
+ month = {1},
+ pages = {425--449},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00017-2},
+ issn = {15724352},
+ keywords = {Assessment, Bentonite, Common clays and shales, Industrial applications, Kaolin, Palygorskite, Physical and chemical properties, Sepiolite, Specifications}
+}
+
+@article{Wuensch2013,
+ title = {{Asymmetric Enzymatic Hydration of Hydroxystyrene Derivatives}},
+ year = {2013},
+ journal = {Angewandte Chemie International Edition},
+ author = {Wuensch, Christiane and Gross, Johannes and Steinkellner, Georg and Gruber, Karl and Glueck, Silvia M. and Faber, Kurt},
+ number = {8},
+ month = {2},
+ pages = {2293--2297},
+ volume = {52},
+ url = {http://doi.wiley.com/10.1002/anie.201207916 http://www.ncbi.nlm.nih.gov/pubmed/23335002 http://doi.wiley.com/10.1002/ange.201207916},
+ isbn = {14337851 (ISSN)},
+ doi = {10.1002/anie.201207916},
+ issn = {14337851},
+ pmid = {23335002},
+ keywords = {biotransformations, catalytic promiscuity, decarboxylases, enzyme catalysis, hydratases}
+}
+
+@article{Neumann2015,
+ title = {{Atom exchange between aqueous Fe(II) and structural Fe in clay minerals}},
+ year = {2015},
+ journal = {Environmental Science and Technology},
+ author = {Neumann, Anke and Wu, Lingling and Li, Weiqiang and Beard, Brian L. and Johnson, Clark M. and Rosso, Kevin M. and Frierdich, Andrew J. and Scherer, Michelle M.},
+ number = {5},
+ month = {3},
+ pages = {2786--2795},
+ volume = {49},
+ publisher = {American Chemical Society},
+ doi = {10.1021/ES504984Q},
+ issn = {15205851},
+ pmid = {25671351}
+}
+
+@article{Holmboe2019,
+ title = {{atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS}},
+ year = {2019},
+ journal = {Clays and Clay Minerals},
+ author = {Holmboe, Michael},
+ number = {5},
+ month = {10},
+ pages = {419--426},
+ volume = {67},
+ publisher = {Springer},
+ url = {moz-extension://c1bb7943-a542-4776-abea-3b772b374491/enhanced-reader.html?pdf=https%3A%2F%2Fbrxt.mendeley.com%2Fdocument%2Fcontent%2F13ed481d-dd6d-3844-9f76-62515b7125be https://link.springer.com/article/10.1007/s42860-019-00043-y},
+ doi = {10.1007/s42860-019-00043-y},
+ issn = {15528367},
+ keywords = {CLAYFF, Gromacs, INTERFACE force field, MATLAB, Molecular dynamics simulations, Monte Carlo}
+}
+
+@article{Holmboe2019a,
+ title = {{atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS}},
+ year = {2019},
+ journal = {Clays and Clay Minerals},
+ author = {Holmboe, Michael},
+ number = {5},
+ month = {10},
+ pages = {419--426},
+ volume = {67},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1007/s42860-019-00043-y},
+ doi = {10.1007/S42860-019-00043-Y/FIGURES/4},
+ issn = {15528367},
+ keywords = {CLAYFF, Gromacs, INTERFACE force field, MATLAB, Molecular dynamics simulations, Monte Carlo}
+}
+
+@article{Ho2017,
+ title = {{Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering}},
+ year = {2017},
+ journal = {Scientific Reports},
+ author = {Ho, Tuan Anh and Greathouse, Jeffery A and Wang, Yifeng and Criscenti, Louise J},
+ number = {1},
+ month = {12},
+ pages = {15286},
+ volume = {7},
+ url = {www.nature.com/scientificreports/ http://www.nature.com/articles/s41598-017-15639-4},
+ doi = {10.1038/s41598-017-15639-4},
+ issn = {2045-2322}
+}
+
+@article{Jo2007,
+ title = {{Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations}},
+ year = {2007},
+ journal = {PLoS ONE},
+ author = {Jo, Sunhwan and Kim, Taehoon and Im, Wonpil},
+ editor = {Yuan, Adam},
+ number = {9},
+ month = {9},
+ pages = {e880},
+ volume = {2},
+ url = {https://dx.plos.org/10.1371/journal.pone.0000880},
+ doi = {10.1371/journal.pone.0000880},
+ issn = {1932-6203}
+}
+
+@article{Vanommeslaeghe2012b,
+ title = {{Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing}},
+ year = {2012},
+ journal = {Journal of Chemical Information and Modeling},
+ author = {Vanommeslaeghe, K. and MacKerell, A. D.},
+ number = {12},
+ month = {12},
+ pages = {3144--3154},
+ volume = {52},
+ url = {https://pubs.acs.org/doi/10.1021/ci300363c},
+ doi = {10.1021/ci300363c},
+ issn = {1549-9596}
+}
+
+@article{Vanommeslaeghe2012,
+ title = {{Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges}},
+ year = {2012},
+ journal = {Journal of Chemical Information and Modeling},
+ author = {Vanommeslaeghe, K. and Raman, E. Prabhu and MacKerell, A. D.},
+ number = {12},
+ month = {12},
+ pages = {3155--3168},
+ volume = {52},
+ url = {https://pubs.acs.org/doi/10.1021/ci3003649},
+ doi = {10.1021/ci3003649},
+ issn = {1549-9596}
+}
+
+@article{Vanommeslaeghe2012a,
+ title = {{Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges}},
+ year = {2012},
+ journal = {Journal of Chemical Information and Modeling},
+ author = {Vanommeslaeghe, K. and Raman, E. Prabhu and MacKerell, A. D.},
+ number = {12},
+ month = {12},
+ pages = {3155--3168},
+ volume = {52},
+ url = {https://pubs.acs.org/doi/10.1021/ci3003649},
+ doi = {10.1021/ci3003649},
+ issn = {1549-9596}
+}
+
+@article{Chipera2001,
+ title = {{Baseline Studies of the Clay Minerals Society Source Clays: Powder X-ray Diffraction Analyses}},
+ year = {2001},
+ journal = {Clays and Clay Minerals},
+ author = {Chipera, Steve J.},
+ number = {5},
+ pages = {398--409},
+ volume = {49},
+ publisher = {Clay Minerals Society},
+ url = {http://link.springer.com/10.1346/CCMN.2001.0490507},
+ doi = {10.1346/CCMN.2001.0490507},
+ issn = {0009-8604}
+}
+
+@article{Lutz2011,
+ title = {{Beyond directed evolution - semi-rational protein engineering and design}},
+ year = {2011},
+ journal = {Current opinion in biotechnology},
+ author = {Lutz, Stefan},
+ number = {6},
+ pages = {734--743},
+ volume = {21},
+ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2982887&tool=pmcentrez&rendertype=abstract},
+ isbn = {1879-0429 (Electronic){\textbackslash}r0958-1669 (Linking)},
+ doi = {10.1016/j.copbio.2010.08.011.Beyond},
+ issn = {1879-0429},
+ pmid = {20869867},
+ keywords = {Biological, Computational Biology, Computational Biology: methods, Computational Biology: trends, Enzymes, Enzymes: chemical synthesis, Enzymes: chemistry, Enzymes: genetics, Enzymes: metabolism, Models, Protein Engineering, Protein Engineering: methods, Protein Engineering: trends, Structure-Activity Relationship}
+}
+
+@article{Palmisano2021,
+ title = {{Binding of azobenzene and p -diaminoazobenzene to the human voltage-gated sodium channel Na v 1.4}},
+ year = {2021},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Palmisano, Vito F. and G{\'{o}}mez-Rodellar, Carlos and Pollak, Hannah and C{\'{a}}rdenas, Gustavo and Corry, Ben and Faraji, Shirin and Nogueira, Juan J.},
+ number = {5},
+ month = {2},
+ pages = {3552--3564},
+ volume = {23},
+ publisher = {Royal Society of Chemistry (RSC)},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2021/cp/d0cp06140a https://pubs.rsc.org/en/content/articlelanding/2021/cp/d0cp06140a http://xlink.rsc.org/?DOI=D0CP06140A},
+ doi = {10.1039/D0CP06140A},
+ issn = {1463-9076}
+}
+
+@book{Bommarius200411,
+ title = {{Biocatalysis}},
+ year = {2004},
+ booktitle = {Applied Organometallic Chemistry},
+ author = {Bommarius, Andreas Sebastian (Andreas Sebastian) and Riebel, Bettina R. (Bettina R.)},
+ number = {7},
+ month = {1},
+ pages = {373},
+ volume = {18},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/aoc.651 http://doi.wiley.com/10.1002/3527602364},
+ address = {Weinheim, FRG},
+ isbn = {9783527602360},
+ doi = {10.1002/3527602364},
+ issn = {0268-2605}
+}
+
+@article{Johnson1999,
+ title = {{Biocatalytic Applications of Hydroxynitrile Lyases}},
+ year = {1999},
+ journal = {Advances In Biochemical Engineering},
+ author = {Johnson, Dean V and Griengl, Herfried},
+ volume = {63},
+ keywords = {molecular cloning, overexpression, reaction mechanism, transhydrocyanation}
+}
+
+@article{Ohta1999,
+ title = {{Biocatalytic asymmetric decarboxylation.}},
+ year = {1999},
+ journal = {Advances in biochemical engineering/biotechnology},
+ author = {Ohta, H},
+ number = {February},
+ pages = {1--30},
+ volume = {63},
+ issn = {0724-6145},
+ pmid = {9933980},
+ keywords = {a -arylpropionic acid, asymmetric decarboxylation, enzyme, reaction mechanism}
+}
+
+@article{OxDict,
+ title = {{Biochemistry and physiology of hexose-6-phosphate knockout mice}},
+ year = {2011},
+ journal = {Molecular and Cellular Endocrinology},
+ author = {Zielinska, Agnieszka E. and Walker, Elizabeth A. and Stewart, Paul M. and Lavery, Gareth G.},
+ number = {1-2},
+ month = {4},
+ pages = {213--218},
+ volume = {336},
+ publisher = {Oxford University Press},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/S0303720710005678 https://linkinghub.elsevier.com/retrieve/pii/S0303720710005678},
+ address = {Oxford},
+ isbn = {0 19 850673 2},
+ doi = {10.1016/j.mce.2010.12.004},
+ issn = {03037207},
+ keywords = {Endoplasmic reticulum, Glucocorticoid, Knockout mice, Metabolism, Muscle}
+}
+
+@article{Zhao2015,
+ title = {{Biological redox cycling of iron in nontronite and its potential application in nitrate removal}},
+ year = {2015},
+ journal = {Environmental Science and Technology},
+ author = {Zhao, Linduo and Dong, Hailiang and Kukkadapu, Ravi K. and Zeng, Qiang and Edelmann, Richard E. and Pentr{\'{a}}k, Martin and Agrawal, Abinash},
+ number = {9},
+ month = {5},
+ pages = {5493--5501},
+ volume = {49},
+ publisher = {American Chemical Society},
+ doi = {10.1021/ACS.EST.5B00131},
+ issn = {15205851},
+ pmid = {25873540}
+}
+
+@article{Dror2012,
+ title = {{Biomolecular Simulation: A Computational Microscope for Molecular Biology}},
+ year = {2012},
+ author = {Dror, Ron O and Dirks, Robert M and Grossman, J P and Xu, Huafeng and Shaw, David E},
+ url = {www.annualreviews.org},
+ doi = {10.1146/annurev-biophys-042910-155245},
+ keywords = {Anton, drug binding, millisecond timescale, molecular dynamics, protein folding}
+}
+
+@article{Ziebuhr1997,
+ title = {{Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase.}},
+ year = {1997},
+ journal = {Journal of virology},
+ author = {Ziebuhr, J and Heusipp, G and Siddell, S G},
+ number = {5},
+ pages = {3992--3997},
+ volume = {71},
+ publisher = {American Society for Microbiology},
+ url = {https://jvi.asm.org/content/71/5/3992},
+ doi = {10.1128/JVI.71.5.3992-3997.1997},
+ issn = {0022-538X},
+ pmid = {9094676}
+}
+
+@article{Adam1999,
+ title = {{Biotransformations with peroxidases.}},
+ year = {1999},
+ journal = {Advances in biochemical engineering/biotechnology},
+ author = {Adam, W and Lazarus, M and Saha-M{\"{o}}ller, C R and Weichold, O and Hoch, U and H{\"{a}}ring, D and Schreier, P},
+ pages = {73--108},
+ volume = {63},
+ isbn = {07246145 (ISSN)},
+ doi = {10.1007/3-540-69791-8{\_}4},
+ issn = {0724-6145},
+ pmid = {9933982},
+ keywords = {asymmetric synthesis, biocatalysis, epoxidation, halogenation, hydroperoxide, hydroxylation, kinetic resolution, peroxidase, phenol coupling, sulfoxidation}
+}
+
+@article{Dufreche2010,
+ title = {{Bridging molecular and continuous descriptions: The case of dynamics in clays}},
+ year = {2010},
+ journal = {Anais da Academia Brasileira de Ciencias},
+ author = {Dufr{\^{e}}che, Jean François and Rotenberg, Benjamin and Marry, Virginie and Turq, Pierre},
+ number = {1},
+ pages = {61--68},
+ volume = {82},
+ publisher = {Academia Brasileira de Ciencias},
+ doi = {10.1590/S0001-37652010000100006},
+ issn = {16782690},
+ pmid = {20209243},
+ keywords = {Brownian model, Clays, Hydrodynamics, Molecular dynamics, Multi-scale modelling}
+}
+
+@article{Izadi2014,
+ title = {{Building Water Models: A Different Approach}},
+ year = {2014},
+ journal = {The Journal of Physical Chemistry Letters},
+ author = {Izadi, Saeed and Anandakrishnan, Ramu and Onufriev, Alexey V.},
+ number = {21},
+ month = {11},
+ pages = {3863--3871},
+ volume = {5},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/jz501780a},
+ doi = {10.1021/jz501780a},
+ issn = {1948-7185},
+ arxivId = {1408.1679},
+ keywords = {electrostatics, liquid structure simulations, optimal point charge approximation, water models}
+}
+
+@article{Salanne2017,
+ title = {{Ca2+-Cl− Association in Water Revisited: the Role of Cation Hydration}},
+ year = {2017},
+ journal = {ChemPhysChem},
+ author = {Salanne, Mathieu and Tazi, Sami and Vuilleumier, Rodolphe and Rotenberg, Benjamin},
+ number = {19},
+ month = {10},
+ pages = {2807--2811},
+ volume = {18},
+ publisher = {Wiley-VCH Verlag},
+ doi = {10.1002/cphc.201700286},
+ issn = {14397641},
+ pmid = {28510283},
+ keywords = {calcium chloride, hydration, ion pair, molecular dynamics, potential of mean force}
+}
+
+@article{Saeki2004,
+ title = {{Ca2+-Fe2+ and Ca2+-Mn2+ exchange selectivity of kaolinite, montmorillonite, and illite}},
+ year = {2004},
+ journal = {Soil Science},
+ author = {Saeki, Kazutoshi and Wada, Shin Ichiro and Shibata, Masahiro},
+ number = {2},
+ pages = {125--132},
+ volume = {169},
+ publisher = {Lippincott Williams and Wilkins},
+ doi = {10.1097/01.ss.0000117786.98510.d4},
+ issn = {0038075X},
+ keywords = {Ca2+, Clay minerals, Fe2+, Ion exchange selectivity coefficient, Mn 2+}
+}
+
+@article{Bornscheuer2004,
+ title = {{Catalytic promiscuity in biocatalysis: Using old enzymes to form new bonds and follow new pathways}},
+ year = {2004},
+ journal = {Angewandte Chemie - International Edition},
+ author = {Bornscheuer, Uwe T. and Kazlauskas, Romas J.},
+ number = {45},
+ pages = {6032--6040},
+ volume = {43},
+ isbn = {14337851 (ISSN)},
+ doi = {10.1002/anie.200460416},
+ issn = {14337851},
+ pmid = {15523680},
+ keywords = {Biosynthesis, Biotransformations, Enzyme catalysis, Molecular modeling, Proteins}
+}
+
+@article{Fornaro2018a,
+ title = {{Catalytic/Protective Properties of Martian Minerals and Implications for Possible Origin of Life on Mars}},
+ year = {2018},
+ journal = {Life},
+ author = {Fornaro, Teresa and Steele, Andrew and Brucato, John},
+ number = {4},
+ month = {11},
+ volume = {8},
+ doi = {10.3390/life8040056},
+ issn = {2075-1729}
+}
+
+@article{Fornaro2018,
+ title = {{Catalytic/Protective Properties of Martian Minerals and Implications for Possible Origin of Life on Mars}},
+ year = {2018},
+ journal = {Life},
+ author = {Fornaro, Teresa and Steele, Andrew and Brucato, John},
+ number = {4},
+ month = {11},
+ pages = {56},
+ volume = {8},
+ publisher = {MDPI AG},
+ url = {http://www.mdpi.com/2075-1729/8/4/56 www.mdpi.com/journal/life},
+ doi = {10.3390/life8040056},
+ issn = {2075-1729},
+ keywords = {Biomarkers, Catalysis, Ionizing radiations, Mars, Minerals, Preservation, biomarkers, catalysis, ionizing radiations, minerals, preservation}
+}
+
+@incollection{Bergaya2013i,
+ title = {{Cation and Anion Exchange}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G. and Vayer, M.},
+ number = {C},
+ month = {1},
+ pages = {333--359},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00013-5},
+ issn = {15724352},
+ keywords = {Analytical techniques, Anion exchange, Binding coefficient, CEC determination, Cation exchange, Cation-exchange capacity, Equimolar exchange, Equivalent exchange, Gapon coefficient, HSAB character, Heterovalent exchange, Hydration, Hysteresis, Ion exchange, Selectivity coefficient, Separation factor, Surface precipitation, Thermodynamics, Vanselow coefficient}
+}
+
+@article{Kandasamy2006,
+ title = {{Cation and anion transport through hydrophilic pores in lipid bilayers}},
+ year = {2006},
+ journal = {Journal of Chemical Physics},
+ author = {Kandasamy, Senthil K. and Larson, Ronald G.},
+ number = {7},
+ volume = {125},
+ doi = {10.1063/1.2217737},
+ issn = {00219606}
+}
+
+@incollection{VanDamme2013,
+ title = {{Cement hydrates}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Van Damme, H. and Pellenq, R. J.M. and Ulm, F. J.},
+ pages = {801--817},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00027-4},
+ issn = {15724352},
+ keywords = {CSH, Cohesion, Double-layer interactions, Hydrates, Ionic correlation forces, LDH, Monte Carlo, Smectites, Swelling}
+}
+
+@article{HPII6667,
+ title = {{Cerium ammonium nitrate-mediated the oxidative dimerization of p-alkenylphenols: a new synthesis of substituted (±)-trans-dihydrobenzofurans}},
+ year = {2013},
+ journal = {Tetrahedron},
+ author = {Chen, Po-Yuan and Wu, Yi-Hua and Hsu, Mon-Huei and Wang, Tzu-Pin and Wang, Eng-Chi},
+ number = {2},
+ month = {1},
+ pages = {653--657},
+ volume = {69},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/S0040402012016663},
+ doi = {10.1016/j.tet.2012.11.006},
+ issn = {00404020}
+}
+
+@article{Mukai2016,
+ title = {{Cesium adsorption/desorption behavior of clay minerals considering actual contamination conditions in Fukushima}},
+ year = {2016},
+ journal = {Scientific Reports},
+ author = {Mukai, Hiroki and Hirose, Atsushi and Motai, Satoko and Kikuchi, Ryosuke and Tanoi, Keitaro and Nakanishi, Tomoko M. and Yaita, Tsuyoshi and Kogure, Toshihiro},
+ number = {1},
+ month = {2},
+ pages = {1--7},
+ volume = {6},
+ publisher = {Nature Publishing Group},
+ url = {www.nature.com/scientificreports/},
+ doi = {10.1038/srep21543},
+ issn = {20452322},
+ keywords = {Environmental sciences, Mineralogy}
+}
+
+@article{Posner1964,
+ title = {{Changes in basal spacing of montmorillonite in electrolyte solutions}},
+ year = {1964},
+ journal = {Journal of Colloid Science},
+ author = {Posner, A. M. and Quirk, J. P.},
+ number = {9},
+ month = {12},
+ pages = {798--812},
+ volume = {19},
+ publisher = {Academic Press},
+ doi = {10.1016/0095-8522(64)90056-X},
+ issn = {0095-8522}
+}
+
+@article{Murray2006e,
+ title = {{Chapter 1 Introduction}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {1--6},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02001-0},
+ issn = {15724352}
+}
+
+@article{Murray2006b,
+ title = {{Chapter 2 Structure and Composition of the Clay Minerals and their Physical and Chemical Properties}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {7--31},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02002-2},
+ issn = {15724352}
+}
+
+@article{Murray2006f,
+ title = {{Chapter 3 Geology and Location of Major Industrial Clay Deposits}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {33--65},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02003-4},
+ issn = {15724352}
+}
+
+@article{Murray2006i,
+ title = {{Chapter 4 Exploration, Mining, and Processing}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {67--83},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02004-6},
+ issn = {15724352}
+}
+
+@article{Murray2006h,
+ title = {{Chapter 5 Kaolin Applications}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {85--109},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02005-8},
+ issn = {15724352}
+}
+
+@article{Murray2006c,
+ title = {{Chapter 6 Bentonite Applications}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {111--130},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02006-X},
+ issn = {15724352}
+}
+
+@article{Murray2006g,
+ title = {{Chapter 7 Palygorskite and Sepiolite Applications}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {131--140},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02007-1},
+ issn = {15724352}
+}
+
+@article{Murray2006k,
+ title = {{Chapter 8 Common Clays}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Murray, Haydn H.},
+ number = {C},
+ pages = {141--145},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02008-3},
+ issn = {15724352}
+}
+
+@article{Elkhalifah2011,
+ title = {{Characterization of different cationic forms of montmorillonite by FTIR, XRD and TGA techniques}},
+ year = {2011},
+ journal = {2011 National Postgraduate Conference - Energy and Sustainability: Exploring the Innovative Minds, NPC 2011},
+ author = {Elkhalifah, Ali E.I. and Murugesan, T. and Bustam, M. Azmi},
+ isbn = {9781457718847},
+ doi = {10.1109/NATPC.2011.6136275},
+ keywords = {Characeterization, FTIR, Montmorillonite, TGA, XRD, exchangeable cation}
+}
+
+@techreport{Scholarship2020,
+ title = {{Characterization of Impactite Clay Minerals with Implications for Characterization of Impactite Clay Minerals with Implications for Mars Geologic Context and Mars Sample Return Mars Geologic Context and Mars Sample Return}},
+ year = {2020},
+ author = {Scholarship, Western and Caudill, Christy M and Gordon Osinski, Supervisor}
+}
+
+@article{McKeown2009,
+ title = {{Characterization of phyllosilicates observed in the central Mawrth Vallis region, Mars, their potential formational processes, and implications for past climate}},
+ year = {2009},
+ journal = {Journal of Geophysical Research},
+ author = {McKeown, Nancy K. and Bishop, Janice L. and Noe Dobrea, Eldar Z. and Ehlmann, Bethany L. and Parente, Mario and Mustard, John F. and Murchie, Scott L. and Swayze, Gregg A. and Bibring, Jean-Pierre and Silver, Eli A.},
+ month = {11},
+ pages = {E00D10},
+ volume = {114},
+ url = {http://doi.wiley.com/10.1029/2008JE003301},
+ doi = {10.1029/2008JE003301},
+ issn = {0148-0227},
+ keywords = {CRISM, Mawrth Vallis, doi:10.1029/2008JE003301, http://dx.doi.org/10.1029/2008JE003301, phyllosilicates}
+}
+
+@incollection{Preocanin2016,
+ title = {{Charging Behavior of Clays and Clay Minerals in Aqueous Electrolyte Solutions — Experimental Methods for Measuring the Charge and Interpreting the Results}},
+ year = {2016},
+ booktitle = {Clays, Clay Minerals and Ceramic Materials Based on Clay Minerals},
+ author = {Preocanin, Tajana and Abdelmonem, Ahmed and Montavon, Gilles and Luetzenkirchen, Johannes},
+ month = {3},
+ publisher = {InTech},
+ url = {http://dx.doi.org/10.5772/62082},
+ doi = {10.5772/62082},
+ keywords = {Mass titration, acid-base properties, adsorption, clay mineral, montmorillonite, smectite, surface charge}
+}
+
+@misc{Vanommeslaeghe2015,
+ title = {{CHARMM additive and polarizable force fields for biophysics and computer-aided drug design}},
+ year = {2015},
+ booktitle = {Biochimica et Biophysica Acta - General Subjects},
+ author = {Vanommeslaeghe, K. and Mackerell, A. D.},
+ number = {5},
+ month = {5},
+ pages = {861--871},
+ volume = {1850},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.bbagen.2014.08.004},
+ issn = {18728006},
+ keywords = {Biophysics, Computer-aided drug design, Empirical force field, Molecular Mechanics, Molecular dynamics, Potential energy function}
+}
+
+@article{Vanommeslaeghe2009,
+ title = {{CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields}},
+ year = {2009},
+ journal = {Journal of Computational Chemistry},
+ author = {Vanommeslaeghe, K. and Hatcher, E. and Acharya, C. and Kundu, S. and Zhong, S. and Shim, J. and Darian, E. and Guvench, O. and Lopes, P. and Vorobyov, I. and Mackerell, A. D.},
+ pages = {NA-NA},
+ url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.21367},
+ doi = {10.1002/jcc.21367},
+ issn = {01928651}
+}
+
+@article{Lee2016,
+ title = {{CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field}},
+ year = {2016},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Lee, Jumin and Cheng, Xi and Swails, Jason M. and Yeom, Min Sun and Eastman, Peter K. and Lemkul, Justin A. and Wei, Shuai and Buckner, Joshua and Jeong, Jong Cheol and Qi, Yifei and Jo, Sunhwan and Pande, Vijay S. and Case, David A. and Brooks, Charles L. and MacKerell, Alexander D. and Klauda, Jeffery B. and Im, Wonpil},
+ number = {1},
+ month = {1},
+ pages = {405--413},
+ volume = {12},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jctc.5b00935},
+ doi = {10.1021/acs.jctc.5b00935},
+ issn = {1549-9618}
+}
+
+@article{Wu2014,
+ title = {{CHARMM-GUI Membrane Builder toward realistic biological membrane simulations}},
+ year = {2014},
+ journal = {Journal of Computational Chemistry},
+ author = {Wu, Emilia L. and Cheng, Xi and Jo, Sunhwan and Rui, Huan and Song, Kevin C. and D{\'{a}}vila-Contreras, Eder M. and Qi, Yifei and Lee, Jumin and Monje-Galvan, Viviana and Venable, Richard M. and Klauda, Jeffery B. and Im, Wonpil},
+ number = {27},
+ month = {10},
+ pages = {1997--2004},
+ volume = {35},
+ url = {http://doi.wiley.com/10.1002/jcc.23702},
+ doi = {10.1002/jcc.23702},
+ issn = {01928651}
+}
+
+@article{Choi2021,
+ title = {{CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems}},
+ year = {2021},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Choi, Yeol Kyo and Kern, Nathan R. and Kim, Seonghan and Kanhaiya, Krishan and Afshar, Yaser and Jeon, Sun Hee and Jo, Sunhwan and Brooks, Bernard R. and Lee, Jumin and Tadmor, Ellad B. and Heinz, Hendrik and Im, Wonpil},
+ month = {12},
+ pages = {acs.jctc.1c00996},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jctc.1c00996},
+ doi = {10.1021/acs.jctc.1c00996},
+ issn = {1549-9618}
+}
+
+@article{Jo2008,
+ title = {{CHARMM-GUI: A web-based graphical user interface for CHARMM}},
+ year = {2008},
+ journal = {Journal of Computational Chemistry},
+ author = {Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil},
+ number = {11},
+ month = {8},
+ pages = {1859--1865},
+ volume = {29},
+ url = {http://doi.wiley.com/10.1002/jcc.20945},
+ doi = {10.1002/jcc.20945},
+ issn = {01928651}
+}
+
+@article{Huang2017,
+ title = {{CHARMM36m: an improved force field for folded and intrinsically disordered proteins}},
+ year = {2017},
+ journal = {Nature Methods},
+ author = {Huang, Jing and Rauscher, Sarah and Nawrocki, Grzegorz and Ran, Ting and Feig, Michael and de Groot, Bert L and Grubm{\"{u}}ller, Helmut and MacKerell, Alexander D.},
+ number = {1},
+ month = {1},
+ pages = {71--73},
+ volume = {14},
+ publisher = {Nature Publishing Group},
+ url = {http://www.nature.com/articles/nmeth.4067},
+ doi = {10.1038/nmeth.4067},
+ issn = {1548-7091}
+}
+
+@article{Yoshizawa1993,
+ title = {{Chavicol and Related Compounds as Nematocides}},
+ year = {1993},
+ journal = {Biosci. Biotech. Biochem},
+ author = {Yoshizawa, Yuko and Kawaii, Satoru and Kanauchi, Masatoshi and Chida, Manami and Mizutani, Junya},
+ number = {9},
+ pages = {1572--1574},
+ volume = {57},
+ url = {http://www.tandfonline.com/doi/pdf/10.1271/bbb.57.1572?needAccess=true}
+}
+
+@article{Ohigashi1976,
+ title = {{Chavicol, as a Larva-growth Inhibitor, from Viburnum japonicum Spreng}},
+ year = {1976},
+ journal = {Agricultural and Biological Chemistry ISSN:},
+ author = {Ohigashi, Hajime and Koshimizu, Koichi},
+ number = {11},
+ pages = {2283--2287},
+ volume = {40},
+ url = {http://www.tandfonline.com/doi/pdf/10.1080/00021369.1976.10862375?needAccess=true},
+ doi = {10.1080/00021369.1976.10862375}
+}
+
+@incollection{Bain1994,
+ title = {{Chemical analysis}},
+ year = {1994},
+ booktitle = {Clay Mineralogy: Spectroscopic and Chemical Determinative Methods},
+ author = {Bain, D. C. and Smith, B. F. L.},
+ pages = {300--332},
+ publisher = {Springer Netherlands},
+ url = {https://link.springer.com/chapter/10.1007/978-94-011-0727-3_8 http://link.springer.com/10.1007/978-94-011-0727-3_8},
+ address = {Dordrecht},
+ doi = {10.1007/978-94-011-0727-3{\_}8}
+}
+
+@article{Srodon1986,
+ title = {{Chemistry of illite/smectite and end-member illite.}},
+ year = {1986},
+ journal = {Clays {\&} Clay Minerals},
+ author = {Srodon, J. and Morgan, D. J. and Eslinger, E. V. and Eberl, D. D. and Karlinger, M. R.},
+ number = {4},
+ pages = {368--378},
+ volume = {34},
+ doi = {10.1346/CCMN.1986.0340403},
+ issn = {0009-8604}
+}
+
+@article{Aspuru-Guzik2005,
+ title = {{Chemistry: Simulated quantum computation of molecular energies}},
+ year = {2005},
+ journal = {Science},
+ author = {Aspuru-Guzik, Alán and Dutoi, Anthony D. and Love, Peter J. and Head-Gordon, Martin},
+ number = {5741},
+ month = {9},
+ pages = {1704--1707},
+ volume = {309},
+ url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1113479},
+ doi = {10.1126/science.1113479},
+ issn = {00368075}
+}
+
+@article{TraniChap21,
+ title = {{Chimeragenesis in Protein Engineering}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Trani, Manuela and Lutz, Stefan},
+ pages = {493--514},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch21},
+ keywords = {Chimeragenesis, Homology-independent recombination, Hybrid enzymes, ITCHY, SCHEMA, SCRATCHY}
+}
+
+@article{Cisneros2014,
+ title = {{Classical Electrostatics for Biomolecular Simulations}},
+ year = {2014},
+ journal = {Chemical Reviews},
+ author = {Cisneros, G. Andrés and Karttunen, Mikko and Ren, Pengyu and Sagui, Celeste},
+ number = {1},
+ month = {1},
+ pages = {779--814},
+ volume = {114},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/cr300461d},
+ doi = {10.1021/cr300461d},
+ issn = {0009-2665},
+ pmid = {23981057}
+}
+
+@article{Tesson2016,
+ title = {{Classical Polarizable Force Field for Clays: Pyrophyllite and Talc}},
+ year = {2016},
+ journal = {Journal of Physical Chemistry C},
+ author = {Tesson, Stéphane and Salanne, Mathieu and Rotenberg, Benjamin and Tazi, Sami and Marry, Virginie},
+ number = {7},
+ month = {2},
+ pages = {3749--3758},
+ volume = {120},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.5b10181},
+ issn = {19327455}
+}
+
+@article{Tesson2017,
+ title = {{Classical Polarizable Force Field to Study Dry Charged Clays and Zeolites}},
+ year = {2017},
+ journal = {Journal of Physical Chemistry C},
+ author = {Tesson, Stéphane and Louisfrema, Wilfried and Salanne, Mathieu and Boutin, Anne and Rotenberg, Benjamin and Marry, Virginie},
+ number = {18},
+ month = {5},
+ pages = {9833--9846},
+ volume = {121},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.7b00270},
+ issn = {19327455}
+}
+
+@article{Tesson2018,
+ title = {{Classical Polarizable Force Field to Study Hydrated Charged Clays and Zeolites}},
+ year = {2018},
+ journal = {Journal of Physical Chemistry C},
+ author = {Tesson, Stéphane and Louisfrema, Wilfried and Salanne, Mathieu and Boutin, Anne and Ferrage, Eric and Rotenberg, Benjamin and Marry, Virginie},
+ number = {43},
+ month = {11},
+ pages = {24690--24704},
+ volume = {122},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.8b06230},
+ issn = {19327455}
+}
+
+@article{Hande2018,
+ title = {{Classical polarizable force field to study hydrated hectorite: Optimization on DFT calculations and validation against XRD data}},
+ year = {2018},
+ journal = {Minerals},
+ author = {H{\aa}nde, Ragnhild and Ramothe, Vivien and Tesson, Stéphane and Dazas, Baptiste and Ferrage, Eric and Lanson, Bruno and Salanne, Mathieu and Rotenberg, Benjamin and Marry, Virginie},
+ number = {5},
+ month = {5},
+ volume = {8},
+ publisher = {MDPI AG},
+ doi = {10.3390/min8050205},
+ issn = {2075163X},
+ keywords = {Ca-, Density functional theory, Hydrated charged clay, Molecular dynamics, Na-, Polarizability, Sr- and Cs-hectorites, X-ray diffraction}
+}
+
+@incollection{Wagner2013a,
+ title = {{Clay Liners and Waste Disposal}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Wagner, J. F.},
+ number = {C},
+ month = {1},
+ pages = {663--676},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00023-8},
+ issn = {15724352},
+ keywords = {Bottom liner, Compacted clay, Contaminant retention, Cover liner, Cut-off wall, Geosynthetic clay liner, Long-term stability}
+}
+
+@article{Bristow2018,
+ title = {{Clay mineral diversity and abundance in sedimentary rocks of Gale crater, Mars}},
+ year = {2018},
+ journal = {Science Advances},
+ author = {Bristow, Thomas F. and Rampe, Elizabeth B. and Achilles, Cherie N. and Blake, David F. and Chipera, Steve J. and Craig, Patricia and Crisp, Joy A. and Des Marais, David J. and Downs, Robert T. and Gellert, Ralf and Grotzinger, John P. and Gupta, Sanjeev and Hazen, Robert M. and Horgan, Briony and Hogancamp, Joanna V. and Mangold, Nicolas and Mahaffy, Paul R. and McAdam, Amy C. and Ming, Doug W. and Morookian, John Michael and Morris, Richard V. and Morrison, Shaunna M. and Treiman, Allan H. and Vaniman, David T. and Vasavada, Ashwin R. and Yen, Albert S.},
+ number = {6},
+ month = {6},
+ volume = {4},
+ doi = {10.1126/sciadv.aar3330},
+ issn = {2375-2548}
+}
+
+@incollection{Lagaly2013,
+ title = {{Clay mineral-organic interactions}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Lagaly, G. and Ogawa, M. and D{\'{e}}k{\'{a}}ny, I.},
+ pages = {435--505},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00015-8},
+ issn = {15724352},
+ keywords = {adsorption, adsorption excess isotherms, adsorption from binary solution, alkylammonium clay minerals, amino acids, displacement reactions, dyes, entraining reactions, hydrophilic/hydrophobic balance, intercalation, layer charge, organic derivatives, organo-clays, phase transitions, polymerisation, polymers, proteins, solvation}
+}
+
+@incollection{Brack2013,
+ title = {{Clay Minerals and the Origin of Life}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Brack, A.},
+ pages = {507--521},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00016-X},
+ issn = {15724352},
+ keywords = {Amino acids, Catalysts, Homochirality, Origins of life, Polynucleotides, Polypeptides, RNA, Vesicles}
+}
+
+@article{Schoonheydt2018,
+ title = {{Clay minerals and their surfaces}},
+ year = {2018},
+ journal = {Developments in Clay Science},
+ author = {Schoonheydt, Robert A. and Johnston, Cliff T. and Bergaya, Faïza},
+ month = {1},
+ pages = {1--21},
+ volume = {9},
+ publisher = {Elsevier},
+ doi = {10.1016/B978-0-08-102432-4.00001-9},
+ issn = {1572-4352},
+ keywords = {Cation exchange, H-bonding, Intercalation, Isomorphous substitution, Lennard-Jones potential, Swelling, TO and TOT clay minerals, van der Waals energy}
+}
+
+@incollection{Mccabe2013,
+ title = {{Clay Minerals as Catalysts}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Mccabe, R. W. and Adams, J. M.},
+ number = {C},
+ month = {1},
+ pages = {491--538},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00019-6},
+ issn = {15724352},
+ keywords = {Br{\o}nsted acidity, Catalysis, Clay minerals, Cycloaddition reactions, Lewis acidity, Microwaves, Reactive intermediates, Redox reactions, Selectivity, Supported catalysts, Supported reagents, Ultrasound}
+}
+
+@incollection{Bergaya2013f,
+ title = {{Clay science: A young discipline and a great perspective}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Beneke, K. and Berry, R. W. and Lagaly, G. and Tankersley, K. B.},
+ pages = {819--855},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00028-6},
+ issn = {15724352},
+ keywords = {Archaeology, Clay groups, Clay meetings, First localities of clay minerals, History, Name of clay minerals, Teaching}
+}
+
+@article{Anderson2010,
+ title = {{Clay swelling — A challenge in the oilfield}},
+ year = {2010},
+ journal = {Earth-Science Reviews},
+ author = {Anderson, R. L. and Ratcliffe, I. and Greenwell, H. C. and Williams, P. A. and Cliffe, S. and Coveney, P. V.},
+ number = {3-4},
+ month = {2},
+ pages = {201--216},
+ volume = {98},
+ publisher = {Elsevier},
+ doi = {10.1016/J.EARSCIREV.2009.11.003},
+ issn = {0012-8252},
+ keywords = {clay swelling, clays, computer simulation, drilling fluid, oil exploration}
+}
+
+@article{Bourg2017a,
+ title = {{Clay, Water, and Salt: Controls on the Permeability of Fine-Grained Sedimentary Rocks}},
+ year = {2017},
+ journal = {Accounts of Chemical Research},
+ author = {Bourg, Ian C. and Ajo-Franklin, Jonathan B.},
+ number = {9},
+ month = {9},
+ pages = {2067--2074},
+ volume = {50},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.accounts.7b00261},
+ issn = {15204898},
+ pmid = {28862427}
+}
+
+@misc{Dong2012,
+ title = {{Clay-microbe interactions and implications for environmental mitigation}},
+ year = {2012},
+ booktitle = {Elements},
+ author = {Dong, Hailiang},
+ number = {2},
+ month = {4},
+ pages = {113--118},
+ volume = {8},
+ doi = {10.2113/gselements.8.2.113},
+ issn = {18115209},
+ keywords = {Clay minerals, Microorganisms, Oxidation, Reduction, Transformation}
+}
+
+@article{Franchi1999,
+ title = {{CLAY-NUCLEIC ACID COMPLEXES: CHARACTERISTICS AND IMPLICATIONS FOR THE PRESERVATION OF GENETIC MATERIAL IN PRIMEVAL HABITATS}},
+ year = {1999},
+ author = {Franchi, Marco and Bramanti, Emilia and Bonzi, Laura Morassi and Orioli, Pier Luigi and Vettori, Cristina and Gallori, Enzo},
+ doi = {https://doi.org/10.1023/A:1006557832574}
+}
+
+@article{Bodine1987,
+ title = {{CLAYFORM: a FORTRAN 77 computer program apportioning the constituents in the chemical analysis of a clay or other silicate mineral into a structural formula}},
+ year = {1987},
+ journal = {Computers {\&} Geosciences},
+ author = {Bodine, Marc W.},
+ number = {1},
+ month = {1},
+ pages = {77--88},
+ volume = {13},
+ publisher = {Pergamon},
+ doi = {10.1016/0098-3004(87)90025-2},
+ issn = {0098-3004},
+ keywords = {Chemical analysis, Clay minerals, Ideal stoichiometries, Silicate structural formula}
+}
+
+@incollection{Yuan2013,
+ title = {{Clays and Clay Minerals for Pollution Control}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Yuan, G. D. and Theng, B. K.G. and Churchman, G. J. and Gates, W. P.},
+ number = {C},
+ month = {1},
+ pages = {587--644},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00021-4},
+ issn = {15724352},
+ keywords = {Environmental materials, Environmental remediation, Heavy metals, Nanoparticles, Organic contaminants, Organoclays}
+}
+
+@techreport{Valaskova2015a,
+ title = {{CLAYS, CLAY MINERALS AND CORDIERITE CERAMICS-A REVIEW}},
+ year = {2015},
+ booktitle = {Original papers Ceramics-Silik{\'{a}}ty},
+ author = {Val{\'{a}}{\v{s}}kov{\'{a}}, Marta},
+ number = {4},
+ pages = {331--340},
+ volume = {59},
+ keywords = {Clay minerals, Clays, Cordierite ceramics, Cordierite polymorphs}
+}
+
+@techreport{Valaskova2015,
+ title = {{CLAYS, CLAY MINERALS AND CORDIERITE CERAMICS-A REVIEW}},
+ year = {2015},
+ booktitle = {Original papers Ceramics-Silik{\'{a}}ty},
+ author = {Val{\'{a}}{\v{s}}kov{\'{a}}, Marta},
+ number = {4},
+ pages = {331--340},
+ volume = {59},
+ keywords = {Clay minerals, Clays, Cordierite ceramics, Cordierite polymorphs}
+}
+
+@incollection{Nir2013,
+ title = {{Clays, Clay Minerals, and Pesticides}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Nir, S. and El-Nahhal, Y. and Undabeytia, T. and Rytwo, G. and Polubesova, T. and Mishael, Y. and Rabinovitz, O. and Rubin, B.},
+ number = {C},
+ month = {1},
+ pages = {645--662},
+ volume = {5},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982595000226},
+ doi = {10.1016/B978-0-08-098259-5.00022-6},
+ keywords = {Adsorption, Clay polymer nanaocomposite, Herbicide formulations, Liposome–clay mineral, Micelle–clay mineral formulations, Octadecyl trimethylammonium, Organoclay formulations, Photostabilization, Slow release formulations, Volatilization}
+}
+
+@incollection{Carretero2013,
+ title = {{Clays, Drugs, and Human Health}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Carretero, M. I. and Gomes, C. S.F. and Tateo, F.},
+ number = {C},
+ month = {1},
+ pages = {711--764},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00025-1},
+ issn = {15724352},
+ keywords = {Active ingredients and excipients, Beneficial effects of clays and clay minerals, Cosmetic products, Harmful effects of clays and clay minerals, Medical applications, Pelotherapy}
+}
+
+@incollection{Tazaki2013,
+ title = {{Clays, micro-organisms and biomineralization}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Tazaki, K.},
+ pages = {613--653},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00019-5},
+ issn = {15724352},
+ keywords = {Biomineralization, electron microscopy, imogolite, oil spill, pisoliths, radioactive minerals}
+}
+
+@misc{Dunn2011,
+ title = {{Cloaking malware with the trusted platform module}},
+ year = {2011},
+ booktitle = {Proceedings of the 20th USENIX Security Symposium},
+ author = {Dunn, Alan M. and Hofmann, Owen S. and Waters, Brent and Witchel, Emmett},
+ pages = {395--410},
+ isbn = {9781931971874}
+}
+
+@article{Carof2014,
+ title = {{Coarse graining the dynamics of nano-confined solutes: The case of ions in clays}},
+ year = {2014},
+ journal = {Molecular Simulation},
+ author = {Carof, Antoine and Marry, Virginie and Salanne, Mathieu and Hansen, Jean Pierre and Turq, Pierre and Rotenberg, Benjamin},
+ number = {1-3},
+ pages = {237--244},
+ volume = {40},
+ doi = {10.1080/08927022.2013.840894},
+ issn = {08927022},
+ keywords = {cesium, clays, confinement, generalised Langevin dynamics, memory function}
+}
+
+@incollection{Lagaly2013a,
+ title = {{Colloid Clay Science}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Lagaly, G. and D{\'{e}}k{\'{a}}ny, I.},
+ pages = {243--345},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00010-9},
+ issn = {15724352},
+ keywords = {Aggregation, Charge distribution, Clay-water interaction, Coagulation, Colloids, DLVO theory, Deflocculation, Delamination, Depletion effect, Diffuse ionic layer, Dispersion, Electrokinetic properties, Electrostatic stabilization, Exfoliation, Filtration, Flocculation, Fractionation, Gel, Hydrates, Ion exchange, Mixed-layer structure, Nanoparticles, Particle shape, Particle size, Peptization, Plastering, Plasticity, Polyanions, Polycations, Polyelectrolytes, Polymers, Rheology, Salt effect, Sealing, Sedimentation, Sol, Steric stabilization, Stirring, Stokes' equations, Surfactants, Thixotropy, van der Waals interaction}
+}
+
+@techreport{Sposito1999a,
+ title = {{Colloquium Paper This paper was presented at the National Academy of Sciences colloquium ''Geology, Mineralogy, and Human Welfare}},
+ year = {1999},
+ author = {Sposito, Garrison and Skipper, Neal T and Sutton, Rebecca and Park, Sung-Ho and Soper, Alan K and Greathouse, Jeffery A},
+ pages = {3358--3364},
+ volume = {96},
+ url = {www.pnas.org.}
+}
+
+@article{Capkova2003,
+ title = {{Combination of modeling and experiment in structure analysis of intercalated layer silicates}},
+ year = {2003},
+ journal = {Journal of Molecular Modeling},
+ author = {{\v{C}}apkov{\'{a}}, Pavla and Posp{\'{i}}{\v{s}}il, Miroslav and Weiss, Zdeněk},
+ number = {3},
+ month = {6},
+ pages = {195--205},
+ volume = {9},
+ url = {http://link.springer.com/10.1007/s00894-002-0106-9},
+ doi = {10.1007/s00894-002-0106-9},
+ issn = {1610-2940},
+ keywords = {Intercalated layer silicates {\textperiodcentered}, Molecular dynamics, Molecular mechanics {\textperiodcentered}, Structure analysis modeling {\textperiodcentered}}
+}
+
+@article{Reetz2001a,
+ title = {{Combinatorial and Evolution-Based Methods in the Creation of Enantioselective Catalysts}},
+ year = {2001},
+ journal = {Angewandte Chemie International Edition},
+ author = {Reetz, Manfred T.},
+ number = {2},
+ month = {1},
+ pages = {284--310},
+ volume = {40},
+ url = {http://doi.wiley.com/10.1002/1521-3773%2820010119%2940%3A2%3C284%3A%3AAID-ANIE284%3E3.0.CO%3B2-N},
+ isbn = {1521-3773},
+ doi = {10.1002/1521-3773(20010119)40:2<284::AID-ANIE284>3.0.CO;2-N},
+ issn = {1433-7851},
+ pmid = {11180317},
+ keywords = {Analytical methods, Asymmetric catalysis, Combinatorial chemistry, Directed evolution, Enzyme catalysis, High-throughput screening}
+}
+
+@article{Reetz2001,
+ title = {{Combinatorial and Evolution-Based Methods in the Creation of Enantioselective Catalysts}},
+ year = {2001},
+ journal = {Angewandte Chemie International Edition},
+ author = {Reetz, Manfred T.},
+ number = {2},
+ month = {1},
+ pages = {284--310},
+ volume = {40},
+ url = {http://doi.wiley.com/10.1002/1521-3773%2820010119%2940%3A2%3C284%3A%3AAID-ANIE284%3E3.0.CO%3B2-N},
+ isbn = {1521-3773},
+ doi = {10.1002/1521-3773(20010119)40:2<284::AID-ANIE284>3.0.CO;2-N},
+ issn = {1433-7851},
+ pmid = {11180317},
+ keywords = {Analytical methods, Asymmetric catalysis, Combinatorial chemistry, Directed evolution, Enzyme catalysis, High-throughput screening}
+}
+
+@article{Wilson2014,
+ title = {{Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance}},
+ year = {2014},
+ journal = {Journal of Chemical Physics},
+ author = {Wilson, Michael A. and Nguyen, Thuy Hien and Pohorille, Andrew},
+ number = {22},
+ month = {12},
+ pages = {22D519},
+ volume = {141},
+ publisher = {American Institute of Physics Inc.},
+ url = {http://aip.scitation.org/doi/10.1063/1.4900879},
+ doi = {10.1063/1.4900879},
+ issn = {00219606},
+ keywords = {biodiffusion, bioelectric phenomena, biomembrane transport, free energy, molecular biophysics, molecular dynamics method, proteins}
+}
+
+@article{Chatterji2005,
+ title = {{Combining molecular dynamics with Lattice Boltzmann: A hybrid method for the simulation of (charged) colloidal systems}},
+ year = {2005},
+ journal = {Journal of Chemical Physics},
+ author = {Chatterji, Apratim and Horbach, Jürgen},
+ number = {18},
+ month = {5},
+ volume = {122},
+ doi = {10.1063/1.1890905},
+ issn = {00219606},
+ arxivId = {cond-mat/0505276}
+}
+
+@misc{Evans1984,
+ title = {{Comment on "Extensions of the molecular dynamics simulation method. II. Isothermal systems"}},
+ year = {1984},
+ booktitle = {The Journal of Chemical Physics},
+ author = {Evans, Denis J. and Morriss, Gary P.},
+ number = {8},
+ pages = {3749--3750},
+ volume = {81},
+ doi = {10.1063/1.448095},
+ issn = {00219606}
+}
+
+@article{Jorgensen1983,
+ title = {{Comparison of simple potential functions for simulating liquid water}},
+ year = {1983},
+ journal = {The Journal of Chemical Physics},
+ author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
+ number = {2},
+ pages = {926--935},
+ volume = {79},
+ doi = {10.1063/1.445869},
+ issn = {00219606}
+}
+
+@article{Yang2020,
+ title = {{Competitive Adsorption of Metal Ions at Smectite/Water Interfaces: Mechanistic Aspects, and Impacts of Co-Ions, Charge Densities, and Charge Locations}},
+ year = {2020},
+ journal = {Journal of Physical Chemistry C},
+ author = {Yang, Sen and Li, Xiong and Li, Qinyi and Gu, Peike and Liu, Xiantang and Yang, Gang},
+ number = {2},
+ month = {1},
+ pages = {1500--1510},
+ volume = {124},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/acs.jpcc.9b10341},
+ issn = {19327455}
+}
+
+@article{Martinez2020,
+ title = {{Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus}},
+ year = {2020},
+ journal = {Antimicrobial Agents and Chemotherapy},
+ author = {Martinez, Miguel Angel},
+ number = {5},
+ month = {3},
+ pages = {00399--20},
+ volume = {64},
+ publisher = {NLM (Medline)},
+ url = {https://aac.asm.org/content/aac/64/5/e00399-20.full.pdf https://aac.asm.org/content/64/5/e00399-20},
+ doi = {10.1128/AAC.00399-20},
+ issn = {0066-4804},
+ pmid = {32152082},
+ keywords = {Antiviral agents, Coronavirus, SARS-CoV-2}
+}
+
+@article{Whitfield2013,
+ title = {{Computational complexity in electronic structure}},
+ year = {2013},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Whitfield, James Daniel and Love, Peter John and Aspuru-Guzik, Alán},
+ number = {2},
+ pages = {397--411},
+ volume = {15},
+ url = {http://xlink.rsc.org/?DOI=C2CP42695A},
+ doi = {10.1039/c2cp42695a},
+ issn = {14639076},
+ arxivId = {1208.3334}
+}
+
+@article{VaissierWelborn2019,
+ title = {{Computational Design of Synthetic Enzymes}},
+ year = {2019},
+ journal = {Chemical Reviews},
+ author = {Vaissier Welborn, Valerie and Head-Gordon, Teresa},
+ number = {11},
+ month = {6},
+ pages = {6613--6630},
+ volume = {119},
+ publisher = {American Chemical Society},
+ url = {http://pubs.acs.org/doi/10.1021/acs.chemrev.8b00399},
+ doi = {10.1021/acs.chemrev.8b00399},
+ issn = {0009-2665}
+}
+
+@article{Kiss2013,
+ title = {{Computational Enzyme Design}},
+ year = {2013},
+ journal = {Angewandte Chemie International Edition},
+ author = {Kiss, Gert and {\c{C}}elebi-{\"{O}}l{\c{c}}{\"{u}}m, Nihan and Moretti, Rocco and Baker, David and Houk, K. N.},
+ number = {22},
+ month = {5},
+ pages = {5700--5725},
+ volume = {52},
+ url = {http://doi.wiley.com/10.1002/anie.201204077},
+ doi = {10.1002/anie.201204077},
+ issn = {14337851},
+ keywords = {active-site design, biomolecular catalysis, non-natural reactions, protein engineering, theozymes}
+}
+
+@article{Mak2014,
+ title = {{Computational enzyme design: Transitioning from catalytic proteins to enzymes}},
+ year = {2014},
+ journal = {Current Opinion in Structural Biology},
+ author = {Mak, Wai Shun and Siegel, Justin B.},
+ number = {1},
+ pages = {87--94},
+ volume = {27},
+ publisher = {Elsevier Ltd},
+ url = {http://dx.doi.org/10.1016/j.sbi.2014.05.010},
+ isbn = {1879-033X (Electronic){\textbackslash}r0959-440X (Linking)},
+ doi = {10.1016/j.sbi.2014.05.010},
+ issn = {1879033X},
+ pmid = {25005925}
+}
+
+@article{Swiderek2015,
+ title = {{Computational strategies for the design of new enzymatic functions}},
+ year = {2015},
+ journal = {Archives of Biochemistry and Biophysics},
+ author = {{\'{S}}widerek, K. and Tu{\~{n}}{\'{o}}n, I. and Moliner, V. and Bertran, J.},
+ month = {9},
+ pages = {68--79},
+ volume = {582},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0003986115001411},
+ doi = {10.1016/j.abb.2015.03.013},
+ issn = {00039861}
+}
+
+@article{Damborsky2014,
+ title = {{Computational tools for designing and engineering enzymes}},
+ year = {2014},
+ journal = {Current Opinion in Chemical Biology},
+ author = {Damborsky, Jiri and Brezovsky, Jan},
+ number = {1},
+ pages = {8--16},
+ volume = {19},
+ publisher = {Elsevier Ltd},
+ url = {http://dx.doi.org/10.1016/j.cbpa.2013.12.003},
+ isbn = {1367-5931},
+ doi = {10.1016/j.cbpa.2013.12.003},
+ issn = {13675931},
+ pmid = {24780274}
+}
+
+@article{Skipper1989,
+ title = {{Computer Calculation of Water-Clay Interactions Using Atomic Pair Potentials}},
+ year = {1989},
+ journal = {Clay Minerals},
+ author = {Skipper, N. T.},
+ number = {2},
+ pages = {411--425},
+ volume = {24},
+ publisher = {Mineralogical Society},
+ doi = {10.1180/claymin.1989.024.2.16},
+ issn = {0009-8558}
+}
+
+@article{Chang1995,
+ title = {{Computer Simulation of Interlayer Molecular Structure in Sodium Montmorillonite Hydrates}},
+ year = {1995},
+ journal = {Langmuir},
+ author = {Chang, Fang-Ru Chou and Skipper, N. T. and Sposito, Garrison},
+ number = {7},
+ month = {7},
+ pages = {2734--2741},
+ volume = {11},
+ url = {https://pubs.acs.org/doi/abs/10.1021/la00007a064},
+ doi = {10.1021/la00007a064},
+ issn = {0743-7463}
+}
+
+@article{Skipper1991,
+ title = {{Computer simulation of interlayer water in 2:1 clays}},
+ year = {1991},
+ journal = {The Journal of Chemical Physics},
+ author = {Skipper, N. T. and Refson, K. and McConnell, J. D.C.},
+ number = {11},
+ pages = {7434--7445},
+ volume = {94},
+ doi = {10.1063/1.460175},
+ issn = {00219606}
+}
+
+@article{Team2010,
+ title = {{Condor {\textregistered} Version 7.4.2 Manual}},
+ year = {2010},
+ author = {Team, Condor}
+}
+
+@article{Houston2013,
+ title = {{Consensus docking: Improving the reliability of docking in a virtual screening context}},
+ year = {2013},
+ journal = {Journal of Chemical Information and Modeling},
+ author = {Houston, Douglas R. and Walkinshaw, Malcolm D.},
+ number = {2},
+ month = {2},
+ pages = {384--390},
+ volume = {53},
+ doi = {10.1021/ci300399w},
+ issn = {15499596}
+}
+
+@article{Gumbart2012,
+ title = {{Constant electric field simulations of the membrane potential illustrated with simple systems}},
+ year = {2012},
+ journal = {Biochimica et Biophysica Acta - Biomembranes},
+ author = {Gumbart, James and Khalili-Araghi, Fatemeh and Sotomayor, Marcos and Roux, Benoît},
+ number = {2},
+ month = {2},
+ pages = {294--302},
+ volume = {1818},
+ doi = {10.1016/j.bbamem.2011.09.030},
+ issn = {00052736},
+ keywords = {Electrodes, Electrostatics, Free energy, Patch clamp}
+}
+
+@article{Martyna1994,
+ title = {{Constant pressure molecular dynamics algorithms}},
+ year = {1994},
+ journal = {The Journal of Chemical Physics},
+ author = {Martyna, Glenn J and Tobias, Douglas J and Klein, Michael L},
+ pages = {8577},
+ volume = {101},
+ doi = {10.1063/1.467468},
+ keywords = {ALGORITHMS, ENSEMBLE, EQUATIONS OF MOTION, FLUCTUATIONS, FULLERENES, INVARIANCE PRINCIPLES, ISOTHERMAL PROCESSES, ISOTROPY, MOLECULAR DYNAMICS CALCULATIONS, PHASE SPACE, PRESSURE, SOLID-FLUID INTERFACES, VOLUME}
+}
+
+@article{Feller1995,
+ title = {{Constant pressure molecular dynamics simulation: The Langevin piston method}},
+ year = {1995},
+ journal = {The Journal of Chemical Physics},
+ author = {Feller, Scott E. and Zhang, Yuhong and Pastor, Richard W. and Brooks, Bernard R.},
+ number = {11},
+ month = {9},
+ pages = {4613--4621},
+ volume = {103},
+ publisher = {American Institute of PhysicsAIP},
+ url = {http://aip.scitation.org/doi/10.1063/1.470648},
+ doi = {10.1063/1.470648},
+ issn = {00219606},
+ keywords = {LANGEVIN EQUATION, MOLECULAR DYNAMICS CALCULATIONS, PISTONS, PRESSURE, SIMULATION}
+}
+
+@article{Gil-Lozano2020,
+ title = {{Constraining the preservation of organic compounds in Mars analog nontronites after exposure to acid and alkaline fluids}},
+ year = {2020},
+ journal = {Scientific Reports},
+ author = {Gil-Lozano, Carolina and Fair{\'{e}}n, Alberto G. and Mu{\~{n}}oz-Iglesias, Victoria and Fern{\'{a}}ndez-Sampedro, Maite and Prieto-Ballesteros, Olga and Gago-Duport, Luis and Losa-Adams, Elisabeth and Carrizo, Daniel and Bishop, Janice L. and Fornaro, Teresa and Mateo-Mart{\'{i}}, Eva},
+ number = {1},
+ month = {12},
+ pages = {1--11},
+ volume = {10},
+ publisher = {Nature Research},
+ url = {https://doi.org/10.1038/s41598-020-71657-9},
+ doi = {10.1038/s41598-020-71657-9},
+ issn = {20452322},
+ pmid = {32934272},
+ keywords = {Astrobiology, Geochemistry, Mineralogy}
+}
+
+@article{Gil-Lozano2020a,
+ title = {{Constraining the preservation of organic compounds in Mars analog nontronites after exposure to acid and alkaline fluids}},
+ year = {2020},
+ journal = {Scientific Reports},
+ author = {Gil-Lozano, Carolina and Fair{\'{e}}n, Alberto G. and Mu{\~{n}}oz-Iglesias, Victoria and Fern{\'{a}}ndez-Sampedro, Maite and Prieto-Ballesteros, Olga and Gago-Duport, Luis and Losa-Adams, Elisabeth and Carrizo, Daniel and Bishop, Janice L. and Fornaro, Teresa and Mateo-Mart{\'{i}}, Eva},
+ number = {1},
+ month = {12},
+ volume = {10},
+ doi = {10.1038/s41598-020-71657-9},
+ issn = {2045-2322}
+}
+
+@incollection{Natta2013,
+ title = {{Contributors}},
+ year = {2013},
+ author = {Natta, Ingegneria Chimica G and Mancinelli, Via},
+ number = {491},
+ pages = {xxiii-xxv},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B978008098259509987X},
+ doi = {10.1016/B978-0-08-098259-5.09987-X}
+}
+
+@incollection{Curie2013,
+ title = {{Contributors}},
+ year = {2013},
+ author = {Curie, Marie and Allard, T and Umr, Cnrs and Balan, E and Umr, Cnrs},
+ number = {127},
+ pages = {xxi-xxiii},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588099892},
+ doi = {10.1016/B978-0-08-098258-8.09989-2}
+}
+
+@article{Jaisi2005,
+ title = {{Control of Fe(III) site occupancy on the rate and extent of microbial reduction of Fe(III) in nontronite}},
+ year = {2005},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Jaisi, Deb P. and Kukkadapu, Ravi K. and Eberl, Dennis D. and Dong, Hailiang},
+ number = {23},
+ month = {12},
+ pages = {5429--5440},
+ volume = {69},
+ publisher = {Pergamon},
+ doi = {10.1016/J.GCA.2005.07.008},
+ issn = {0016-7037}
+}
+
+@techreport{Ding2002,
+ title = {{Controlled rate thermal analysis of nontronite}},
+ year = {2002},
+ booktitle = {Thermochimica Acta},
+ author = {Ding, Z and Frost, R L},
+ number = {2},
+ pages = {185--193},
+ volume = {389},
+ keywords = {controlled rate thermal analysis, differential thermogravimetric analysis, ferruginous smectite, nontronite}
+}
+
+@article{Sebastiani2020,
+ title = {{Cooperativity and ion pairing in magnesium sulfate aqueous solutions from the dilute regime to the solubility limit}},
+ year = {2020},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Sebastiani, Federico and Verde, Ana Vila and Heyden, Matthias and Schwaab, Gerhard and Havenith, Martina},
+ number = {21},
+ month = {6},
+ pages = {12140--12153},
+ volume = {22},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2020/cp/c9cp06845g https://pubs.rsc.org/en/content/articlelanding/2020/cp/c9cp06845g},
+ doi = {10.1039/C9CP06845G},
+ issn = {1463-9084}
+}
+
+@article{Anand2003,
+ title = {{Coronavirus main proteinase (3CLpro) Structure: Basis for design of anti-SARS drugs}},
+ year = {2003},
+ journal = {Science},
+ author = {Anand, Kanchan and Ziebuhr, John and Wadhwani, Parvesh and Mesters, Jeroen R. and Hilgenfeld, Rolf},
+ number = {5626},
+ month = {6},
+ pages = {1763--1767},
+ volume = {300},
+ publisher = {American Association for the Advancement of Science},
+ doi = {10.1126/science.1085658},
+ issn = {00368075}
+}
+
+@article{Tang2020,
+ title = {{Coronavirus membrane fusion mechanism offers a potential target for antiviral development}},
+ year = {2020},
+ journal = {Antiviral Research},
+ author = {Tang, Tiffany and Bidon, Miya and Jaimes, Javier A. and Whittaker, Gary R. and Daniel, Susan},
+ number = {104792},
+ month = {6},
+ pages = {0166--3542},
+ volume = {178},
+ publisher = {Elsevier B.V.},
+ url = {https://doi.org/10.1016/j.antiviral.2020.104792 https://linkinghub.elsevier.com/retrieve/pii/S0166354220302060},
+ doi = {10.1016/j.antiviral.2020.104792},
+ issn = {01663542},
+ pmid = {32272173},
+ keywords = {COVID-19, Fusion peptide, Middle east respiratory syndrome, SARS-CoV-2, Severe acute respiratory syndrome, Spike protein}
+}
+
+@article{Zumla2016,
+ title = {{Coronaviruses — drug discovery and therapeutic options}},
+ year = {2016},
+ journal = {Nature Reviews Drug Discovery},
+ author = {Zumla, Alimuddin and Chan, Jasper F. W. and Azhar, Esam I. and Hui, David S. C. and Yuen, Kwok-Yung},
+ number = {5},
+ month = {5},
+ pages = {327--347},
+ volume = {15},
+ publisher = {Nature Publishing Group},
+ url = {http://www.nature.com/articles/nrd.2015.37},
+ doi = {10.1038/nrd.2015.37},
+ issn = {1474-1776}
+}
+
+@article{Zumla2016a,
+ title = {{Coronaviruses-drug discovery and therapeutic options}},
+ year = {2016},
+ journal = {Nature Reviews Drug Discovery},
+ author = {Zumla, Alimuddin and Chan, Jasper F.W. and Azhar, Esam I. and Hui, David S.C. and Yuen, Kwok Yung},
+ number = {5},
+ month = {5},
+ pages = {327--347},
+ volume = {15},
+ publisher = {Nature Publishing Group},
+ doi = {10.1038/nrd.2015.37},
+ issn = {14741784}
+}
+
+@article{Emami2015,
+ title = {{Correction to Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution}},
+ year = {2015},
+ journal = {Chemistry of Materials},
+ author = {Emami, Fateme S. and Puddu, Valeria and Berry, Rajiv J. and Varshney, Vikas and Patwardhan, Siddharth V. and Perry, Carole C. and Heinz, Hendrik},
+ number = {1},
+ month = {1},
+ pages = {406--407},
+ volume = {28},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/acs.chemmater.5b04760},
+ doi = {10.1021/ACS.CHEMMATER.5B04760},
+ issn = {15205002}
+}
+
+@article{Ertem2010,
+ title = {{Correlation Between the Extent of Catalytic Activity and Charge Density of Montmorillonites}},
+ year = {2010},
+ journal = {Astrobiology},
+ author = {Ertem, Gözen and Steudel, Annett and Emmerich, Katja and Lagaly, Gerhard and Schuhmann, Rainer},
+ number = {7},
+ month = {9},
+ pages = {743--749},
+ volume = {10},
+ url = {www.clays.org http://www.liebertpub.com/doi/10.1089/ast.2009.0436},
+ doi = {10.1089/ast.2009.0436},
+ issn = {1531-1074},
+ keywords = {743-749}
+}
+
+@incollection{Bergaya2013c,
+ title = {{Critical Assessment of Analytical Techniques of Clays and Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ number = {C},
+ month = {1},
+ pages = {9--10},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00002-0},
+ issn = {15724352},
+ keywords = {Clay mineral characterization, Electron microscopy, Ion exchange, Smectite characterization, Spectroscopic techniques, Thermal analysis}
+}
+
+@article{Ponder2010,
+ title = {{Current status of the AMOEBA polarizable force field}},
+ year = {2010},
+ journal = {Journal of Physical Chemistry B},
+ author = {Ponder, Jay W. and Wu, Chuanjie and Ren, Pengyu and Pande, Vijay S. and Chodera, John D. and Schnieders, Michael J. and Haque, Imran and Mobley, David L. and Lambrecht, Daniel S. and Distasio, Robert A. and Head-Gordon, Martin and Clark, Gary N.I. and Johnson, Margaret E. and Head-Gordon, Teresa},
+ number = {8},
+ month = {3},
+ pages = {2549--2564},
+ volume = {114},
+ publisher = {American Chemical Society},
+ doi = {10.1021/jp910674d},
+ issn = {15205207}
+}
+
+@article{Kries2013,
+ title = {{De novo enzymes by computational design}},
+ year = {2013},
+ journal = {Current Opinion in Chemical Biology},
+ author = {Kries, Hajo and Blomberg, Rebecca and Hilvert, Donald},
+ number = {2},
+ pages = {221--228},
+ volume = {17},
+ publisher = {Elsevier Ltd},
+ url = {http://dx.doi.org/10.1016/j.cbpa.2013.02.012},
+ isbn = {13675931 (ISSN)},
+ doi = {10.1016/j.cbpa.2013.02.012},
+ issn = {13675931},
+ pmid = {23498973}
+}
+
+@article{Povedano-Priego2021,
+ title = {{Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept}},
+ year = {2021},
+ journal = {Journal of Hazardous Materials},
+ author = {Povedano-Priego, Cristina and Jroundi, Fadwa and Lopez-Fernandez, Margarita and Shrestha, Rojina and Spanek, Roman and Mart{\'{i}}n-S{\'{a}}nchez, Inés and Villar, María Victoria and {\v{S}}evců, Alena and Dopson, Mark and Merroun, Mohamed L.},
+ month = {4},
+ pages = {124600},
+ volume = {408},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.jhazmat.2020.124600},
+ issn = {18733336},
+ pmid = {33339698},
+ keywords = {Compaction, DGR, DNA extraction, Microbial diversity, Protocol, Sequencing}
+}
+
+@article{Lanson1997,
+ title = {{Decomposition of Experimental X-ray Diffraction Patterns (Profile Fitting): A Convenient Way to Study Clay Minerals}},
+ year = {1997},
+ journal = {Clays and Clay Minerals},
+ author = {Lanson, Bruno},
+ number = {2},
+ pages = {132--146},
+ volume = {45},
+ url = {http://link.springer.com/10.1346/CCMN.1997.0450202},
+ doi = {10.1346/CCMN.1997.0450202},
+ issn = {0009-8604},
+ keywords = {Clay Minerals, Decomposition, Mixed Layering, Simulation, X-ray Powder Diffraction}
+}
+
+@article{Lindholm2019,
+ title = {{Deconvolution of Smectite Hydration Isotherms}},
+ year = {2019},
+ journal = {ACS Earth and Space Chemistry},
+ author = {Lindholm, Jerry and Boily, Jean-François and Holmboe, Michael},
+ number = {11},
+ month = {11},
+ pages = {2490--2498},
+ volume = {3},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acsearthspacechem.9b00178},
+ doi = {10.1021/acsearthspacechem.9b00178},
+ issn = {2472-3452},
+ keywords = {XRD, adsorption, clays, ion hydration, montmorillonite, water vapor}
+}
+
+@article{Bergaya2013d,
+ title = {{Dedication}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {Bergaya, Faïza},
+ month = {1},
+ pages = {v},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/b978-0-08-098259-5.09990-x},
+ issn = {15724352}
+}
+
+@article{Sigmund2020,
+ title = {{Deep Learning Neural Network Approach for Predicting the Sorption of Ionizable and Polar Organic Pollutants to a Wide Range of Carbonaceous Materials}},
+ year = {2020},
+ journal = {Environmental Science and Technology},
+ author = {Sigmund, Gabriel and Gharasoo, Mehdi and H{\"{u}}ffer, Thorsten and Hofmann, Thilo},
+ number = {7},
+ month = {4},
+ pages = {4583--4591},
+ volume = {54},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.est.9b06287},
+ issn = {15205851},
+ pmid = {32124609}
+}
+
+@article{Frost2000,
+ title = {{Dehydration and dehydroxylation of nontronites and ferruginous smectite}},
+ year = {2000},
+ journal = {Thermochimica Acta},
+ author = {Frost, Ray L. and Ruan, Huada and Theo Kloprogge, J. and Gates, W.P},
+ number = {1-2},
+ month = {3},
+ pages = {63--72},
+ volume = {346},
+ publisher = {Elsevier},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0040603199003664},
+ doi = {10.1016/S0040-6031(99)00366-4},
+ issn = {00406031},
+ keywords = {Differential thermal analysis, Differential thermogravimetry, Infrared absorption spectroscopy, Montmorillonite, Nontronite, Smectite}
+}
+
+@article{Yong2016,
+ title = {{Descriptions and Implementations of DL{\_}F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations}},
+ year = {2016},
+ journal = {Journal of Chemical Information and Modeling},
+ author = {Yong, Chin W.},
+ number = {8},
+ month = {8},
+ pages = {1405--1409},
+ volume = {56},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jcim.6b00323},
+ doi = {10.1021/acs.jcim.6b00323},
+ issn = {1549-9596}
+}
+
+@article{Joung2008,
+ title = {{Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations}},
+ year = {2008},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Joung, In Suk and Cheatham, Thomas E.},
+ number = {30},
+ month = {7},
+ pages = {9020--9041},
+ volume = {112},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/jp8001614},
+ doi = {10.1021/jp8001614},
+ issn = {1520-6106}
+}
+
+@article{Xiao2013,
+ title = {{Development of an effective polarizable bond method for biomolecular simulation}},
+ year = {2013},
+ journal = {Journal of Physical Chemistry B},
+ author = {Xiao, Xudong and Zhu, Tong and Ji, Chang G. and Zhang, John Z.H.},
+ number = {48},
+ month = {12},
+ pages = {14885--14893},
+ volume = {117},
+ publisher = {American Chemical Society},
+ doi = {10.1021/jp4080866},
+ issn = {15206106}
+}
+
+@article{Cabaleiro-Lago1999,
+ title = {{Development of an intermolecular potential function for interactions in formamide clusters based on ab initio calculations}},
+ year = {1999},
+ journal = {Journal of Chemical Physics},
+ author = {Cabaleiro-Lago, Enrique M. and R{\'{i}}os, Miguel A.},
+ number = {14},
+ pages = {6782--6791},
+ volume = {110},
+ doi = {10.1063/1.478582},
+ issn = {00219606}
+}
+
+@article{Li2019,
+ title = {{DFT and 2D-CA methods unravelling the mechanism of interfacial interaction between amino acids and Ca-montmorillonite}},
+ year = {2019},
+ journal = {Applied Clay Science},
+ author = {Li, Hai-long and Bian, Liang and Dong, Fa-qin and Li, Wei-min and Song, Mian-xin and Nie, Jia-nan and Liu, Xiao-nan and Huo, Ting-ting and Zhang, Hong-ping and Xu, Bing and Riehle, Frank S. and Sun, Shu-hui},
+ month = {12},
+ volume = {183},
+ doi = {10.1016/j.clay.2019.105356},
+ issn = {01691317}
+}
+
+@book{Singleton2010Dict,
+ title = {{Dictionary of DNA and Genome Technology}},
+ year = {2009},
+ author = {Singleton, Paul},
+ month = {11},
+ pages = {433},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {http://books.google.cz/books?id=gDBefDaF0rAC http://doi.wiley.com/10.1002/9780470689127},
+ address = {Chichester, UK},
+ isbn = {9780470689127},
+ doi = {10.1002/9780470689127},
+ keywords = {0470747315{\textbackslash}r{\textbackslash}n9780470747315{\textbackslash}r{\textbackslash}n0470747323{\textbackslash}r{\textbackslash}n978-0}
+}
+
+@book{Singleton2010,
+ title = {{Dictionary of DNA and Genome Technology}},
+ year = {2009},
+ author = {Singleton, Paul},
+ month = {11},
+ pages = {433},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {http://books.google.cz/books?id=gDBefDaF0rAC http://doi.wiley.com/10.1002/9780470689127},
+ address = {Chichester, UK},
+ isbn = {9780470689127},
+ doi = {10.1002/9780470689127},
+ keywords = {0470747315{\textbackslash}r{\textbackslash}n9780470747315{\textbackslash}r{\textbackslash}n0470747323{\textbackslash}r{\textbackslash}n978-0}
+}
+
+@article{Koster1977,
+ title = {{Die Berechnung kristallchemischer Strukturformeln von 2:1-Schichtsilikaten unter Ber{\"{u}}cksichtigung der gemessenen Zwischenschichtladungen und Kationenumtauschkapazit{\"{a}}ten, sowie die Darstellung der Ladungsverteilung in der Struktur mittels Dreieckskoordinat}},
+ year = {1977},
+ journal = {Clay Minerals},
+ author = {K{\"{o}}ster, Heinrich Martin},
+ number = {1},
+ month = {3},
+ pages = {45--54},
+ volume = {12},
+ publisher = {Mineralogical Society},
+ doi = {10.1180/claymin.1977.012.1.03},
+ issn = {0009-8558}
+}
+
+@article{Tazi2012b,
+ title = {{Diffusion coefficient and shear viscosity of rigid water models}},
+ year = {2012},
+ journal = {Journal of Physics Condensed Matter},
+ author = {Tazi, Sami and Boan, Alexandru and Salanne, Mathieu and Marry, Virginie and Turq, Pierre and Rotenberg, Benjamin},
+ number = {28},
+ month = {7},
+ volume = {24},
+ doi = {10.1088/0953-8984/24/28/284117},
+ issn = {09538984},
+ pmid = {22739097},
+ arxivId = {1204.2501}
+}
+
+@book{Karger2012,
+ title = {{Diffusion in Nanoporous Materials}},
+ year = {2012},
+ booktitle = {Diffusion in Nanoporous Materials},
+ author = {K{\"{a}}rger, Jörg and Ruthven, Douglas M. and Theodorou, Doros N.},
+ month = {4},
+ publisher = {Wiley-VCH},
+ isbn = {9783527310241},
+ doi = {10.1002/9783527651276}
+}
+
+@article{Simonnin2017,
+ title = {{Diffusion under Confinement: Hydrodynamic Finite-Size Effects in Simulation}},
+ year = {2017},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Simonnin, Pauline and Noetinger, Benolt and Nieto-Draghi, Carlos and Marry, Virginie and Rotenberg, Benjamin},
+ number = {6},
+ month = {6},
+ pages = {2881--2889},
+ volume = {13},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jctc.7b00342},
+ issn = {15499626},
+ pmid = {28535342},
+ arxivId = {1703.05261}
+}
+
+@article{Daskin2018,
+ title = {{Direct application of the phase estimation algorithm to find the eigenvalues of the Hamiltonians}},
+ year = {2018},
+ journal = {Chemical Physics},
+ author = {Daskin, Ammar and Kais, Sabre},
+ month = {10},
+ pages = {87--94},
+ volume = {514},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0301010417309497},
+ doi = {10.1016/j.chemphys.2018.01.002},
+ issn = {03010104}
+}
+
+@article{Skipper1995,
+ title = {{Direct measurement of the electric double-layer structure in hydrated lithium vermiculite clays by neutron diffraction}},
+ year = {1995},
+ journal = {Journal of Physical Chemistry},
+ author = {Skipper, N. T. and Smalley, M. V. and Williams, G. D. and Soper, A. K. and Thompson, C. H.},
+ number = {39},
+ pages = {14201--14204},
+ volume = {99},
+ doi = {10.1021/j100039a003},
+ issn = {00223654}
+}
+
+@article{Bornscheuer2001,
+ title = {{Directed Evolution of Enzymes for Biocatalytic Applications}},
+ year = {2001},
+ journal = {Biocatalysis and Biotransformation},
+ author = {Bornscheuer, Uwe T.},
+ number = {2},
+ month = {1},
+ pages = {85--97},
+ volume = {19},
+ url = {http://www.tandfonline.com/doi/full/10.3109/10242420109003638},
+ doi = {10.3109/10242420109003638},
+ issn = {1024-2422},
+ keywords = {directed evolution, dna-shuffling, enzymes, error-prone pcr, high-throughput, molecular evolution, screening}
+}
+
+@article{Leemhuis2009,
+ title = {{Directed evolution of enzymes: Library screening strategies}},
+ year = {2009},
+ journal = {IUBMB Life},
+ author = {Leemhuis, Hans and Kelly, Ronan M. and Dijkhuizen, Lubbert},
+ number = {3},
+ month = {3},
+ pages = {222--228},
+ volume = {61},
+ url = {http://doi.wiley.com/10.1002/iub.165},
+ isbn = {1521-6551},
+ doi = {10.1002/iub.165},
+ issn = {15216543},
+ pmid = {19180668},
+ keywords = {Cell surface display, DNA shuffling, Enzymology, Error-prone PCR, High-throughput, In vitro compartmentalization, Protein engineering, Saturation mutagenesis, Screening}
+}
+
+@article{Leemhuis2009b,
+ title = {{Directed evolution of enzymes: Library screening strategies}},
+ year = {2009},
+ journal = {IUBMB Life},
+ author = {Leemhuis, Hans and Kelly, Ronan M. and Dijkhuizen, Lubbert},
+ number = {3},
+ month = {3},
+ pages = {222--228},
+ volume = {61},
+ url = {http://doi.wiley.com/10.1002/iub.165 http://www.ncbi.nlm.nih.gov/pubmed/19180668},
+ isbn = {1521-6551},
+ doi = {10.1002/iub.165},
+ issn = {15216543},
+ pmid = {19180668},
+ keywords = {Cell surface display, DNA shuffling, Enzyme catalysis, Enzymology, Error-prone PCR, High-throughput, In vitro compartmentalization, Molecular evolution, Mutagenesis, Protein engineering, Saturation mutagenesis, Screening}
+}
+
+@incollection{Jacobs2010,
+ title = {{Discovery of non-covalent inhibitors of the SARS main proteinase 3CLpro}},
+ year = {2010},
+ booktitle = {Probe Reports from the NIH Molecular Libraries Program},
+ author = {Jacobs, J and Zhou, S and Dawson, E and Daniels, J S and Hodder, P and Tokars, V and Mesecar, A and Lindsley, C W and Stauffer, S R},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/23658941},
+ address = {Bethesda (MD)},
+ pmid = {23658941}
+}
+
+@article{Jacobs2013,
+ title = {{Discovery, Synthesis, And Structure-Based Optimization of a Series of N -( tert -Butyl)-2-( N -arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3}},
+ year = {2013},
+ journal = {Journal of Medicinal Chemistry},
+ author = {Jacobs, Jon and Grum-Tokars, Valerie and Zhou, Ya and Turlington, Mark and Saldanha, S. Adrian and Chase, Peter and Eggler, Aimee and Dawson, Eric S. and Baez-Santos, Yahira M. and Tomar, Sakshi and Mielech, Anna M. and Baker, Susan C. and Lindsley, Craig W. and Hodder, Peter and Mesecar, Andrew and Stauffer, Shaun R.},
+ number = {2},
+ month = {1},
+ pages = {534--546},
+ volume = {56},
+ publisher = {NIH Public Access},
+ url = {https://pubs.acs.org/doi/10.1021/jm301580n},
+ doi = {10.1021/jm301580n},
+ issn = {0022-2623}
+}
+
+@article{Todorov2006,
+ title = {{DL{\_}POLY{\_}3: New dimensions in molecular dynamics simulations via massive parallelism}},
+ year = {2006},
+ journal = {Journal of Materials Chemistry},
+ author = {Todorov, Ilian T. and Smith, William and Trachenko, Kostya and Dove, Martin T.},
+ number = {20},
+ month = {5},
+ pages = {1911--1918},
+ volume = {16},
+ publisher = {The Royal Society of Chemistry},
+ doi = {10.1039/b517931a},
+ issn = {09599428}
+}
+
+@article{Yang2006,
+ title = {{Drug Design Targeting the Main Protease, the Achilles Heel of Coronaviruses}},
+ year = {2006},
+ journal = {Current Pharmaceutical Design},
+ author = {Yang, Haitao and Bartlam, Mark and Rao, Zihe},
+ number = {35},
+ month = {12},
+ pages = {4573--4590},
+ volume = {12},
+ publisher = {Bentham Science Publishers Ltd.},
+ url = {http://www.eurekaselect.com/openurl/content.php?genre=article&issn=1381-6128&volume=12&issue=35&spage=4573},
+ doi = {10.2174/138161206779010369},
+ issn = {13816128}
+}
+
+@misc{Malikova2010,
+ title = {{Dynamics in clays - Combining neutron scattering and microscopic simulation}},
+ year = {2010},
+ booktitle = {Zeitschrift fur Physikalische Chemie},
+ author = {Malikova, Natalie and Dubois, Emmanuelle and Marry, Virginie and Rotenberg, Benjamin and Turq, Pierre},
+ number = {1-2},
+ pages = {153--181},
+ volume = {224},
+ publisher = {Oldenbourg Wissenschaftsverlag GmbH},
+ doi = {10.1524/zpch.2010.6097},
+ issn = {09429352},
+ keywords = {Clays, Microscopic simulation, QENS}
+}
+
+@article{Newton,
+ title = {{Edge Structure of Montmorillonite from Atomistic Simulations}},
+ year = {2016},
+ journal = {Minerals},
+ author = {Newton, Aric and Kwon, Kideok and Cheong, Dae-Kyo},
+ number = {2},
+ month = {3},
+ pages = {25},
+ volume = {6},
+ url = {www.mdpi.com/journal/minerals http://www.mdpi.com/2075-163X/6/2/25},
+ doi = {10.3390/min6020025},
+ issn = {2075-163X},
+ keywords = {Na-montmorillonite, atomistic simulation, clay edge, density functional theory, mineral surfaces, molecular dynamics, nanoporous minerals}
+}
+
+@article{Newton2016,
+ title = {{Edge Structure of Montmorillonite from Atomistic Simulations}},
+ year = {2016},
+ journal = {Minerals},
+ author = {Newton, Aric and Kwon, Kideok and Cheong, Dae-Kyo},
+ number = {2},
+ month = {3},
+ pages = {25},
+ volume = {6},
+ url = {www.mdpi.com/journal/minerals http://www.mdpi.com/2075-163X/6/2/25},
+ doi = {10.3390/min6020025},
+ issn = {2075-163X},
+ keywords = {Na-montmorillonite, atomistic simulation, clay edge, density functional theory, mineral surfaces, molecular dynamics, nanoporous minerals}
+}
+
+@article{Amorim2007,
+ title = {{Effect of clay-water interactions on clay swelling by X-ray diffraction}},
+ year = {2007},
+ journal = {Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment},
+ author = {Amorim, C. L.G. and Lopes, R. T. and Barroso, R. C. and Queiroz, J. C. and Alves, D. B. and Perez, C. A. and Schelin, H. R.},
+ number = {1 SPEC. ISS.},
+ month = {9},
+ pages = {768--770},
+ volume = {580},
+ publisher = {Elsevier},
+ keywords = {Clay swelling, Formation damage, Interplanar spacing, Osmotic swelling, Smectite, X-ray diffraction}
+}
+
+@article{Fialips2002,
+ title = {{Effect of Fe oxidation state on the IR spectra of Garfield nontronite}},
+ year = {2002},
+ journal = {American Mineralogist},
+ author = {Fialips, Claire Isabelle and Huo, Dongfang and Yan, Laibin and Wu, Jun and Stucki, Joseph W.},
+ number = {5-6},
+ pages = {630--641},
+ volume = {87},
+ publisher = {Mineralogical Society of America},
+ doi = {10.2138/AM-2002-5-605},
+ issn = {0003004X}
+}
+
+@article{Shahriari2018,
+ title = {{Effect of nanoparticles Brownian motion and uniform sinusoidal roughness elements on natural convection in an enclosure}},
+ year = {2018},
+ journal = {Journal of Thermal Analysis and Calorimetry},
+ author = {Shahriari, Alireza and Jahanshahi Javaran, Ebrahim and Rahnama, Mohammad},
+ number = {3},
+ month = {3},
+ pages = {2865--2884},
+ volume = {131},
+ publisher = {Springer Netherlands},
+ url = {https://doi.org/10.1007/s10973-017-6787-1},
+ doi = {10.1007/s10973-017-6787-1},
+ issn = {15882926},
+ keywords = {Brownian motion, Lattice Boltzmann method, Nanofluid, Natural convection, Sinusoidal roughness}
+}
+
+@article{Sainz-Diaz2004,
+ title = {{Effect of the Tetrahedral Charge on the Order-disorder of the Cation Distribution in the Octahedral Sheet of Smectites and Illites by Computational Methods}},
+ year = {2004},
+ journal = {Clays and Clay Minerals},
+ author = {Sainz-D{\'{i}}az, C. I. and Palin, E. J. and Hern{\'{a}}ndez-Laguna, A. and Dove, M T},
+ number = {3},
+ month = {6},
+ pages = {357--374},
+ volume = {52},
+ url = {http://link.springer.com/10.1346/CCMN.2004.0520311},
+ doi = {10.1346/CCMN.2004.0520311},
+ issn = {00098604},
+ keywords = {Cation Ordering, Clay Minerals, Illites, Monte Carlo Simulations, Smectites}
+}
+
+@article{Sato1992,
+ title = {{Effects of Layer Charge, Charge Location, and Energy Change on Expansion Properties of Dioctahedral Smectites}},
+ year = {1992},
+ journal = {Clays and Clay Minerals},
+ author = {Sato, Tsutomu and Watanabe, Takashi and Otsuka, Ryohei},
+ number = {1},
+ month = {2},
+ pages = {103--113},
+ volume = {40},
+ publisher = {Clay Minerals Society},
+ url = {https://link.springer.com/article/10.1346/CCMN.1992.0400111 http://link.springer.com/10.1346/CCMN.1992.0400111},
+ doi = {10.1346/CCMN.1992.0400111},
+ issn = {0009-8604},
+ keywords = {Charge location, Ethylene glycol, Expanded phase, Expansion energy, Glycerol, Layer charge, Relative humidity, Smectite}
+}
+
+@article{Liu2008,
+ title = {{Effects of layer-charge distribution on the thermodynamic and microscopic properties of Cs-smectite}},
+ year = {2008},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Liu, Xiandong and Lu, Xiancai and Wang, Rucheng and Zhou, Huiqun},
+ number = {7},
+ pages = {1837--1847},
+ volume = {72},
+ doi = {10.1016/j.gca.2008.01.028},
+ issn = {00167037}
+}
+
+@article{Yang2012,
+ title = {{Effects of redox cycling of iron in nontronite on reduction of technetium}},
+ year = {2012},
+ journal = {Chemical Geology},
+ author = {Yang, Junjie and Kukkadapu, Ravi K. and Dong, Hailiang and Shelobolina, Evgenya S. and Zhang, Jing and Kim, Jinwook},
+ month = {1},
+ pages = {206--216},
+ volume = {291},
+ doi = {10.1016/j.chemgeo.2011.10.013},
+ issn = {00092541},
+ keywords = {Fe species, Nontronite, Redox cycles, Technetium}
+}
+
+@article{Pedreira-Segade2018a,
+ title = {{Effects of salinity on the adsorption of nucleotides onto phyllosilicates}},
+ year = {2018},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Pedreira-Segade, Ulysse and Michot, Laurent J. and Daniel, Isabelle},
+ number = {3},
+ month = {1},
+ pages = {1938--1952},
+ volume = {20},
+ publisher = {Royal Society of Chemistry},
+ url = {http://xlink.rsc.org/?DOI=C7CP07004G},
+ doi = {10.1039/C7CP07004G},
+ issn = {1463-9076}
+}
+
+@article{Fernandez2013,
+ title = {{Effects of thermal and mechanical treatments on montmorillonite homoionized with mono- and polyvalent cations: Insight into the surface and structural changes}},
+ year = {2013},
+ journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
+ author = {Fern{\'{a}}ndez, M. and Alba, M. D. and Torres S{\'{a}}nchez, R. M.},
+ month = {4},
+ pages = {1--10},
+ volume = {423},
+ publisher = {Elsevier},
+ doi = {10.1016/J.COLSURFA.2013.01.040},
+ issn = {0927-7757},
+ keywords = {Homoionized montmorillonite, Mechanical and thermal treatments, Montmorillonite, RMN, Zeta potential}
+}
+
+@article{Eastman2009,
+ title = {{Efficient nonbonded interactions for molecular dynamics on a graphics processing unit}},
+ year = {2009},
+ journal = {Journal of Computational Chemistry},
+ author = {Eastman, Peter and Pande, Vijay S.},
+ pages = {NA-NA},
+ url = {http://doi.wiley.com/10.1002/jcc.21413},
+ doi = {10.1002/jcc.21413},
+ issn = {01928651}
+}
+
+@incollection{Hille2012,
+ title = {{Electrical Excitability and Ion Channels}},
+ year = {2012},
+ booktitle = {Basic Neurochemistry},
+ author = {Hille, Bertil and Catterall, William A.},
+ month = {1},
+ pages = {63--80},
+ publisher = {Elsevier},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780123749475000043},
+ isbn = {9780123749475},
+ doi = {10.1016/B978-0-12-374947-5.00004-3}
+}
+
+@article{Sander2015,
+ title = {{Electrochemical analyses of redox-active iron minerals: A review of nonmediated and mediated approaches}},
+ year = {2015},
+ journal = {Environmental Science and Technology},
+ author = {Sander, Michael and Hofstetter, Thomas B. and Gorski, Christopher A.},
+ number = {10},
+ month = {5},
+ pages = {5862--5878},
+ volume = {49},
+ publisher = {American Chemical Society},
+ doi = {10.1021/ACS.EST.5B00006},
+ issn = {15205851},
+ pmid = {25856208}
+}
+
+@article{Alexandrov2013a,
+ title = {{Electron Exchange and Conduction in Nontronite from First-Principles}},
+ year = {2013},
+ author = {Alexandrov, Vitaly and Neumann, Anke and Scherer, Michelle M and Rosso, Kevin M},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/jp3110776}
+}
+
+@article{Alexandrov2013,
+ title = {{Electron Exchange and Conduction in Nontronite from First-Principles}},
+ year = {2013},
+ journal = {Journal of Physical Chemistry C},
+ author = {Alexandrov, Vitaly and Neumann, Anke and Scherer, Michelle M. and Rosso, Kevin M.},
+ number = {5},
+ month = {2},
+ pages = {2032--2040},
+ volume = {117},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/jp3110776},
+ doi = {10.1021/JP3110776},
+ issn = {19327447}
+}
+
+@incollection{Kogure2013,
+ title = {{Electron Microscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Kogure, T.},
+ number = {C},
+ month = {1},
+ pages = {275--317},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00011-1},
+ issn = {15724352},
+ pmid = {13880167},
+ keywords = {High-resolution imaging, Phyllosilicates, Radiation damage, Sample preparation, Scanning electron microscopy, Transmission electron microscopy}
+}
+
+@article{Hult2003,
+ title = {{Engineered enzymes for improved organic synthesis}},
+ year = {2003},
+ journal = {Current Opinion in Biotechnology},
+ author = {Hult, Karl and Berglund, Per},
+ number = {4},
+ pages = {395--400},
+ volume = {14},
+ isbn = {0958-1669},
+ doi = {10.1016/S0958-1669(03)00095-8},
+ issn = {09581669},
+ pmid = {12943848}
+}
+
+@article{Kazlauskas2005,
+ title = {{Enhancing catalytic promiscuity for biocatalysis}},
+ year = {2005},
+ journal = {Current Opinion in Chemical Biology},
+ author = {Kazlauskas, Romas J.},
+ number = {2},
+ pages = {195--201},
+ volume = {9},
+ isbn = {1367-5931},
+ doi = {10.1016/j.cbpa.2005.02.008},
+ issn = {13675931},
+ pmid = {15811805}
+}
+
+@article{Khersonsky2006,
+ title = {{Enzyme promiscuity: evolutionary and mechanistic aspects}},
+ year = {2006},
+ journal = {Current Opinion in Chemical Biology},
+ author = {Khersonsky, Olga and Roodveldt, Cintia and Tawfik, Dan S.},
+ number = {5},
+ pages = {498--508},
+ volume = {10},
+ isbn = {1367-5931 (Print){\textbackslash}r1367-5931 (Linking)},
+ doi = {10.1016/j.cbpa.2006.08.011},
+ issn = {13675931},
+ pmid = {16939713}
+}
+
+@article{Hult2007,
+ title = {{Enzyme promiscuity: mechanism and applications}},
+ year = {2007},
+ journal = {Trends in Biotechnology},
+ author = {Hult, Karl and Berglund, Per},
+ number = {5},
+ month = {5},
+ pages = {231--238},
+ volume = {25},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/S016777990700073X},
+ isbn = {0167-7799},
+ doi = {10.1016/j.tibtech.2007.03.002},
+ issn = {01677799},
+ pmid = {17379338}
+}
+
+@article{Orru1999,
+ title = {{Epoxide hydrolases and their synthetic applications.}},
+ year = {1999},
+ journal = {Advances in biochemical engineering/biotechnology},
+ author = {Orru, R V and Archelas, a and Furstoss, R and Faber, K},
+ pages = {145--167},
+ volume = {63},
+ isbn = {0724-6145 (Print){\textbackslash}r0724-6145 (Linking)},
+ issn = {0724-6145},
+ pmid = {9933984},
+ keywords = {biocatalysis, enantio-convergent, epoxide, epoxide hydrolase, vicinal diol}
+}
+
+@incollection{ethylene,
+ title = {{Ethanol}},
+ year = {2011},
+ booktitle = {Ullmann's Encyclopedia of Industrial Chemistry},
+ author = {Kosaric, Naim and Duvnjak, Zdravko and Farkas, Adalbert and Sahm, Hermann and Bringer-Meyer, Stephanie and Goebel, Otto and Mayer, Dieter},
+ month = {10},
+ pages = {1--72},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/14356007.a09_587.pub2},
+ address = {Weinheim, Germany},
+ doi = {10.1002/14356007.a09{\_}587.pub2}
+}
+
+@article{Neumann2011,
+ title = {{Evaluation of redox-active iron sites in smectites using middle and near infrared spectroscopy}},
+ year = {2011},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Neumann, Anke and Petit, Sabine and Hofstetter, Thomas B.},
+ number = {9},
+ month = {5},
+ pages = {2336--2355},
+ volume = {75},
+ publisher = {Pergamon},
+ url = {https://reader.elsevier.com/reader/sd/pii/S0016703711000883?token=63DA0BB56BD765E3453D2755B61E6C807E85441E48093A4D609D35C4F8D95281659872357C25DC31B3325E8169A90C95&originRegion=eu-west-1&originCreation=20211208135728 https://linkinghub.elsevier.com/retriev},
+ doi = {10.1016/j.gca.2011.02.009},
+ issn = {00167037}
+}
+
+@article{Zheng2010,
+ title = {{Evolution of the interlayer space of hydrated montmorillonite as a function of temperature}},
+ year = {2010},
+ journal = {American Mineralogist},
+ author = {Zheng, Y. and Zaoui, A. and Shahrour, I.},
+ number = {10},
+ month = {10},
+ pages = {1493--1499},
+ volume = {95},
+ publisher = {Walter de Gruyter GmbH},
+ url = {https://www.degruyter.com/document/doi/10.2138/am.2010.3541/html},
+ doi = {10.2138/am.2010.3541},
+ issn = {0003-004X}
+}
+
+@article{Becke2005,
+ title = {{Exchange-hole dipole moment and the dispersion interaction}},
+ year = {2005},
+ journal = {Journal of Chemical Physics},
+ author = {Becke, Axel D. and Johnson, Erin R.},
+ number = {15},
+ volume = {122},
+ doi = {10.1063/1.1884601},
+ issn = {00219606}
+}
+
+@book{Nagi2005,
+ title = {{Exercise and Sport in Diabetes}},
+ year = {2005},
+ booktitle = {Exercise and Sport in Diabetes: Second Edition},
+ author = {Nagi, Dinesh},
+ editor = {Nagi, Dinesh},
+ number = {December 2012},
+ month = {12},
+ pages = {2012},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {http://doi.wiley.com/10.1002/0470022086},
+ address = {Chichester, UK},
+ isbn = {9780470022085},
+ doi = {10.1002/0470022086}
+}
+
+@article{Renata2015,
+ title = {{Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution}},
+ year = {2015},
+ journal = {Angewandte Chemie International Edition},
+ author = {Renata, Hans and Wang, Z. Jane and Arnold, Frances H.},
+ number = {11},
+ month = {3},
+ pages = {3351--3367},
+ volume = {54},
+ url = {http://doi.wiley.com/10.1002/anie.201409470},
+ doi = {10.1002/anie.201409470},
+ issn = {14337851}
+}
+
+@article{Yu2012,
+ title = {{Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations}},
+ year = {2012},
+ journal = {Journal of Computational Chemistry},
+ author = {Yu, Wenbo and He, Xibing and Vanommeslaeghe, Kenno and MacKerell, Alexander D.},
+ number = {31},
+ month = {12},
+ pages = {2451--2468},
+ volume = {33},
+ url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.23067},
+ doi = {10.1002/jcc.23067},
+ issn = {01928651}
+}
+
+@article{Haile1983,
+ title = {{Extensions of the molecular dynamics simulation method. II. Isothermal systems}},
+ year = {1983},
+ journal = {The Journal of Chemical Physics},
+ author = {Haile, J. M. and Gupta, S.},
+ number = {6},
+ pages = {3067--3076},
+ volume = {79},
+ doi = {10.1063/1.446137},
+ issn = {00219606}
+}
+
+@article{Chaplain,
+ title = {{Fate of Pesticides in Soils: Toward an Integrated Approach of Influential Factors}},
+ author = {Chaplain, Véronique and Mamy, Laure and Vieubl{\'{e}}-Gonod, Laure and Mougin, Christian and Benoit, Pierre and Barriuso, Enrique and N{\'{e}}lieu, Sylvie},
+ url = {www.intechopen.com}
+}
+
+@article{Jaisi2008,
+ title = {{Fe 2+ sorption onto nontronite (NAu-2)}},
+ year = {2008},
+ author = {Jaisi, Deb P and Liu, Chongxuan and Dong, Hailiang and Blake, Ruth E and Fein, Jeremy B},
+ url = {www.elsevier.com/locate/gca},
+ doi = {10.1016/j.gca.2008.08.022}
+}
+
+@article{Decarreau2014,
+ title = {{Fe 3+ /Al 3+ partitioning between tetrahedral and octahedral sites in dioctahedral smectites}},
+ year = {2014},
+ journal = {Clay Minerals},
+ author = {Decarreau, A. and Petit, S.},
+ number = {5},
+ month = {12},
+ pages = {657--665},
+ volume = {49},
+ publisher = {Mineralogical Society},
+ url = {https://www.cambridge.org/core/product/identifier/S0009855800011808/type/journal_article},
+ doi = {10.1180/claymin.2014.049.5.03},
+ issn = {0009-8558}
+}
+
+@incollection{Ruiz-Hitzky2013,
+ title = {{Fibrous clay mineral-polymer nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Ruiz-Hitzky, E. and Aranda, P. and Darder, M. and Fernandes, F. M.},
+ pages = {721--741},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00023-7},
+ issn = {15724352},
+ keywords = {Bionanocomposites, Clay-polymer nanocomposites, Nanofillers, Palygorskite, Polymer-clay nanocomposites, Sepiolite}
+}
+
+@article{Heinz2005,
+ title = {{Force field for mica-type silicates and dynamics of octadecylammonium chains grafted to montmorillonite}},
+ year = {2005},
+ journal = {Chemistry of Materials},
+ author = {Heinz, Hendrik and Koerner, Hilmar and Anderson, Kelly L. and Vaia, Richard A. and Farmer, B. L.},
+ number = {23},
+ month = {11},
+ pages = {5658--5669},
+ volume = {17},
+ publisher = { American Chemical Society },
+ url = {https://pubs.acs.org/doi/full/10.1021/cm0509328},
+ doi = {10.1021/CM0509328/SUPPL{\_}FILE/CM0509328SI20050802{\_}050932.PDF},
+ issn = {08974756}
+}
+
+@article{Baker2017,
+ title = {{Formation of the ferruginous smectite SWa-1 by alteration of soil clays}},
+ year = {2017},
+ journal = {American Mineralogist},
+ author = {Baker, Leslie L.},
+ number = {1},
+ month = {1},
+ pages = {33--41},
+ volume = {102},
+ publisher = {Walter de Gruyter GmbH},
+ url = {https://www.degruyter.com/document/doi/10.2138/am-2017-5735/html},
+ doi = {10.2138/am-2017-5735},
+ issn = {0003-004X},
+ keywords = {Columbia River Basalts, Mars, Nontronite, SWa-1, clay minerals}
+}
+
+@article{Catterall2017,
+ title = {{Forty Years of Sodium Channels: Structure, Function, Pharmacology, and Epilepsy}},
+ year = {2017},
+ journal = {Neurochemical Research},
+ author = {Catterall, William A},
+ number = {9},
+ month = {9},
+ pages = {2495--2504},
+ volume = {42},
+ url = {http://link.springer.com/10.1007/s11064-017-2314-9},
+ doi = {10.1007/s11064-017-2314-9},
+ issn = {0364-3190}
+}
+
+@incollection{Petit2013,
+ title = {{Fourier Transform Infrared Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Petit, S. and Madejova, J.},
+ number = {C},
+ month = {1},
+ pages = {213--231},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00009-3},
+ issn = {15724352},
+ keywords = {Characterization, Clay mineral identification, Crystal-chemistry, Mid-infrared, Near-infrared, Structural changes}
+}
+
+@article{GBussi2015,
+ title = {{Free-energy calculations with metadynamics: theory and practice}},
+ year = {2015},
+ journal = {Rev. Comput. Chem.},
+ author = {G Bussi, D Branduardi},
+ pages = {1--49},
+ volume = {28}
+}
+
+@article{BoestenI2000,
+ title = {{From laboratory to field: Uses and limitations of pesticide behaviour models for the soil/plant system}},
+ year = {2000},
+ journal = {Weed Research},
+ author = {Boesten I, J. J.T.},
+ number = {1},
+ month = {2},
+ pages = {123--138},
+ volume = {40},
+ doi = {10.1046/j.1365-3180.2000.00158.x},
+ issn = {00431737},
+ keywords = {Environmental fate, Modelling, Pesticides, Soils}
+}
+
+@article{Rotenberg2010a,
+ title = {{From lcalized orbitals to material properties: Building classical force fields for nonmetallic condensed matter systems}},
+ year = {2010},
+ journal = {Physical Review Letters},
+ author = {Rotenberg, Benjamin and Salanne, Mathieu and Simon, Christian and Vuilleumier, Rodolphe},
+ number = {13},
+ month = {3},
+ volume = {104},
+ doi = {10.1103/PhysRevLett.104.138301},
+ issn = {00319007}
+}
+
+@misc{Blumberger2020,
+ title = {{Frontiers in molecular simulation of solvated ions, molecules and interfaces}},
+ year = {2020},
+ booktitle = {Physical Chemistry Chemical Physics},
+ author = {Blumberger, J. and Gaigeot, M. P. and Sulpizi, M. and Vuilleumier, R.},
+ number = {19},
+ month = {5},
+ pages = {10393--10396},
+ volume = {22},
+ publisher = {Royal Society of Chemistry},
+ doi = {10.1039/d0cp90091e},
+ issn = {14639076},
+ pmid = {32352136}
+}
+
+@article{Madejova2003,
+ title = {{FTIR techniques in clay mineral studies}},
+ year = {2003},
+ journal = {Vibrational Spectroscopy},
+ author = {Madejov{\'{a}}, J.},
+ number = {1},
+ month = {1},
+ pages = {1--10},
+ volume = {31},
+ publisher = {Elsevier},
+ doi = {10.1016/S0924-2031(02)00065-6},
+ issn = {0924-2031},
+ keywords = {ATR, Clay minerals, DRIFT, Smectites, Transmission and reflection methods}
+}
+
+@incollection{Emmerich2013,
+ title = {{Full Characterization of Smectites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Emmerich, K.},
+ number = {C},
+ month = {1},
+ pages = {381--404},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00015-9},
+ issn = {15724352},
+ keywords = {2:1 layer silicates, Classification, Montmorillonite, Smectite}
+}
+
+@article{Linke2018,
+ title = {{Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations}},
+ year = {2018},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Linke, Max and K{\"{o}}finger, Jürgen and Hummer, Gerhard},
+ number = {21},
+ month = {5},
+ pages = {5630--5639},
+ volume = {122},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b11988 https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acs.jpcb.7b11988},
+ doi = {10.1021/acs.jpcb.7b11988},
+ issn = {1520-6106},
+ pmid = {29382197}
+}
+
+@article{Furini2011,
+ title = {{Gating at the selectivity filter of ion channels that conduct Na + and K + ions}},
+ year = {2011},
+ journal = {Biophysical Journal},
+ author = {Furini, Simone and Domene, Carmen},
+ number = {7},
+ month = {10},
+ pages = {1623--1631},
+ volume = {101},
+ doi = {10.1016/j.bpj.2011.08.035},
+ issn = {00063495}
+}
+
+@incollection{Bergaya2013,
+ title = {{General Introduction}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {1},
+ pages = {1--19},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588000018},
+ doi = {10.1016/B978-0-08-098258-8.00001-8},
+ keywords = {Aggregates, Associated phases, Classification, Clay, Clay mineral, Delamination, Exfoliation, Formulae, Inorganic polymer, Names of clay minerals, Names of clays, Particles, Porous layered (hydr)oxides, Properties, Salts with 2D polyanion, Swelling}
+}
+
+@incollection{Galan2013,
+ title = {{Genesis of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Gal{\'{a}}n, E. and Ferrell, R. E.},
+ pages = {83--126},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00003-1},
+ issn = {15724352},
+ keywords = {Clay minerals, Geological environments, Isotopic geochemistry, Martian clays, Statistical analysis}
+}
+
+@article{Keeling2000,
+ title = {{Geology and Characterization of Two Hydrothermal Nontronites from Weathered Metamorphic Rocks at the Uley Graphite Mine, South Australia}},
+ year = {2000},
+ journal = {Clays and Clay Minerals},
+ author = {Keeling, John L.},
+ number = {5},
+ pages = {537--548},
+ volume = {48},
+ publisher = {Clay Minerals Soc},
+ url = {http://link.springer.com/10.1346/CCMN.2000.0480506},
+ doi = {10.1346/CCMN.2000.0480506},
+ issn = {0009-8604},
+ keywords = {Amphibole alteration, Biotite alteration, Hydrothermal alteration, Infrared spectroscopy, NAu-1, NAu-2, Nontronite, Weathering, X-ray diffraction}
+}
+
+@article{Bandfield2002,
+ title = {{Global mineral distributions on Mars}},
+ year = {2002},
+ journal = {Journal of Geophysical Research},
+ author = {Bandfield, Joshua L.},
+ number = {E6},
+ month = {6},
+ pages = {5042},
+ volume = {107},
+ publisher = {American Geophysical Union},
+ url = {http://doi.wiley.com/10.1029/2001JE001510},
+ doi = {10.1029/2001JE001510},
+ issn = {0148-0227},
+ keywords = {Infrared spectroscopy, Mars, Remote sensing, Surface mineralogy}
+}
+
+@article{Huang2009,
+ title = {{Gold nanorods: From synthesis and properties to biological and biomedical applications}},
+ year = {2009},
+ journal = {Advanced Materials},
+ author = {Huang, Xiaohua and Neretina, Svetlana and El-Sayed, Mostafa A.},
+ number = {48},
+ pages = {4880--4910},
+ volume = {21},
+ isbn = {1521-4095},
+ doi = {10.1002/adma.200802789},
+ issn = {09359648},
+ pmid = {25378252}
+}
+
+@article{Cho2019a,
+ title = {{Google claims quantum computing milestone}},
+ year = {2019},
+ journal = {Science},
+ author = {Cho, Adrian},
+ number = {6460},
+ pages = {1364--1364},
+ volume = {365},
+ doi = {10.1126/science.365.6460.1364},
+ issn = {0036-8075},
+ keywords = {Science Magazine Article}
+}
+
+@article{Lindahl2021,
+ title = {{GROMACS 2021.4 Manual}},
+ year = {2021},
+ author = {{Lindahl} and {Abraham} and {Hess} and Spoel, van der},
+ month = {11},
+ url = {https://zenodo.org/record/5636522},
+ doi = {10.5281/ZENODO.5636522},
+ keywords = {Software MD Documentation}
+}
+
+@article{BERENDSEN199543,
+ title = {{GROMACS: A message-passing parallel molecular dynamics implementation}},
+ year = {1995},
+ journal = {Computer Physics Communications},
+ author = {Berendsen, H.J.C. and van der Spoel, D and van Drunen, R},
+ number = {1-3},
+ month = {9},
+ pages = {43--56},
+ volume = {91},
+ url = {http://www.sciencedirect.com/science/article/pii/001046559500042E https://linkinghub.elsevier.com/retrieve/pii/001046559500042E},
+ doi = {10.1016/0010-4655(95)00042-E},
+ issn = {00104655},
+ keywords = {Molecular dynamics, Parallel computing}
+}
+
+@article{Fraschini1998,
+ title = {{H ⋯ H model potential for exchange-repulsion energy of methane dimer}},
+ year = {1998},
+ journal = {Journal of Computational Chemistry},
+ author = {Fraschini, Elena and Stone, Anthony J.},
+ number = {8},
+ pages = {847--857},
+ volume = {19},
+ doi = {10.1002/(SICI)1096-987X(199806)19:8<847::AID-JCC4>3.0.CO;2-P},
+ issn = {01928651},
+ keywords = {Anisotropic model potential, Exchange-repulsion, Methane, Methane dimer, Potential energy surface}
+}
+
+@article{Gauglitz2014,
+ title = {{Handbook of Spectroscopy: Second, Enlarged Edition}},
+ year = {2014},
+ journal = {Handbook of Spectroscopy: Second, Enlarged Edition},
+ author = {Gauglitz, Günter and Moore, David S.},
+ month = {6},
+ pages = {1--1878},
+ volume = {1-4},
+ publisher = {Wiley Blackwell},
+ url = {https://onlinelibrary.wiley.com/doi/10.1002/9783527654703},
+ isbn = {9783527654703},
+ doi = {10.1002/9783527654703}
+}
+
+@article{Tschapek1989,
+ title = {{Handy methods for determining the isoelectric point of soils}},
+ year = {1989},
+ journal = {Zeitschrift f{\"{u}}r Pflanzenern{\"{a}}hrung und Bodenkunde},
+ author = {Tschapek, M. and Sanchez, R. M.Torres and Wasowski, C.},
+ number = {1},
+ pages = {73--76},
+ volume = {152},
+ doi = {10.1002/JPLN.19891520113/FORMAT/PDF},
+ issn = {15222624}
+}
+
+@techreport{Mcgeoch,
+ title = {{Hemolithin: a Meteoritic Protein containing Iron and Lithium}},
+ author = {Mcgeoch, Malcolm W and Dikler, Sergei and Mcgeoch, Julie E M},
+ doi = {https://doi.org/10.48550/arXiv.2002.11688}
+}
+
+@article{Koopmeiners2017,
+ title = {{HheG, a Halohydrin Dehalogenase with Activity on Cyclic Epoxides}},
+ year = {2017},
+ journal = {ACS Catalysis},
+ author = {Koopmeiners, Julia and Diederich, Christina and Solarczek, Jennifer and Vo{\ss}, Hauke and Mayer, Janine and Blankenfeldt, Wulf and Schallmey, Anett},
+ number = {10},
+ month = {10},
+ pages = {6877--6886},
+ volume = {7},
+ publisher = {American Chemical Society},
+ url = {https://doi.org/10.1021/acscatal.7b01854},
+ doi = {10.1021/acscatal.7b01854}
+}
+
+@techreport{2002NoTitle,
+ title = {{(No Title)}},
+ year = {2002},
+ url = {http://www.nature.com/naturestructuralbiology}
+}
+
+@article{N-end2006-acetyl--cysteine,
+ title = {{-acetyl- l -cysteine}},
+ year = {2006},
+ author = {N-end, The},
+ number = {1}
+}
+
+@article{The-alkylguanine-DNAAlkyltransferase,
+ title = {{-alkylguanine-DNA alkyltransferase}},
+ author = {The, A and Chem, Biol and Ca, Carlsbad},
+ pages = {167--171}
+}
+
+@book{Any2013-CysteineC,
+ title = {{-Cysteine (alternative to Cys). C}},
+ year = {2013},
+ author = {Any, C-degron and One, Plos and Mrsa, Ca-mrsa Community-acquired and Dnase, C A D Caspase-activated and Biol, B M C and Res, Genome and Res, Nucleic Acids and Cap, Cage},
+ number = {2009},
+ volume = {37},
+ isbn = {1201501091},
+ doi = {10.1021/jm8014298.}
+}
+
+@misc{1_2289Hazen.inddReader,
+ title = {{1{\_}2289Hazen.indd | Enhanced Reader}}
+}
+
+@article{Krull20003Release,
+ title = {{3 C depth profiles from paleosols across the Permian-Triassic boundary: Evidence for methane release}},
+ year = {2000},
+ journal = {GSA Bulletin},
+ author = {Krull, Evelyn S and Retallack, Gregory J},
+ number = {9},
+ pages = {1459--1472},
+ url = {http://pubs.geoscienceworld.org/gsa/gsabulletin/article-pdf/112/9/1459/3385510/i0016-7606-112-9-1459.pdf},
+ keywords = {Permian, Triassic, boundary, carbon-13, methane, paleosols}
+}
+
+@article{Steinle200933Synthetases,
+ title = {{33 Cyanophycin Synthetases}},
+ year = {2009},
+ author = {Steinle, Anna},
+ isbn = {9783527318506}
+}
+
+@article{Bornscheuer20098Engineering,
+ title = {{8 Structural Frameworks Suitable for Engineering}},
+ year = {2009},
+ author = {Bornscheuer, Uwe T},
+ isbn = {9783527318506}
+}
+
+@article{Rogge2015AFrameworks,
+ title = {{A Comparison of Barostats for the Mechanical Characterization of Metal−Organic Frameworks}},
+ year = {2015},
+ author = {Rogge, S M J and Vanduyfhuys, L and Ghysels, A and Waroquier, M and Verstraelen, T and Maurin, G and Speybroeck, V Van},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/acs.jctc.5b00748}
+}
+
+@article{McMahon2018AMars,
+ title = {{A Field Guide to Finding Fossils on Mars}},
+ year = {2018},
+ journal = {Journal of Geophysical Research: Planets},
+ author = {McMahon, S. and Bosak, T. and Grotzinger, J. P. and Milliken, R. E. and Summons, R. E. and Daye, M. and Newman, S. A. and Fraeman, A. and Williford, K. H. and Briggs, D. E. G.},
+ number = {5},
+ month = {5},
+ pages = {1012--1040},
+ volume = {123},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1029/2017JE005478 https://onlinelibrary.wiley.com/doi/abs/10.1029/2017JE005478 https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2017JE005478 http://doi.wiley.com/10.1029/2017JE005478},
+ doi = {10.1029/2017JE005478},
+ issn = {21699097},
+ keywords = {Mars, astrobiology, fossils}
+}
+
+@article{McMahon2018AMarsb,
+ title = {{A Field Guide to Finding Fossils on Mars}},
+ year = {2018},
+ journal = {Journal of Geophysical Research: Planets},
+ author = {McMahon, S. and Bosak, T and Grotzinger, J P and Milliken, R E and Summons, R E and Daye, M and Newman, S A and Fraeman, A and Williford, K H and Briggs, D E G},
+ number = {5},
+ month = {5},
+ pages = {1012--1040},
+ volume = {123},
+ url = {https://doi.org/10.1029/2017JE005478 http://doi.wiley.com/10.1029/2017JE005478},
+ doi = {10.1029/2017JE005478},
+ issn = {21699097}
+}
+
+@article{Moshiri2010APathogens,
+ title = {{A fluorescence-based reporter substrate for monitoring RNA editing in trypanosomatid pathogens}},
+ year = {2010},
+ journal = {Nucleic Acids Research},
+ author = {Moshiri, Houtan and Salavati, Reza},
+ number = {13},
+ volume = {38},
+ isbn = {1362-4962 (Electronic){\textbackslash}r0305-1048 (Linking)},
+ doi = {10.1093/nar/gkq333},
+ issn = {03051048},
+ pmid = {20444864}
+}
+
+@article{Russell1994ALife,
+ title = {{A hydrothermally precipitated catalytic iron sulphide membrane as a first step toward life}},
+ year = {1994},
+ journal = {Journal of Molecular Evolution},
+ author = {Russell, Michael J. and Daniel, Roy M. and Hall, Allan J. and Sherringham, John A.},
+ number = {3},
+ pages = {231--243},
+ volume = {39},
+ doi = {10.1007/BF00160147},
+ issn = {14321432},
+ keywords = {Botryoid, Chemiosmosis, Ferredoxin, Greigite, Hydrothermal, Iron sulphides, Membrane, Origin of life, Protocell, Proton motive force}
+}
+
+@book{Reetz2009AEvolution.pdf,
+ title = {{A Method for Rapid Directed Evolution.pdf}},
+ year = {2009},
+ author = {Reetz, Manfred T},
+ isbn = {9783527318506}
+}
+
+@article{Perez-Sanchez2018AHydroxides,
+ title = {{A molecular dynamics framework to explore the structure and dynamics of layered double hydroxides}},
+ year = {2018},
+ journal = {Applied Clay Science},
+ author = {P{\'{e}}rez-S{\'{a}}nchez, Germán and Galv{\~{a}}o, Tiago L.P. and Tedim, João and Gomes, José R.B.},
+ month = {10},
+ pages = {164--177},
+ volume = {163},
+ publisher = {Elsevier},
+ doi = {10.1016/J.CLAY.2018.06.037},
+ issn = {0169-1317},
+ keywords = {CLAYFF, Density functional theory, Force field, LDH, Molecular dynamics}
+}
+
+@article{Bone2011AGSK-3,
+ title = {{A novel chemically directed route for the generation of definitive endoderm from human embryonic stem cells based on inhibition of GSK-3}},
+ year = {2011},
+ journal = {Journal of Cell Science},
+ author = {Bone, H. K. and Nelson, A. S. and Goldring, C. E. and Tosh, D. and Welham, M. J.},
+ number = {12},
+ pages = {1992--2000},
+ volume = {124},
+ url = {http://jcs.biologists.org/cgi/doi/10.1242/jcs.081679},
+ isbn = {0021-9533},
+ doi = {10.1242/jcs.081679},
+ issn = {0021-9533},
+ pmid = {21610099}
+}
+
+@article{Liu2014ANontronite,
+ title = {{A novel photosensitized Fenton reaction catalyzed by sandwiched iron in synthetic nontronite}},
+ year = {2014},
+ journal = {RSC Advances},
+ author = {Liu, Renlan and Xiao, Dongxue and Guo, Yaoguang and Wang, Zhaohui and Liu, Jianshe},
+ number = {25},
+ month = {3},
+ pages = {12958--12963},
+ volume = {4},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2014/ra/c3ra47359g https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra47359g},
+ doi = {10.1039/C3RA47359G},
+ issn = {2046-2069}
+}
+
+@article{Lange2021ASamples,
+ title = {{A Novel Proteomics-Based Strategy for the Investigation of Peptide Sequences in Extraterrestrial Samples}},
+ year = {2021},
+ journal = {Journal of Proteome Research},
+ author = {Lange, Justin and Djago, Fabiola and Eddhif, Balkis and Remaury, Quentin B. and Ruf, Alexander and Leitner, Nathalie K.V. and Hendecourt, Louis L.S. and Danger, Grégoire and Rodier, Claude G. and Papot, Sébastien and Poinot, Pauline},
+ number = {2},
+ month = {2},
+ volume = {20},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00700},
+ doi = {10.1021/ACS.JPROTEOME.0C00700/SUPPL{\_}FILE/PR0C00700{\_}SI{\_}001.PDF},
+ issn = {15353907},
+ pmid = {33078610}
+}
+
+@article{Miller11953AConditions,
+ title = {{A Production of Amino Acids Under Possible Primitive Earth Conditions}},
+ year = {1953},
+ author = {Miller1', Stanley L and Jones, G H},
+ url = {https://www.science.org/doi/10.1126/science.117.3046.528},
+ doi = {10.1126/science.117.3046.528}
+}
+
+@article{Payer2018A4-Hydroxystyrenes,
+ title = {{A Rational Active-Site Redesign Converts a Decarboxylase into a C═C Hydratase: “Tethered Acetate” Supports Enantioselective Hydration of 4-Hydroxystyrenes}},
+ year = {2018},
+ journal = {ACS Catalysis},
+ author = {Payer, Stefan E. and Pollak, Hannah and Glueck, Silvia M. and Faber, Kurt},
+ number = {3},
+ month = {3},
+ pages = {2438--2442},
+ volume = {8},
+ url = {https://pubs.acs.org/doi/10.1021/acscatal.7b04293},
+ doi = {10.1021/acscatal.7b04293},
+ issn = {2155-5435},
+ keywords = {biocatalysis, decarboxylase, enzyme engineering, hydratase, hydration}
+}
+
+@article{Res2006ASite,
+ title = {{A site}},
+ year = {2006},
+ author = {Res, Nucleic Acids and Atpases, These and Ca, La Jolla and The, V and Res, Nucleic Acids},
+ number = {1},
+ pages = {2504--2506},
+ volume = {49}
+}
+
+@article{Polymerases2013ACommon,
+ title = {{A specifi c indicator of ambiguity in the recognition site of a – or in another nucleic acid seq- ence; ‘B’ indicates C or G or T in DNA, C or G or U in RNA. B-DNA The form of DNA that appears to be the most common}},
+ year = {2013},
+ author = {Polymerases, D N A and Family, A and Family, X and Family, Y and House, Flock and Endonuclease, Restriction},
+ doi = {10.1093/nar/gkp962.}
+}
+
+@article{Saladino2019AChemistry,
+ title = {{A Universal Geochemical Scenario for Formamide Condensation and Prebiotic Chemistry}},
+ year = {2019},
+ journal = {Chemistry – A European Journal},
+ author = {Saladino, Raffaele and Di Mauro, Ernesto and Garc{\'{i}}a-Ruiz, Juan Manuel},
+ number = {13},
+ month = {3},
+ pages = {3181--3189},
+ volume = {25},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/chem.201803889 https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201803889 https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/chem.201803889},
+ doi = {10.1002/CHEM.201803889},
+ issn = {1521-3765},
+ pmid = {30230056},
+ keywords = {biomorphs, formamide, geochemistry, origin of life, prebiotic chemistry, serpentinization}
+}
+
+@book{Komadel2013AcidMinerals,
+ title = {{Acid activation of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Komadel, P. and Madejov{\'{a}}, J.},
+ edition = {2},
+ pages = {385--409},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00013-4},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00013-4},
+ issn = {15724352},
+ keywords = {Acid sites, Acid treatment, FTIR spectroscopy, Structural modification, Surface area}
+}
+
+@article{2017Acknowledgements,
+ title = {{Acknowledgements}},
+ year = {2017},
+ pages = {xiv-xv},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780081003558099999},
+ doi = {10.1016/B978-0-08-100355-8.09999-9}
+}
+
+@article{Huber1997ActivatedConditions,
+ title = {{Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions}},
+ year = {1997},
+ journal = {Science},
+ author = {Huber, Claudia and W{\"{a}}chtersh{\"{a}}user, Günter},
+ number = {5310},
+ month = {4},
+ pages = {245--247},
+ volume = {276},
+ publisher = {American Association for the Advancement of Science},
+ doi = {10.1126/SCIENCE.276.5310.245},
+ issn = {00368075},
+ pmid = {9092471}
+}
+
+@article{Taylor2011ActivityFamily,
+ title = {{Activity, specificity and structure of I-Bth0305I: A representative of a new homing endonuclease family}},
+ year = {2011},
+ journal = {Nucleic Acids Research},
+ author = {Taylor, Gregory K. and Heiter, Daniel F. and Pietrokovski, Shmuel and Stoddard, Barry L.},
+ number = {22},
+ pages = {9705--9719},
+ volume = {39},
+ isbn = {1362-4962 (Electronic){\textbackslash}r0305-1048 (Linking)},
+ doi = {10.1093/nar/gkr669},
+ issn = {03051048},
+ pmid = {21890897}
+}
+
+@article{Lambert2008AdsorptionReview,
+ title = {{Adsorption and Polymerization of Amino Acids on Mineral Surfaces: A Review}},
+ year = {2008},
+ journal = {Origins of Life and Evolution of Biospheres},
+ author = {Lambert, Jean-François},
+ number = {3},
+ month = {6},
+ pages = {211--242},
+ volume = {38},
+ url = {http://link.springer.com/10.1007/s11084-008-9128-3},
+ doi = {10.1007/s11084-008-9128-3},
+ issn = {0169-6149},
+ pmid = {18344011},
+ keywords = {Adsorption, Amino acids, Bernal's hypothesis, Oxide minerals, Surface polymerization}
+}
+
+@article{Brunauer1938AdsorptionLayers,
+ title = {{Adsorption of Gases in Multimolecular Layers}},
+ year = {1938},
+ journal = {Journal of the American Chemical Society},
+ author = {Brunauer, Stephen and Emmett, P. H. and Teller, Edward},
+ number = {2},
+ month = {2},
+ pages = {309--319},
+ volume = {60},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/ja01269a023},
+ doi = {10.1021/ja01269a023},
+ issn = {0002-7863}
+}
+
+@article{Mignon2020AdsorptionSalts,
+ title = {{Adsorption of nucleotides on clay surfaces: Effects of mineral composition, pH and solution salts}},
+ year = {2020},
+ journal = {Applied Clay Science},
+ author = {Mignon, Pierre and Corbin, Gwenaëlle and Le Crom, Sébastien and Marry, Virginie and Hao, Jihua and Daniel, Isabelle},
+ month = {6},
+ pages = {105544},
+ volume = {190},
+ publisher = {Elsevier},
+ doi = {10.1016/J.CLAY.2020.105544},
+ issn = {0169-1317},
+ keywords = {Adsorption, Modelling, Nucleotide, Origin of life}
+}
+
+@article{Pedreira-Segade2016AdsorptionLife,
+ title = {{Adsorption of nucleotides onto ferromagnesian phyllosilicates: Significance for the origin of life}},
+ year = {2016},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Pedreira-Segade, Ulysse and Feuillie, Cécile and Pelletier, Manuel and Michot, Laurent J. and Daniel, Isabelle},
+ month = {3},
+ pages = {81--95},
+ volume = {176},
+ publisher = {Pergamon},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S001670371500719X},
+ doi = {10.1016/j.gca.2015.12.025},
+ issn = {00167037}
+}
+
+@article{Yu2013AdsorptionReview,
+ title = {{Adsorption of proteins and nucleic acids on clay minerals and their interactions: A review}},
+ year = {2013},
+ journal = {Applied Clay Science},
+ author = {Yu, Wei Hua and Li, Na and Tong, Dong Shen and Zhou, Chun Hui and Lin, Chun Xiang and Xu, Chuan Yun},
+ month = {8},
+ pages = {443--452},
+ volume = {80-81},
+ publisher = {Elsevier},
+ doi = {10.1016/J.CLAY.2013.06.003},
+ issn = {0169-1317},
+ keywords = {Adsorption, Biomolecule, Clay mineral, Mechanism, Nucleic acids, Protein}
+}
+
+@article{Michalkova2011AdsorptionWater,
+ title = {{Adsorption of thymine and uracil on 1 : 1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water}},
+ year = {2011},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Michalkova, A. and Robinson, T. L. and Leszczynski, J.},
+ number = {17},
+ month = {4},
+ pages = {7862--7881},
+ volume = {13},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2011/cp/c1cp00008j https://pubs.rsc.org/en/content/articlelanding/2011/cp/c1cp00008j},
+ doi = {10.1039/C1CP00008J},
+ issn = {1463-9084},
+ pmid = {21437301}
+}
+
+@article{Stepanow2011Allele-specificMCHR1,
+ title = {{Allele-specific, age-dependent and BMI-associated DNA methylation of human MCHR1}},
+ year = {2011},
+ journal = {PLoS ONE},
+ author = {Stepanow, Stefanie and Reichwald, Kathrin and Huse, Klaus and Gausmann, Ulrike and Nebel, Almut and Rosenstiel, Philip and Wabitsch, Martin and Fischer-Posovszky, Pamela and Platzer, Matthias},
+ number = {5},
+ volume = {6},
+ isbn = {1932-6203 (Electronic){\textbackslash}r1932-6203 (Linking)},
+ doi = {10.1371/journal.pone.0017711},
+ issn = {19326203},
+ pmid = {21637341}
+}
+
+@article{Rimola2007AluminosilicateMethods,
+ title = {{Aluminosilicate surfaces as promoters for peptide bond formation: an assessment of Bernal's hypothesis by ab initio methods}},
+ year = {2007},
+ journal = {Journal of the American Chemical Society},
+ author = {Rimola, Albert and Sodupe, Mariona and Ugliengo, Piero},
+ number = {26},
+ month = {7},
+ pages = {8333--8344},
+ volume = {129},
+ publisher = {J Am Chem Soc},
+ url = {https://pubmed.ncbi.nlm.nih.gov/17552521/},
+ doi = {10.1021/JA070451K},
+ issn = {0002-7863},
+ pmid = {17552521},
+ keywords = {Albert Rimola, Aluminum Silicates / chemistry*, Chemical*, Glycine / chemistry, MEDLINE, Mariona Sodupe, Models, Molecular, Molecular Structure, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Non-U.S. Gov't, Peptides / chemistry*, Piero Ugliengo, Protein Binding, PubMed Abstract, Research Support, Surface Properties, doi:10.1021/ja070451k, pmid:17552521}
+}
+
+@article{Benetoli2007AminoInvestigations,
+ title = {{Amino acid interaction with and adsorption on clays: FT-IR and M{\"{o}}ssbauer spectroscopy and X-ray diffractometry investigations}},
+ year = {2007},
+ journal = {Origins of Life and Evolution of Biospheres},
+ author = {Benetoli, Luís O.B. and De Souza, Cláudio M.D. and Da Silva, Klébson L. and De Souza, Ivan G. and De Santana, Henrique and Paesano, Andrea and Da Costa, Antonio C.S. and Zaia, Cássia Thaïs B.V. and Zaia, Dimas A.M.},
+ number = {6},
+ month = {12},
+ pages = {479--493},
+ volume = {37},
+ doi = {10.1007/S11084-007-9072-7},
+ issn = {01696149},
+ pmid = {17578677},
+ keywords = {Adsorption, Amino acids, Clays, FT-IR spectroscopy, M{\"{o}}ssbauer spectroscopy, X-ray diffractometry}
+}
+
+@techreport{Laird1977AnalysisClays,
+ title = {{Analysis of Layer Charge, Cation and Anion Exchange Capacities, and Synthesis of Reduced Charge Clays}},
+ year = {1977},
+ booktitle = {Methods of Soil Analysis. Part 5. Mineralogical Methods. SSSA Book Series},
+ author = {Laird, David and Fleming, Pierce},
+ number = {5},
+ publisher = {MacEwan and Wilson}
+}
+
+@article{Laird2015AnalysisClays,
+ title = {{Analysis of layer charge, cation and anion exchange capacities, and synthesis of reduced charge clays}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Laird, David and Fleming, Pierce},
+ number = {5},
+ month = {10},
+ pages = {485--508},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C16},
+ keywords = {Alkylammonium method, Anion exchange capacities, Cation exchange capacity, Layer charge estimates, Reduced charge clays, Structural formula method}
+}
+
+@article{He2017AnalysisMinerals,
+ title = {{Analysis of Organoclays and Organic Adsorption by Clay Minerals}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {He, H. P. and Zhu, J.},
+ pages = {310--342},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00010-2},
+ issn = {15724352},
+ keywords = {Basal spacing, Cation exchange capacity, Clay mineral, Hybrid, IR, IR spectroscopy, Intercalation, Molecular environment, Organoclay, Quaternary ammonium cation}
+}
+
+@article{Kelly2015AnalysisSpectroscopy,
+ title = {{Analysis of soils and minerals using x-ray absorption spectroscopy}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Kelly, S. D. and Hesterberg, D. and Ravel, B.},
+ month = {10},
+ pages = {387--463},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C14},
+ keywords = {Data analysis, Electronic transitions, Extended x-ray absorption fine structure spectroscopy, Mineral-associated chemical species, Sample preparation, Sample preservation, Soil minerals, X-ray absorption near edge structure spectroscopy}
+}
+
+@article{AlteromonasAppendix:Genera,
+ title = {{Appendix: alphabetical list of genera}},
+ author = {Alteromonas, Agropyron and Apis, Anguina and Astacus, Aschersonia and Beta, Beggiatoa and Achlya, Acanthamoeba and Alnus, Albugo and Anopheles, Amanita and Ascosphaera, Arabidopsis and Boletus, Belononlaimus Bifidobacterium and Buchnera, Brassica and Callithrix, Brochothrix Byssochlamys and Caulobacter, Cardiobacterium Caseobacter and Alcaligenes, Aeromonas Agrobacterium and Arcella, Aphelenchoides and Avena, Arthrobacter and Bos, Bombyx},
+ pages = {293--297}
+}
+
+@article{AppendixAppendix:Genera,
+ title = {{Appendix: Alphabetical list of genera}},
+ author = {Appendix, The},
+ number = {C},
+ pages = {505--510}
+}
+
+@incollection{2005ApplicationPharmaceuticals,
+ title = {{Application of Enzymes as Catalysts: Basic Chemicals, Fine Chemicals, Food, Crop Protection, Bulk Pharmaceuticals}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {159--208},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch7},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch7}
+}
+
+@article{Kloprogge2017ApplicationSynthesis,
+ title = {{Application of Vibrational Spectroscopy in Clay Minerals Synthesis}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Kloprogge, J. T.},
+ pages = {222--287},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00008-4},
+ issn = {15724352},
+ keywords = {Clay mineral, IR, IR spectroscopy, Raman, Raman Spectroscopy, Synthesis, Synthetic clay minerals}
+}
+
+@book{Galimberti2013ApplicationsNanocomposites,
+ title = {{Applications of Clay–Polymer Nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Galimberti, M. and Cipolletti, V. R. and Coombs, M.},
+ edition = {2},
+ number = {C},
+ pages = {539--586},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00020-2},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00020-2},
+ issn = {15724352},
+ keywords = {Applications, Automotive, Barrier properties, Biomedicine, Cables, Clay polymer nanocomposites, Coatings, Degradation properties, Fuel cells, Mechanical properties, Packaging, Rheological properties, Sporting goods, Thermal properties, Tyres, Wire}
+}
+
+@article{Board2007ApplicationsCatalysis,
+ title = {{Applications of Density Functional Theory to Heterogeneous Catalysis}},
+ year = {2007},
+ author = {Board, Editorial},
+ pages = {108--160},
+ doi = {10.1039/9781847555267-00108}
+}
+
+@incollection{2005ApplicationsFeed,
+ title = {{Applications of Enzymes as Bulk Actives: Detergents, Textiles, Pulp and Paper, Animal Feed}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {135--158},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch6},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch6}
+}
+
+@article{Chipot2007ApplicationsBiology,
+ title = {{Applications of free energy calculations to chemistry and biology}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Chipot, Christophe and Mark, Alan E. and Pande, Vijay S. and Simonson, Thomas},
+ pages = {463--501},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}13},
+ issn = {01726218}
+}
+
+@incollection{2005ArtificialEnzymes,
+ title = {{Artificial Enzymes}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {511--537},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch18},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch18}
+}
+
+@article{Desai2011AssessingCatalysts,
+ title = {{Assessing and Exploiting the Persistence of Substrate Ambiguity in Modern Protein Catalysts}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Desai, Kevin K. and Miller, Brian G.},
+ pages = {343--362},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch13},
+ keywords = {Metagenomics, Overexpression library, Substrate ambiguity, Substrate specificity}
+}
+
+@article{Laio2005AssessingMetadynamics,
+ title = {{Assessing the Accuracy of Metadynamics†}},
+ year = {2005},
+ journal = {Journal of Physical Chemistry B},
+ author = {Laio, Alessandro and Rodriguez-Fortea, Antonio and Gervasio, Francesco Luigi and Ceccarelli, Matteo and Parrinello, Michele},
+ number = {14},
+ month = {4},
+ pages = {6714--6721},
+ volume = {109},
+ publisher = { American Chemical Society },
+ url = {https://pubs.acs.org/doi/full/10.1021/jp045424k},
+ doi = {10.1021/JP045424K},
+ issn = {15206106}
+}
+
+@article{Illingworth2008AssessingDocking,
+ title = {{Assessing the role of polarization in docking}},
+ year = {2008},
+ journal = {Journal of Physical Chemistry A},
+ author = {Illingworth, Christopher J.R. and Morris, Garrett M. and Parkes, Kevin E.B. and Snell, Christopher R. and Reynolds, Christopher A.},
+ number = {47},
+ month = {11},
+ pages = {12157--12163},
+ volume = {112},
+ doi = {10.1021/jp710169m},
+ issn = {10895639}
+}
+
+@book{Christidis2013AssessmentClays,
+ title = {{Assessment of Industrial Clays}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Christidis, G. E.},
+ edition = {2},
+ number = {C},
+ pages = {425--449},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00017-2},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00017-2},
+ issn = {15724352},
+ keywords = {Assessment, Bentonite, Common clays and shales, Industrial applications, Kaolin, Palygorskite, Physical and chemical properties, Sepiolite, Specifications}
+}
+
+@article{Achour2021AssistedStudy,
+ title = {{Assisted dipeptide bond formation: glycine as a case study}},
+ year = {2021},
+ journal = {Heliyon},
+ author = {Achour, Sofiene and Hosni, Zied and Darghouthi, Sarra and Syme, Christopher},
+ number = {6},
+ month = {6},
+ volume = {7},
+ publisher = {Heliyon},
+ url = {https://pubmed.ncbi.nlm.nih.gov/34195408/},
+ doi = {10.1016/J.HELIYON.2021.E07276},
+ issn = {2405-8440},
+ pmid = {34195408},
+ keywords = {Christopher Syme, MEDLINE, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, PMC8225972, PubMed Abstract, Sofiene Achour, Zied Hosni, doi:10.1016/j.heliyon.2021.e07276, pmid:34195408}
+}
+
+@article{dIschia2019AstrochemistryWonderland,
+ title = {{Astrochemistry and astrobiology: Materials science in wonderland?}},
+ year = {2019},
+ journal = {International Journal of Molecular Sciences},
+ author = {d’Ischia, Marco and Manini, Paola and Moracci, Marco and Saladino, Raffaele and Ball, Vincent and Thissen, Helmut and Evans, Richard A. and Puzzarini, Cristina and Barone, Vincenzo},
+ number = {17},
+ month = {9},
+ volume = {20},
+ publisher = {MDPI AG},
+ doi = {10.3390/IJMS20174079},
+ issn = {14220067},
+ pmid = {31438518},
+ keywords = {Aminomalononitrile, Computational methods, Formamide, Hybrid functional materials, Nanostructures, Polycyclic aromatic hydrocarbons, Prebiotic processes, Solid-state photochemistry, Surface functionalization, Volcanic fumaroles}
+}
+
+@article{Wuensch2013AsymmetricDerivatives,
+ title = {{Asymmetric enzymatic hydration of hydroxystyrene derivatives}},
+ year = {2013},
+ journal = {Angewandte Chemie - International Edition},
+ author = {Wuensch, Christiane and Gross, Johannes and Steinkellner, Georg and Gruber, Karl and Glueck, Silvia M. and Faber, Kurt},
+ isbn = {14337851 (ISSN)},
+ doi = {10.1002/anie.201207916},
+ issn = {14337851},
+ pmid = {23335002},
+ keywords = {biotransformations, catalytic promiscuity, decarboxylases, enzyme catalysis, hydratases}
+}
+
+@article{Xue2004AsymmetricComplex,
+ title = {{Asymmetric hydration of alkenes catalyzed by wool-palladium complex}},
+ year = {2004},
+ journal = {Polymers for Advanced Technologies},
+ author = {Xue, Lei and Jia, Bin and Tang, Li and Ji, Xiao Feng and Huang, Mei Yu and Jiang, Ying Yan},
+ number = {6},
+ month = {6},
+ pages = {346--349},
+ volume = {15},
+ url = {http://doi.wiley.com/10.1002/pat.440},
+ doi = {10.1002/pat.440},
+ issn = {1042-7147}
+}
+
+@article{Hanna1999BacillusAnthracis,
+ title = {{Bacillus anthracis}},
+ year = {1999},
+ author = {Hanna, Philip C and Ireland, John A W},
+ number = {99},
+ pages = {180--182}
+}
+
+@article{Christ2010BasicReview,
+ title = {{Basic ingredients of free energy calculations: A review}},
+ year = {2010},
+ journal = {Journal of Computational Chemistry},
+ author = {Christ, Clara D. and Mark, Alan E. and Van Gunsteren, Wilfred F.},
+ number = {8},
+ month = {6},
+ pages = {1569--1582},
+ volume = {31},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21450 https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21450 https://onlinelibrary.wiley.com/doi/10.1002/jcc.21450},
+ doi = {10.1002/JCC.21450},
+ issn = {1096-987X},
+ keywords = {affinity, free energy, molecular simulation, sampling}
+}
+
+@article{Berezovsky2017BasicFunction,
+ title = {{Basic units of protein structure, folding, and function}},
+ year = {2017},
+ journal = {Progress in Biophysics and Molecular Biology},
+ author = {Berezovsky, Igor N. and Guarnera, Enrico and Zheng, Zejun},
+ month = {9},
+ pages = {85--99},
+ volume = {128},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/J.PBIOMOLBIO.2016.09.009},
+ issn = {00796107},
+ pmid = {27697476},
+ keywords = {Closed loops, Evolution, Hierarchy of domain structure, Protein folding, Protein function, Protein structure}
+}
+
+@article{Berezovsky2017BasicFunctionb,
+ title = {{Basic units of protein structure, folding, and function}},
+ year = {2017},
+ journal = {Progress in Biophysics and Molecular Biology},
+ author = {Berezovsky, Igor N. and Guarnera, Enrico and Zheng, Zejun},
+ month = {9},
+ pages = {85--99},
+ volume = {128},
+ publisher = {Pergamon},
+ doi = {10.1016/J.PBIOMOLBIO.2016.09.009},
+ issn = {0079-6107},
+ pmid = {27697476},
+ keywords = {Closed loops, Evolution, Hierarchy of domain structure, Protein folding, Protein function, Protein structure}
+}
+
+@article{2017Bibliography,
+ title = {{Bibliography}},
+ year = {2017},
+ pages = {515--591},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780081003558099896},
+ doi = {10.1016/B978-0-08-100355-8.09989-6}
+}
+
+@incollection{2005BiocatalysisMedia,
+ title = {{Biocatalysis in Non-conventional Media}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {339--372},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch12},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch12}
+}
+
+@article{Payne2009BioengineeringFunction,
+ title = {{Bioengineering of Sequence - Repetitive Polypeptides : Synthetic Routes to Protein - Based Materials of Novel Structure and Function}},
+ year = {2009},
+ author = {Payne, Sonha C and Patterson, Melissa and Conticello, Vincent P},
+ pages = {915--938},
+ isbn = {9783527318506}
+}
+
+@incollection{2005Bioinformatics,
+ title = {{Bioinformatics}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {413--432},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch14},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch14}
+}
+
+@article{Hays2017BiosignatureEnvironments,
+ title = {{Biosignature Preservation and Detection in Mars Analog Environments}},
+ year = {2017},
+ journal = {Astrobiology},
+ author = {Hays, Lindsay E. and Graham, Heather V. and Des Marais, David J. and Hausrath, Elisabeth M. and Horgan, Briony and McCollom, Thomas M. and Parenteau, M. Niki and Potter-McIntyre, Sally L. and Williams, Amy J. and Lynch, Kennda L.},
+ number = {4},
+ month = {4},
+ pages = {363--400},
+ volume = {17},
+ publisher = {Mary Ann Liebert Inc.},
+ doi = {10.1089/AST.2016.1627},
+ issn = {15311074},
+ pmid = {28177270}
+}
+
+@book{Cavalazzi2019BiosignaturesAstrobiology,
+ title = {{Biosignatures for Astrobiology}},
+ year = {2019},
+ author = {Cavalazzi, Barbara and Westall, Frances},
+ editor = {Cavalazzi, Barbara and Westall, Frances},
+ series = {Advances in Astrobiology and Biogeophysics},
+ publisher = {Springer International Publishing},
+ url = {http://www.springer.com/series/5118 http://link.springer.com/10.1007/978-3-319-96175-0},
+ address = {Cham},
+ isbn = {978-3-319-96174-3},
+ doi = {10.1007/978-3-319-96175-0}
+}
+
+@article{Schmidt-Dannert2008BiosyntheticStrategies,
+ title = {{Biosynthetic Pathway Engineering Strategies}},
+ year = {2008},
+ journal = {Protein Engineering Handbook},
+ author = {Schmidt-Dannert, Claudia and Pisarchik, Alexander},
+ pages = {849--876},
+ url = {http://dx.doi.org/10.1002/9783527634026.ch34},
+ isbn = {9783527634026},
+ doi = {10.1002/9783527634026.ch34},
+ keywords = {biosynthesis, diversification, isoprenoids, metabolic engineering, metabolic network, pathway engineering}
+}
+
+@incollection{2005BiotechnologicalManufacture,
+ title = {{Biotechnological Processing Steps for Enzyme Manufacture}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {209--242},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch8},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch8}
+}
+
+@article{Eaborn1964BottEflects,
+ title = {{Bott, Eaborn, and Walton: Substituent Eflects}},
+ year = {1964},
+ author = {Eaborn, C},
+ number = {384},
+ pages = {384--388}
+}
+
+@article{CagingC,
+ title = {{C value (}},
+ author = {Caging, P and Invest, Clin and Popstats, D N A and Database, Population and Gc, The and The, A},
+ pages = {33--53}
+}
+
+@article{Chipot2007CalculatingTheory,
+ title = {{Calculating free energy differences using perturbation theory}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Chipot, Christophe and Pohorille, Andrew},
+ pages = {33--75},
+ volume = {86},
+ publisher = {Springer New York},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}2},
+ issn = {01726218}
+}
+
+@article{Holt2011CalculationWater,
+ title = {{Calculation of the molecular and atomic properties of selected anions in water}},
+ year = {2011},
+ journal = {Journal of Physical Chemistry B},
+ author = {Holt, Asbjørn and Karlstr{\"{o}}m, Gunnar and Hermida-Ram{\'{o}}n, José Manuel},
+ number = {5},
+ month = {2},
+ pages = {1098--1104},
+ volume = {115},
+ publisher = {American Chemical Society},
+ doi = {10.1021/jp1107763},
+ issn = {15205207}
+}
+
+@article{Boersma2010CatalyticCatalyst,
+ title = {{Catalytic enantioselective syn hydration of enones in water using a DNA-based catalyst}},
+ year = {2010},
+ journal = {Nature Chemistry},
+ author = {Boersma, Arnold J. and Coqui{\`{e}}re, David and Geerdink, Danny and Rosati, Fiora and Feringa, Ben L. and Roelfes, Gerard},
+ number = {11},
+ month = {11},
+ pages = {991--995},
+ volume = {2},
+ url = {http://www.nature.com/doifinder/10.1038/nchem.819},
+ doi = {10.1038/nchem.819},
+ issn = {1755-4330}
+}
+
+@article{Fornaro2018Catalytic/ProtectiveMars,
+ title = {{Catalytic/Protective Properties of Martian Minerals and Implications for Possible Origin of Life on Mars}},
+ year = {2018},
+ journal = {Life},
+ author = {Fornaro, Teresa and Steele, Andrew and Brucato, John},
+ number = {4},
+ month = {11},
+ pages = {56},
+ volume = {8},
+ url = {www.mdpi.com/journal/life http://www.mdpi.com/2075-1729/8/4/56},
+ doi = {10.3390/life8040056},
+ issn = {2075-1729},
+ keywords = {Mars, biomarkers, catalysis, ionizing radiations, minerals, preservation}
+}
+
+@book{Bergaya2013CationExchange,
+ title = {{Cation and Anion Exchange}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G. and Vayer, M.},
+ edition = {2},
+ number = {C},
+ pages = {333--359},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00013-5},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00013-5},
+ issn = {15724352},
+ keywords = {Analytical techniques, Anion exchange, Binding coefficient, CEC determination, Cation exchange, Cation-exchange capacity, Equimolar exchange, Equivalent exchange, Gapon coefficient, HSAB character, Heterovalent exchange, Hydration, Hysteresis, Ion exchange, Selectivity coefficient, Separation factor, Surface precipitation, Thermodynamics, Vanselow coefficient}
+}
+
+@book{VanDamme2013CementHydrates,
+ title = {{Cement hydrates}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Van Damme, H. and Pellenq, R. J.M. and Ulm, F. J.},
+ edition = {2},
+ pages = {801--817},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00027-4},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00027-4},
+ issn = {15724352},
+ keywords = {CSH, Cohesion, Double-layer interactions, Hydrates, Ionic correlation forces, LDH, Monte Carlo, Smectites, Swelling}
+}
+
+@article{Reetz2004ChangingEvolution,
+ title = {{Changing the enantioselectivity of enzymes by directed evolution}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Reetz, Manfred T.},
+ number = {1982},
+ pages = {238--256},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88021-2},
+ issn = {00766879},
+ pmid = {15289076}
+}
+
+@article{Kelly2008ChapterSpectroscopy,
+ title = {{Chapter 14 - Analysis of Soils and Minerals Using X-ray Absorption Spectroscopy}},
+ year = {2008},
+ journal = {Methods of Soil Analysis: Mineralogical methods},
+ author = {Kelly, S D and D., Hesterberg and B., Ravel},
+ pages = {387--464},
+ series = {Soil Science Society of America Book Series},
+ volume = {5},
+ publisher = {Soil Science Society of America},
+ url = {http://ag.udel.edu/soilchem/Kelley08MethodsPt5.pdf},
+ isbn = {9780891188469}
+}
+
+@incollection{1973ChapterStructure,
+ title = {{Chapter 17 Relations of Composition to Structure}},
+ year = {1973},
+ booktitle = {Developments in Sedimentology},
+ number = {C},
+ month = {1},
+ pages = {173--187},
+ volume = {15},
+ publisher = {Elsevier},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0070457109700202},
+ doi = {10.1016/S0070-4571(09)70020-2},
+ issn = {0070-4571}
+}
+
+@article{Lagaly2006ChapterScience,
+ title = {{Chapter 5 Colloid Clay Science}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ author = {Lagaly, G.},
+ number = {C},
+ month = {1},
+ pages = {141--245},
+ volume = {1},
+ publisher = {Elsevier},
+ doi = {10.1016/S1572-4352(05)01005-6},
+ issn = {1572-4352}
+}
+
+@incollection{Bommarius2005CharacterizationBio-catalyst,
+ title = {{Characterization of a (Bio-)catalyst}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ author = {Bommarius, Andreas Sebastian and Riebel, Bettina R.},
+ month = {1},
+ pages = {19--42},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch2},
+ address = {Weinheim, FRG},
+ isbn = {9783527602360},
+ doi = {10.1002/3527602364.ch2}
+}
+
+@article{2001ChemicallySmectites,
+ title = {{Chemically modified smectites}},
+ year = {2001},
+ doi = {10.1180/0009855033810083},
+ keywords = {H-smectites, Li fixation, acid dissolution, charge modification, reduction}
+}
+
+@article{He2012ChiralDerivatives,
+ title = {{Chiral phosphoric acid catalyzed inverse-electron-demand aza-Diels-Alder reaction of isoeugenol derivatives}},
+ year = {2012},
+ journal = {Organic Letters},
+ author = {He, Long and Bekkaye, Mathieu and Retailleau, Pascal and Masson, Géraldine},
+ isbn = {1523-7060},
+ doi = {10.1021/ol301251h},
+ issn = {15237060},
+ pmid = {22671430}
+}
+
+@article{Meister2011CircularProteins,
+ title = {{Circular Permutation of Proteins}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Meister, Glenna E. and Kanwar, Manu and Ostermeier, Marc},
+ pages = {453--471},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch18},
+ keywords = {Circular permutation, Directed evolution, Genetic rearrangement, Protein engineering, Protein evolution, Random circular permutation}
+}
+
+@book{Wagner2013ClayDisposal,
+ title = {{Clay Liners and Waste Disposal}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Wagner, J. F.},
+ edition = {2},
+ number = {C},
+ pages = {663--676},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00023-8},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00023-8},
+ issn = {15724352},
+ keywords = {Bottom liner, Compacted clay, Contaminant retention, Cover liner, Cut-off wall, Geosynthetic clay liner, Long-term stability}
+}
+
+@book{Lagaly2013ClayInteractions,
+ title = {{Clay mineral-organic interactions}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Lagaly, G. and Ogawa, M. and D{\'{e}}k{\'{a}}ny, I.},
+ pages = {435--505},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00015-8},
+ issn = {15724352},
+ keywords = {adsorption, adsorption excess isotherms, adsorption from binary solution, alkylammonium clay minerals, amino acids, displacement reactions, dyes, entraining reactions, hydrophilic/hydrophobic balance, intercalation, layer charge, organic derivatives, organo-clays, phase transitions, polymerisation, polymers, proteins, solvation}
+}
+
+@article{1994ClayMethods,
+ title = {{Clay Mineralogy: Spectroscopic and Chemical Determinative Methods}},
+ year = {1994},
+ isbn = {9789401043137},
+ doi = {10.1007/978-94-011-0727-3}
+}
+
+@incollection{Brack2013ClayLife,
+ title = {{Clay Minerals and the Origin of Life}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Brack, A.},
+ edition = {1},
+ pages = {507--521},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B978008098258800016X},
+ doi = {10.1016/B978-0-08-098258-8.00016-X},
+ keywords = {Amino acids, Catalysts, Homochirality, Origins of life, Polynucleotides, Polypeptides, RNA, Vesicles}
+}
+
+@article{Schoonheydt2018ClaySurfaces,
+ title = {{Clay minerals and their surfaces}},
+ year = {2018},
+ journal = {Developments in Clay Science},
+ author = {Schoonheydt, Robert A. and Johnston, Cliff T. and Bergaya, Faïza},
+ month = {1},
+ pages = {1--21},
+ volume = {9},
+ publisher = {Elsevier},
+ doi = {10.1016/B978-0-08-102432-4.00001-9},
+ issn = {1572-4352},
+ keywords = {Cation exchange, H-bonding, Intercalation, Isomorphous substitution, Lennard-Jones potential, Swelling, TO and TOT clay minerals, van der Waals energy}
+}
+
+@book{Mccabe2013ClayCatalysts,
+ title = {{Clay Minerals as Catalysts}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Mccabe, R. W. and Adams, J. M.},
+ edition = {2},
+ number = {C},
+ pages = {491--538},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00019-6},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00019-6},
+ issn = {15724352},
+ keywords = {Br{\o}nsted acidity, Catalysis, Clay minerals, Cycloaddition reactions, Lewis acidity, Microwaves, Reactive intermediates, Redox reactions, Selectivity, Supported catalysts, Supported reagents, Ultrasound}
+}
+
+@book{Bergaya2013ClayPerspective,
+ title = {{Clay science: A young discipline and a great perspective}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Beneke, K. and Berry, R. W. and Lagaly, G. and Tankersley, K. B.},
+ edition = {2},
+ pages = {819--855},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00028-6},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00028-6},
+ issn = {15724352},
+ keywords = {Archaeology, Clay groups, Clay meetings, First localities of clay minerals, History, Name of clay minerals, Teaching}
+}
+
+@book{Yuan2013ClaysControl,
+ title = {{Clays and Clay Minerals for Pollution Control}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Yuan, G. D. and Theng, B. K.G. and Churchman, G. J. and Gates, W. P.},
+ edition = {2},
+ number = {C},
+ pages = {587--644},
+ volume = {5},
+ publisher = {Copyright {\&}copy; 2013, 2006 Elsevier Ltd. All rights reserved.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00021-4},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00021-4},
+ issn = {15724352},
+ keywords = {Environmental materials, Environmental remediation, Heavy metals, Nanoparticles, Organic contaminants, Organoclays}
+}
+
+@book{Nir2013ClaysPesticides,
+ title = {{Clays, Clay Minerals, and Pesticides}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Nir, S. and El-Nahhal, Y. and Undabeytia, T. and Rytwo, G. and Polubesova, T. and Mishael, Y. and Rabinovitz, O. and Rubin, B.},
+ edition = {2},
+ number = {C},
+ pages = {645--662},
+ volume = {5},
+ publisher = {Copyright {\&}copy; 2013, 2006 Elsevier Ltd. All rights reserved.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00022-6},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00022-6},
+ issn = {15724352},
+ keywords = {Adsorption, Clay polymer nanaocomposite, Herbicide formulations, Liposome–clay mineral, Micelle–clay mineral formulations, Octadecyl trimethylammonium, Organoclay formulations, Photostabilization, Slow release formulations, Volatilization}
+}
+
+@book{Carretero2013ClaysHealth,
+ title = {{Clays, Drugs, and Human Health}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Carretero, M. I. and Gomes, C. S.F. and Tateo, F.},
+ edition = {2},
+ number = {C},
+ pages = {711--764},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00025-1},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00025-1},
+ issn = {15724352},
+ keywords = {Active ingredients and excipients, Beneficial effects of clays and clay minerals, Cosmetic products, Harmful effects of clays and clay minerals, Medical applications, Pelotherapy}
+}
+
+@book{Tazaki2013ClaysBiomineralization,
+ title = {{Clays, micro-organisms and biomineralization}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Tazaki, K.},
+ edition = {2},
+ pages = {613--653},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00019-5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00019-5},
+ issn = {15724352},
+ keywords = {Biomineralization, electron microscopy, imogolite, oil spill, pisoliths, radioactive minerals}
+}
+
+@article{Benders2010CloningYeast,
+ title = {{Cloning whole bacterial genomes in yeast}},
+ year = {2010},
+ journal = {Nucleic Acids Research},
+ author = {Benders, Gwynedd A. and Noskov, Vladimir N. and Denisova, Evgeniya A. and Lartigue, Carole and Gibson, Daniel G. and Assad-Garcia, Nacyra and Chuang, Ray Yuan and Carrera, William and Moodie, Monzia and Algire, Mikkel A. and Phan, Quang and Alperovich, Nina and Vashee, Sanjay and Merryman, Chuck and Venter, J. Craig and Smith, Hamilton O. and Glass, John I. and Hutchison, Clyde A.},
+ number = {8},
+ pages = {2558--2569},
+ volume = {38},
+ isbn = {1362-4962 (Electronic){\textbackslash}r0305-1048 (Linking)},
+ doi = {10.1093/nar/gkq119},
+ issn = {03051048},
+ pmid = {20211840}
+}
+
+@article{Endonuclease2013Co,
+ title = {{Co}},
+ year = {2013},
+ author = {Endonuclease, Restriction},
+ number = {1},
+ doi = {10.1093/nar.gkq279}
+}
+
+@book{Lagaly2013ColloidScience,
+ title = {{Colloid Clay Science}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Lagaly, G. and D{\'{e}}k{\'{a}}ny, I.},
+ pages = {243--345},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00010-9},
+ issn = {15724352},
+ keywords = {Aggregation, Charge distribution, Clay-water interaction, Coagulation, Colloids, DLVO theory, Deflocculation, Delamination, Depletion effect, Diffuse ionic layer, Dispersion, Electrokinetic properties, Electrostatic stabilization, Exfoliation, Filtration, Flocculation, Fractionation, Gel, Hydrates, Ion exchange, Mixed-layer structure, Nanoparticles, Particle shape, Particle size, Peptization, Plastering, Plasticity, Polyanions, Polycations, Polyelectrolytes, Polymers, Rheology, Salt effect, Sealing, Sedimentation, Sol, Steric stabilization, Stirring, Stokes' equations, Surfactants, Thixotropy, van der Waals interaction}
+}
+
+@book{Reymond2009ColorimetricScreening,
+ title = {{Colorimetric and Fluorescence - Based Screening}},
+ year = {2009},
+ booktitle = {Protein Engineering Handbook},
+ author = {Reymond, Jean Louis},
+ volume = {c},
+ isbn = {9783527318506}
+}
+
+@article{Wooden2008CometarySources,
+ title = {{Cometary Refractory Grains: Interstellar and Nebular Sources}},
+ year = {2008},
+ journal = {Space Science Reviews},
+ author = {Wooden, D H},
+ number = {1-4},
+ month = {7},
+ pages = {75--108},
+ volume = {138},
+ url = {http://link.springer.com/10.1007/s11214-008-9424-2},
+ doi = {10.1007/s11214-008-9424-2},
+ issn = {0038-6308}
+}
+
+@incollection{2005ComparisonProcesses,
+ title = {{Comparison of Biological and Chemical Catalysts for Novel Processes}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {569--592},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch20},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch20}
+}
+
+@article{Kaufhold2006ComparisonMontmorillonites,
+ title = {{Comparison of methods for the determination of the layer charge density (LCD) of montmorillonites}},
+ year = {2006},
+ journal = {Applied Clay Science},
+ author = {Kaufhold, S.},
+ number = {1-4},
+ month = {10},
+ pages = {14--21},
+ volume = {34},
+ publisher = {Elsevier},
+ doi = {10.1016/J.CLAY.2006.02.006},
+ issn = {0169-1317},
+ keywords = {Cation exchange capacity, Inner surface area, Layer charge density, Montmorillonite content}
+}
+
+@article{Barlow2003ComplexChirality,
+ title = {{Complex organic molecules at metal surfaces: bonding, organisation and chirality}},
+ year = {2003},
+ journal = {Surface Science Reports},
+ author = {Barlow, S. M. and Raval, R.},
+ number = {6-8},
+ month = {8},
+ pages = {201--341},
+ volume = {50},
+ publisher = {North-Holland},
+ doi = {10.1016/S0167-5729(03)00015-3},
+ issn = {0167-5729}
+}
+
+@article{Biczysko2018ComputationalAstrochemistry,
+ title = {{Computational challenges in Astrochemistry}},
+ year = {2018},
+ journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
+ author = {Biczysko, Malgorzata and Bloino, Julien and Puzzarini, Cristina},
+ number = {3},
+ month = {5},
+ volume = {8},
+ publisher = {Blackwell Publishing Inc.},
+ doi = {10.1002/WCMS.1349},
+ issn = {17590884}
+}
+
+@article{Saven2008ComputationalDesign,
+ title = {{Computational Protein Design}},
+ year = {2008},
+ author = {Saven, J. G.},
+ number = {1},
+ pages = {401--423},
+ isbn = {9789812778772},
+ doi = {10.1142/9789812778789{\_}0014}
+}
+
+@article{Illingworth2010ComputationalChannels,
+ title = {{Computational studies on polarization effects and selectivity in K + channels}},
+ year = {2010},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Illingworth, Christopher J.R. and Furini, Simone and Domene, Carmen},
+ number = {12},
+ month = {12},
+ pages = {3780--3792},
+ volume = {6},
+ publisher = { American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/ct100276c},
+ doi = {10.1021/ct100276c},
+ issn = {15499618}
+}
+
+@article{Rimola2012COMPUTATIONALPARTICLES,
+ title = {{COMPUTATIONAL STUDY OF INTERSTELLAR GLYCINE FORMATION OCCURRING AT RADICAL SURFACES OF WATER-ICE DUST PARTICLES}},
+ year = {2012},
+ journal = {The Astrophysical Journal},
+ author = {Rimola, Albert and Sodupe, Mariona and Ugliengo, Piero},
+ number = {1},
+ month = {7},
+ pages = {24},
+ volume = {754},
+ url = {https://iopscience.iop.org/article/10.1088/0004-637X/754/1/24},
+ doi = {10.1088/0004-637X/754/1/24},
+ issn = {0004-637X},
+ keywords = {ISM, astrochemistry-cosmic rays-ISM, molecules-molecular processes-ultraviolet}
+}
+
+@book{Haupts2009ConfocalEngineering,
+ title = {{Confocal and Conventional Fluorescence - Based High Throughput Screening in Protein Engineering}},
+ year = {2009},
+ author = {Haupts, Ulrich and Hesse, Oliver and Strerath, Michael and Walla, Peter J and Coco, Wayne M},
+ isbn = {9783527318506}
+}
+
+@article{Steipe2004Consensus-basedEnzymes,
+ title = {{Consensus-based engineering of protein stability: From intrabodies to thermostable enzymes}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Steipe, Boris},
+ number = {1994},
+ pages = {176--186},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88016-9},
+ issn = {00766879},
+ pmid = {15289071}
+}
+
+@article{Gil-Lozano2020ConstrainingFluids,
+ title = {{Constraining the preservation of organic compounds in Mars analog nontronites after exposure to acid and alkaline fluids}},
+ year = {2020},
+ journal = {Scientific Reports 2020 10:1},
+ author = {Gil-Lozano, Carolina and Fair{\'{e}}n, Alberto G. and Mu{\~{n}}oz-Iglesias, Victoria and Fern{\'{a}}ndez-Sampedro, Maite and Prieto-Ballesteros, Olga and Gago-Duport, Luis and Losa-Adams, Elisabeth and Carrizo, Daniel and Bishop, Janice L. and Fornaro, Teresa and Mateo-Mart{\'{i}}, Eva},
+ number = {1},
+ month = {9},
+ pages = {1--11},
+ volume = {10},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s41598-020-71657-9},
+ isbn = {0123456789},
+ doi = {10.1038/s41598-020-71657-9},
+ issn = {2045-2322},
+ pmid = {32934272},
+ keywords = {Astrobiology, Geochemistry, Mineralogy}
+}
+
+@article{Paschon2004ConstructionTruncation,
+ title = {{Construction of protein fragment complementation libraries using incremental truncation}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Paschon, David E. and Ostermeier, Marc},
+ number = {1995},
+ pages = {103--116},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88010-8},
+ issn = {00766879},
+ pmid = {15289065}
+}
+
+@incollection{2013Contributors,
+ title = {{Contributors}},
+ year = {2013},
+ pages = {xxi-xxiii},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588099892},
+ doi = {10.1016/B978-0-08-098258-8.09989-2}
+}
+
+@incollection{2013Contributorsb,
+ title = {{Contributors}},
+ year = {2013},
+ pages = {xxiii-xxv},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B978008098259509987X},
+ doi = {10.1016/B978-0-08-098259-5.09987-X}
+}
+
+@article{2017Contributors,
+ title = {{Contributors}},
+ year = {2017},
+ pages = {xiii},
+ doi = {10.1016/B978-0-08-100355-8.09988-4}
+}
+
+@article{BiologyContributors194,
+ title = {{Contributors to Volume 194}},
+ journal = {New York},
+ author = {Biology, Cellular and Insti-, Massachusetts and Johns, The and Genetics, Molecular and Biology, Cell and Pharmaceuti-, Vertex and Univer-, Comell and Insti-, Howard Hughes Medical and Chemistry, Physiological and Ge-, Molecular and Re-, Collaborative and Biologie, Molekulare and Labora-, Lewis Thomas and Repub-, Federal},
+ number = {17},
+ pages = {12--15},
+ volume = {194}
+}
+
+@article{2013Copyright,
+ title = {{Copyright}},
+ year = {2013},
+ pages = {iv},
+ isbn = {9780080982595},
+ doi = {10.1016/b978-0-08-098259-5.09991-1}
+}
+
+@incollection{2013Copyrightb,
+ title = {{Copyright}},
+ year = {2013},
+ pages = {iv},
+ doi = {10.1016/b978-0-08-098258-8.09992-2}
+}
+
+@incollection{2013Copyrightc,
+ title = {{Copyright}},
+ year = {2013},
+ pages = {iv},
+ doi = {10.1016/b978-0-08-098259-5.09991-1}
+}
+
+@article{2017Copyright,
+ title = {{Copyright}},
+ year = {2017},
+ pages = {iv},
+ doi = {10.1016/B978-0-08-100355-8.09996-3}
+}
+
+@article{Tang2020CoronavirusDevelopment,
+ title = {{Coronavirus membrane fusion mechanism offers a potential target for antiviral development}},
+ year = {2020},
+ journal = {Antiviral Research},
+ author = {Tang, Tiffany and Bidon, Miya and Jaimes, Javier A. and Whittaker, Gary R. and Daniel, Susan},
+ number = {April},
+ pages = {104792},
+ volume = {178},
+ publisher = {Elsevier},
+ url = {https://doi.org/10.1016/j.antiviral.2020.104792},
+ doi = {10.1016/j.antiviral.2020.104792},
+ issn = {18729096},
+ pmid = {32272173},
+ keywords = {COVID-19, Fusion peptide, Middle east respiratory syndrome, SARS-CoV-2, Severe acute respiratory syndrome, Spike protein}
+}
+
+@book{Bergaya2013CriticalMinerals,
+ title = {{Critical Assessment of Analytical Techniques of Clays and Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {2},
+ number = {C},
+ pages = {9--10},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00002-0},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00002-0},
+ issn = {15724352},
+ keywords = {Clay mineral characterization, Electron microscopy, Ion exchange, Smectite characterization, Spectroscopic techniques, Thermal analysis}
+}
+
+@article{Singleton2007DA,
+ title = {{D (1) A specific indicator of ambiguity in the recognition site of a}},
+ year = {2007},
+ author = {Singleton, Paul},
+ number = {1},
+ pages = {393--394},
+ volume = {14},
+ isbn = {9780470747322},
+ doi = {10.1093/nar/gkp725.}
+}
+
+@article{Singleton2007DAb,
+ title = {{D (1) A specific indicator of ambiguity in the recognition site of a}},
+ year = {2007},
+ author = {Singleton, Paul},
+ number = {1},
+ pages = {393--394},
+ volume = {14},
+ isbn = {9780470747322},
+ doi = {10.1093/nar/gkp725.}
+}
+
+@article{Adn2006DLoop,
+ title = {{D loop}},
+ year = {2006},
+ author = {Adn, D D},
+ number = {1},
+ pages = {86--100},
+ volume = {34}
+}
+
+@article{Mckinney2010DataPython,
+ title = {{Data Structures for Statistical Computing in Python}},
+ year = {2010},
+ author = {Mckinney, Wes},
+ keywords = {Index Terms-data structure, R, statistics}
+}
+
+@article{2017Dedication,
+ title = {{Dedication}},
+ year = {2017},
+ pages = {v},
+ doi = {10.1016/B978-0-08-100355-8.09998-7}
+}
+
+@article{NodeDemethylationFluoride,
+ title = {{Demethylation of Aliphatic Methyl Ethers with a Thiol and Boron Tri- fluoride}},
+ author = {Node, Manabu and Hori, Hitoshi and Fujita, Eiichi and Ayer, W A and Bowman, W R and Joseph, T L and Smith, P},
+ doi = {10.1039/P19760002237}
+}
+
+@article{Mancini2020DesignBundle,
+ title = {{Design of a Fe4S4 cluster into the core of a de novo four-helix bundle}},
+ year = {2020},
+ journal = {Biotechnology and Applied Biochemistry},
+ author = {Mancini, Joshua A. and Pike, Douglas H. and Tyryshkin, Alexei M. and Haramaty, Liti and Wang, Michael S. and Poudel, Saroj and Hecht, Michael and Nanda, Vikas},
+ number = {4},
+ pages = {574--585},
+ volume = {67},
+ doi = {10.1002/bab.2003},
+ issn = {14708744},
+ pmid = {32770861},
+ keywords = {combinatorial library, de novo protein, electron transfer, iron–sulfur cluster, oxidoreductase, protein design}
+}
+
+@incollection{2005DesignProcesses,
+ title = {{Design of Biocatalytic Processes}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {539--568},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch19},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch19}
+}
+
+@article{Sagermann2011DesigningSwitches,
+ title = {{Designing Programmable Protein Switches}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Sagermann, Martin},
+ pages = {363--389},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch14},
+ keywords = {Conformational switches, Effector control, Engineering allostery, Protein design}
+}
+
+@article{Joung2008DeterminationSimulations,
+ title = {{Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations}},
+ year = {2008},
+ journal = {Journal of Physical Chemistry B},
+ author = {Joung, In Suk and Cheatham, Thomas E.},
+ number = {30},
+ month = {7},
+ pages = {9020--9041},
+ volume = {112},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/jp8001614},
+ doi = {10.1021/JP8001614/SUPPL{\_}FILE/JP8001614-FILE003.PDF},
+ issn = {15206106}
+}
+
+@article{Yan2011DeterminationMeasurements,
+ title = {{Determination of anisotropic surface characteristics of different phyllosilicates by direct force measurements}},
+ year = {2011},
+ journal = {Langmuir},
+ author = {Yan, Lujie and Englert, Alexandre H. and Masliyah, Jacob H. and Xu, Zhenghe},
+ number = {21},
+ month = {11},
+ pages = {12996--13007},
+ volume = {27},
+ doi = {10.1021/LA2027829},
+ issn = {07437463}
+}
+
+@article{Michot2018DeterminationMinerals,
+ title = {{Determination of surface areas and textural properties of clay minerals}},
+ year = {2018},
+ journal = {Developments in Clay Science},
+ author = {Michot, Laurent J.},
+ month = {1},
+ pages = {23--47},
+ volume = {9},
+ publisher = {Elsevier},
+ doi = {10.1016/B978-0-08-102432-4.00002-0},
+ issn = {1572-4352},
+ keywords = {Basal faces, Edge faces, Gas adsorption, Mesopores, Micropores, Small angle X-ray scattering, Surface area, Swelling}
+}
+
+@article{GatesW.KloproggeJ.T.MadejovaJ.Bergaya2017Dev.Minerals,
+ title = {{Dev. Clay Sci. vol. 8. Infrared and Raman Spectroscopies of Clay Minerals}},
+ year = {2017},
+ author = {Gates, W., Kloprogge, J.T., Madejova, J., Bergaya, F. (eds)},
+ editor = {Gates, W.P., Kloprogge, J.T, Madejova, J., Bergaya, F.},
+ pages = {604},
+ publisher = {Elsevier Ltd},
+ isbn = {978-0-08-100355-8}
+}
+
+@misc{DevelopmentsElsevier,
+ title = {{Developments in Clay Science | Applied Clay Mineralogy - Occurrences, Processing and Application of Kaolins, Bentonites, Palygorskite-Sepiolite, and Common Clays | ScienceDirect.com by Elsevier}},
+ url = {https://www.sciencedirect.com/bookseries/developments-in-clay-science/vol/2/suppl/C}
+}
+
+@misc{DevelopmentsElsevierb,
+ title = {{Developments in Clay Science | Infrared and Raman Spectroscopies of Clay Minerals | ScienceDirect.com by Elsevier}},
+ url = {https://www.sciencedirect.com/bookseries/developments-in-clay-science/vol/8/suppl/C}
+}
+
+@article{Ishida2009DIDSExchange,
+ title = {{DIDS, a chemical compound that inhibits RAD51-mediated homologous pairing and strand exchange}},
+ year = {2009},
+ journal = {Nucleic Acids Research},
+ author = {Ishida, Takako and Takizawa, Yoshimasa and Kainuma, Takashi and Inoue, Jin and Mikawa, Tsutomu and Shibata, Takehiko and Suzuki, Hidekazu and Tashiro, Satoshi and Kurumizaka, Hitoshi},
+ number = {10},
+ pages = {3367--3376},
+ volume = {37},
+ isbn = {1362-4962},
+ doi = {10.1093/nar/gkp200},
+ issn = {03051048},
+ pmid = {19336413}
+}
+
+@article{Torrent2015DiffuseSpectroscopy,
+ title = {{Diffuse reflectance spectroscopy}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Torrent, José and Barr{\'{o}}n, Vidal},
+ month = {10},
+ pages = {367--385},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C13},
+ keywords = {Diffuse reflectance spectroscopy, Kubelka-Munk theory, Particle size, Sample preparation, Soil minerals, UV-visible spectrophotometer}
+}
+
+@article{Vandenbygaart2015DigitalMicromorphology,
+ title = {{Digital image analysis of soil micromorphology}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Vandenbygaart, A. J. and Protz, R. and Duke, C.},
+ month = {10},
+ pages = {227--234},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C8},
+ keywords = {Genetic processes, Multisource image analysis, Multispectral image analysis, Quantitative digital image analysis, Soil micromorphology, Thin section preparation}
+}
+
+@article{Franke2004DirectedAldolases,
+ title = {{Directed evolution of aldolases}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Franke, Dirk and Hsu, Che Chang and Wong, Chi Huey},
+ number = {2000},
+ pages = {224--238},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88020-0},
+ issn = {00766879},
+ pmid = {18230325}
+}
+
+@article{Schmidt2004DirectedEsterases,
+ title = {{Directed evolution of lipases and esterases}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Schmidt, Marlen and Baumann, Markus and Henke, Erik and Konarzycka-Bessler, Monika and Bornscheuer, Uwe T.},
+ number = {1994},
+ pages = {199--207},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88018-2},
+ issn = {00766879},
+ pmid = {15289073}
+}
+
+@article{Reetz2002DirectedCatalysts,
+ title = {{Directed evolution of selective enzymes and hybrid catalysts}},
+ year = {2002},
+ journal = {Tetrahedron},
+ author = {Reetz, Manfred T.},
+ number = {32},
+ pages = {6595--6602},
+ volume = {58},
+ isbn = {2083062000},
+ doi = {10.1016/S0040-4020(02)00668-3},
+ issn = {00404020},
+ keywords = {Enantioselectivity, Enzymes, Lipases, Screening, Transition metal catalysts}
+}
+
+@book{Reetz2016DirectedBiotechnology,
+ title = {{Directed evolution of selective enzymes: Catalysts for organic chemistry and biotechnology}},
+ year = {2016},
+ booktitle = {Directed Evolution of Selective Enzymes: Catalysts for Organic Chemistry and Biotechnology},
+ author = {Reetz, Manfred T.},
+ pages = {1--308},
+ isbn = {9783527655465},
+ doi = {10.1002/9783527655465}
+}
+
+@article{TrifonovDistinctAnalysis,
+ title = {{Distinct Stages of Protein Evolution as Suggested by Protein Sequence Analysis}},
+ author = {Trifonov, Edward N and Kirzhner, Alla and Kirzhner, Valery M and Berezovsky, Igor N},
+ doi = {10.1007/s002390010229},
+ keywords = {Amino acid chronol-ogy-, Autocorrelation-DNA ring closure-, Closed loops-, Codon chronology-, Early evolution-, Gene splicing, Heteropeptides-, Homopep-tides-, Multidomain proteins-, Pro-tein folds-, Sequence mosaic-, Triplet code-}
+}
+
+@article{Boersma2010DNA-basedCatalysis,
+ title = {{DNA-based asymmetric catalysis}},
+ year = {2010},
+ journal = {Chemical Society Reviews},
+ author = {Boersma, Arnold J. and Megens, Rik P. and Feringa, Ben L. and Roelfes, Gerard},
+ number = {6},
+ pages = {2083},
+ volume = {39},
+ url = {http://xlink.rsc.org/?DOI=b811349c},
+ doi = {10.1039/b811349c},
+ issn = {0306-0012}
+}
+
+@misc{Doi:10.1016/j.acha.2006.04.006Reader,
+ title = {{doi:10.1016/j.acha.2006.04.006 | Elsevier Enhanced Reader}},
+ url = {https://reader.elsevier.com/reader/sd/pii/S1063520306000546?token=F95A55580D3000893DA573112AFF485893CEC041DB307CE97D7517B3E08F9086CBBDCC447F591AC90B82DB6B5D8FCDEE}
+}
+
+@article{Hayhurst2004E.Coli,
+ title = {{E. Coli}},
+ year = {2004},
+ author = {Hayhurst, Chris},
+ number = {18064},
+ pages = {64},
+ url = {https://books.google.com/books?id=rYnj-FXH01MC&pgis=1},
+ isbn = {0823942015},
+ keywords = {erscript ii reverse transcriptase}
+}
+
+@article{Li2017ElectricIons,
+ title = {{Electric fields within clay materials: How to affect the adsorption of metal ions}},
+ year = {2017},
+ journal = {Journal of Colloid and Interface Science},
+ author = {Li, Xiong and Li, Hang and Yang, Gang},
+ month = {9},
+ pages = {54--59},
+ volume = {501},
+ publisher = {Academic Press},
+ doi = {10.1016/J.JCIS.2017.04.040},
+ issn = {0021-9797},
+ pmid = {28433885},
+ keywords = {Electric fields, Hofmeister effects, Molecular dynamics, Polarization effects, Potential of mean force}
+}
+
+@article{Guillemette2015ElectronTechniques,
+ title = {{Electron microprobe techniques}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Guillemette, Renald N.},
+ month = {10},
+ pages = {335--365},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C12},
+ keywords = {Electron detectors, Electron optics system, Electron probe microanalyzer, Qualitative analysis, Quantitative analysis, Sample requirements, Soil materials, Vacuum system, Wavelength-dispersive spectrometry, X-ray spectrometers}
+}
+
+@book{Kogure2013ElectronMicroscopy,
+ title = {{Electron Microscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Kogure, T.},
+ edition = {2},
+ number = {C},
+ pages = {275--317},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00011-1},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00011-1},
+ issn = {15724352},
+ pmid = {13880167},
+ keywords = {High-resolution imaging, Phyllosilicates, Radiation damage, Sample preparation, Scanning electron microscopy, Transmission electron microscopy}
+}
+
+@article{Bliznyuk2004ElectronicChannel,
+ title = {{Electronic effects in biomolecular simulations: Investigation of the KcsA potassium ion channel}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry B},
+ author = {Bliznyuk, Andrey A. and Rendell, Alistair P.},
+ number = {36},
+ month = {9},
+ pages = {13866--13873},
+ volume = {108},
+ doi = {10.1021/jp0487298},
+ issn = {15206106}
+}
+
+@article{Pollak2018ElementalTrasimeno,
+ title = {{Elemental Analysis of Sediment Samples from Lake Trasimeno}},
+ year = {2018},
+ author = {Pollak, Hannah},
+ pages = {1--12}
+}
+
+@article{Chen2015EnantioselectiveWater,
+ title = {{Enantioselective Michael Addition of Water}},
+ year = {2015},
+ journal = {Chemistry - A European Journal},
+ author = {Chen, Bi-Shuang and Resch, Verena and Otten, Linda G. and Hanefeld, Ulf},
+ number = {7},
+ month = {2},
+ pages = {3020--3030},
+ volume = {21},
+ publisher = {WILEY‐VCH Verlag},
+ url = {http://doi.wiley.com/10.1002/chem.201405579},
+ doi = {10.1002/chem.201405579},
+ issn = {09476539},
+ keywords = {Michael addition, biocatalysis, enantioselectivity, hydratases, water}
+}
+
+@article{Chen2015EnantioselectiveWaterb,
+ title = {{Enantioselective Michael Addition of Water}},
+ year = {2015},
+ author = {Chen, Bi-Shuang and Resch, Verena and Otten, Linda G. and Hanefeld, Ulf},
+ number = {7},
+ pages = {3020--3030},
+ volume = {21},
+ publisher = {WILEY‐VCH Verlag},
+ url = {http://doi.wiley.com/10.1002/chem.201405579 http://doi.wiley.com/10.1002/chin.201527192},
+ doi = {10.1002/chin.201527192},
+ keywords = {Michael addition, biocatalysis, enantioselectivity, hydratases, water}
+}
+
+@book{Kazlauskas2008EngineeringReactions,
+ title = {{Engineering Enantioselectivity in Enzyme - Catalyzed Reactions}},
+ year = {2008},
+ author = {Kazlauskas, Romas},
+ isbn = {9783527318506}
+}
+
+@article{Turunen2004EngineeringMutagenesis,
+ title = {{Engineering the thermotolerance and pH optimum of family 11 xylanases by site-directed mutagenesis}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Turunen, Ossi and J{\"{a}}nis, Janne and Fenel, Fred and Leisola, Matti},
+ number = {1994},
+ pages = {156--167},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88014-5},
+ issn = {00766879},
+ pmid = {15289069}
+}
+
+@incollection{2005EnzymeEngineering,
+ title = {{Enzyme Reaction Engineering}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {91--134},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch5},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch5}
+}
+
+@article{Neuenschwander2011EquippingStringency,
+ title = {{Equipping in vivo Selection Systems with Tunable Stringency}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Neuenschwander, Martin and Kleeb, Andreas C. and Kast, Peter and Hilvert, Donald},
+ pages = {537--561},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch23},
+ keywords = {Catalyst concentration control, Directed evolution, Enzyme degradation, Genetic complementation, Inducible protein production, Metabolic engineering, Random gene library, Tetracycline promoter}
+}
+
+@article{Red2009EscherichiaColi,
+ title = {{Escherichia coli}},
+ year = {2009},
+ author = {Red, Amplex},
+ isbn = {9783527318506}
+}
+
+@article{Prakash2018EssentialInvestigation,
+ title = {{Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation}},
+ year = {2018},
+ journal = {Biochemical and Biophysical Research Communications},
+ author = {Prakash, Arushi and Sprenger, K. G. and Pfaendtner, Jim},
+ number = {2},
+ month = {3},
+ pages = {274--281},
+ volume = {498},
+ publisher = {Academic Press},
+ doi = {10.1016/J.BBRC.2017.07.066},
+ issn = {0006-291X},
+ pmid = {28720500},
+ keywords = {Adsorption, Metadynamics, Molecular dynamics simulations}
+}
+
+@article{Meiner2015EstimationExperiments,
+ title = {{Estimation of the free energy of adsorption of a polypeptide on amorphous SiO2 from molecular dynamics simulations and force spectroscopy experiments}},
+ year = {2015},
+ journal = {Soft Matter},
+ author = {Mei{\ss}ner, Robert Horst and Wei, Gang and Ciacchi, Lucio Colombi},
+ number = {31},
+ month = {7},
+ pages = {6254--6265},
+ volume = {11},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2015/sm/c5sm01444a https://pubs.rsc.org/en/content/articlelanding/2015/sm/c5sm01444a},
+ doi = {10.1039/C5SM01444A},
+ issn = {1744-6848},
+ pmid = {26158561}
+}
+
+@article{Laird2015EvaluationCharge,
+ title = {{Evaluation of the Structural Formula and Alkylammonium Methods of Determining Layer Charge}},
+ year = {2015},
+ journal = {Layer Charge Characteristics of 2:1 Silicate Clay Minerals},
+ author = {Laird, David A.},
+ month = {4},
+ pages = {79--103},
+ publisher = {Clay Minerals Society},
+ doi = {10.1346/CMS-WLS-6.3}
+}
+
+@incollection{2005EvolutionFunction,
+ title = {{Evolution of Biocatalytic Function}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {457--486},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch16},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch16}
+}
+
+@article{Eggert2011EvolutionLipase,
+ title = {{Evolution of Enantioselective Bacillus subtilis Lipase}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Eggert, Thorsten and Funke, Susanne A. and Andexer, Jennifer N. and Reetz, Manfred T. and Jaeger, Karl Erich},
+ pages = {441--451},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch17},
+ keywords = {Bacillus subtilis lipase, Complete site-saturation mutagenesis, Directed evolution, Enantioselectivity, Error-prone PCR}
+}
+
+@article{Paul2012ExpandingHirsuta,
+ title = {{Expanding the regioselective enzymatic repertoire: oxidative mono-cleavage of dialkenes catalyzed by Trametes hirsuta}},
+ year = {2012},
+ journal = {Chemical Communications},
+ author = {Paul, Caroline E. and Rajagopalan, Aashrita and Lavandera, Iván and Gotor-Fern{\'{a}}ndez, Vicente and Kroutil, Wolfgang and Gotor, Vicente},
+ doi = {10.1039/c2cc17572j},
+ issn = {1359-7345},
+ pmid = {22358469}
+}
+
+@article{Paul2012ExpandingHirsutab,
+ title = {{Expanding the regioselective enzymatic repertoire: oxidative mono-cleavage of dialkenes catalyzed by Trametes hirsuta}},
+ year = {2012},
+ journal = {Chemical Communications},
+ author = {Paul, Caroline E. and Rajagopalan, Aashrita and Lavandera, Iván and Gotor-Fern{\'{a}}ndez, Vicente and Kroutil, Wolfgang and Gotor, Vicente},
+ doi = {10.1039/c2cc17572j},
+ issn = {1359-7345},
+ pmid = {22358469}
+}
+
+@article{Altair2021ExperimentalVents.,
+ title = {{Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents.}},
+ year = {2021},
+ journal = {Life (Basel, Switzerland)},
+ author = {Altair, Thiago and Borges, Luiz G F and Galante, Douglas and Varela, Hamilton},
+ number = {8},
+ month = {7},
+ volume = {11},
+ publisher = {MDPI AG},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/34440521 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC8401828},
+ doi = {10.3390/life11080777},
+ issn = {2075-1729},
+ pmid = {34440521},
+ keywords = {bioenergetics, catalysis, electrochemistry, hydrothermal reactor, hydrothermal vents, interface, origin of life}
+}
+
+@article{Payer2017Exploring4-Hydroxystyrene,
+ title = {{Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene}},
+ year = {2017},
+ journal = {Advanced Synthesis {\&} Catalysis},
+ author = {Payer, Stefan E. and Sheng, Xiang and Pollak, Hannah and Wuensch, Christiane and Steinkellner, Georg and Himo, Fahmi and Glueck, Silvia M. and Faber, Kurt},
+ number = {12},
+ month = {6},
+ pages = {2066--2075},
+ volume = {359},
+ url = {http://doi.wiley.com/10.1002/adsc.201700247},
+ doi = {10.1002/adsc.201700247},
+ issn = {16154150},
+ keywords = {biocatalysis, catalytic promiscuity, decarboxylase, hydration, hydroxystyrene, nucleophile addition}
+}
+
+@article{Payer2017Exploring4-Hydroxystyreneb,
+ title = {{Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene}},
+ year = {2017},
+ journal = {Advanced Synthesis and Catalysis},
+ author = {Payer, Stefan E. and Sheng, Xiang and Pollak, Hannah and Wuensch, Christiane and Steinkellner, Georg and Himo, Fahmi and Glueck, Silvia M. and Faber, Kurt},
+ number = {12},
+ month = {6},
+ pages = {2066--2075},
+ volume = {359},
+ url = {http://doi.wiley.com/10.1002/adsc.201700247},
+ doi = {10.1002/adsc.201700247},
+ issn = {16154169},
+ keywords = {biocatalysis, catalytic promiscuity, decarboxylase, hydration, hydroxystyrene, nucleophile addition}
+}
+
+@article{Payer2017Exploring4-Hydroxystyrenec,
+ title = {{Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene}},
+ year = {2017},
+ journal = {Advanced Synthesis {\&} Catalysis},
+ author = {Payer, Stefan E. and Sheng, Xiang and Pollak, Hannah and Wuensch, Christiane and Steinkellner, Georg and Himo, Fahmi and Glueck, Silvia M. and Faber, Kurt},
+ number = {12},
+ month = {6},
+ pages = {2066--2075},
+ volume = {359},
+ url = {http://doi.wiley.com/10.1002/adsc.201700247},
+ doi = {10.1002/adsc.201700247},
+ issn = {16154150},
+ keywords = {biocatalysis, catalytic promiscuity, decarboxylase, hydration, hydroxystyrene, nucleophile addition}
+}
+
+@article{Martins2011ExtractionUtah,
+ title = {{Extraction of amino acids from soils close to the Mars Desert Research Station (MDRS), Utah}},
+ year = {2011},
+ journal = {International Journal of Astrobiology},
+ author = {Martins, Z. and Sephton, M. A. and Foing, B. H. and Ehrenfreund, P.},
+ number = {3},
+ month = {7},
+ pages = {231--238},
+ volume = {10},
+ publisher = {Cambridge University Press},
+ url = {https://www.cambridge.org/core/journals/international-journal-of-astrobiology/article/extraction-of-amino-acids-from-soils-close-to-the-mars-desert-research-station-mdrs-utah/D6B9ED4EB283ACDC16FEB86E5B4FC6DF},
+ doi = {10.1017/S1473550410000431},
+ issn = {1475-3006},
+ keywords = {Mars Desert Research Station, Mars analogue soils, amino acids}
+}
+
+@article{FRecipient,
+ title = {{F − recipient}},
+ number = {Ii},
+ pages = {83--90},
+ volume = {1}
+}
+
+@article{Dudev2010FactorsChannels,
+ title = {{Factors Governing the Na + vs K + Selectivity in Sodium Ion Channels}},
+ year = {2010},
+ journal = {Journal of the American Chemical Society},
+ author = {Dudev, Todor and Lim, Carmay},
+ number = {7},
+ month = {2},
+ pages = {2321--2332},
+ volume = {132},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/ja909280g},
+ doi = {10.1021/ja909280g},
+ issn = {0002-7863}
+}
+
+@book{Ruiz-Hitzky2013FibrousNanocomposites,
+ title = {{Fibrous clay mineral-polymer nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Ruiz-Hitzky, E. and Aranda, P. and Darder, M. and Fernandes, F. M.},
+ edition = {2},
+ pages = {721--741},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00023-7},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00023-7},
+ issn = {15724352},
+ keywords = {Bionanocomposites, Clay-polymer nanocomposites, Nanofillers, Palygorskite, Polymer-clay nanocomposites, Sepiolite}
+}
+
+@misc{FileDocumentation,
+ title = {{File formats — GROMACS 2018.8 documentation}},
+ url = {https://manual.gromacs.org/documentation/2018-current/user-guide/file-formats.html?highlight=gro}
+}
+
+@article{Heinz2005ForceMontmorillonite,
+ title = {{Force field for mica-type silicates and dynamics of octadecylammonium chains grafted to montmorillonite}},
+ year = {2005},
+ journal = {Chemistry of Materials},
+ author = {Heinz, Hendrik and Koerner, Hilmar and Anderson, Kelly L. and Vaia, Richard A. and Farmer, B. L.},
+ number = {23},
+ month = {11},
+ pages = {5658--5669},
+ volume = {17},
+ publisher = { American Chemical Society },
+ url = {https://pubs.acs.org/doi/full/10.1021/cm0509328},
+ doi = {10.1021/CM0509328/SUPPL{\_}FILE/CM0509328SI20050802{\_}050932.PDF},
+ issn = {08974756}
+}
+
+@article{Rimola2009FormationLife,
+ title = {{Formation versus hydrolysis of the peptide bond from a quantum-mechanical viewpoint: The role of mineral surfaces and implications for the origin of life}},
+ year = {2009},
+ journal = {International journal of molecular sciences},
+ author = {Rimola, Albert and Ugliengo, Piero and Sodupe, Mariona},
+ number = {3},
+ month = {3},
+ pages = {746--760},
+ volume = {10},
+ publisher = {Int J Mol Sci},
+ url = {https://pubmed.ncbi.nlm.nih.gov/19399219/},
+ doi = {10.3390/IJMS10030746},
+ issn = {1422-0067},
+ pmid = {19399219},
+ keywords = {Albert Rimola, Aluminum Silicates / chemistry, Glycine / chemistry, Hydrolysis, MEDLINE, Mariona Sodupe, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Non-U.S. Gov't, PMC2672000, Peptides / chemistry*, Peptides / metabolism, Piero Ugliengo, Potassium Compounds / chemistry, PubMed Abstract, Quantum Theory*, Research Support, Silicates / chemistry, Surface Properties, Thermodynamics, Water / chemistry, doi:10.3390/ijms10030746, pmid:19399219}
+}
+
+@article{Duval2019Fougerite:Cells,
+ title = {{Fougerite: the not so simple progenitor of the first cells}},
+ year = {2019},
+ journal = {Interface focus},
+ author = {Duval, Simon and Baymann, Frauke and Schoepp-Cothenet, Barbara and Trolard, Fabienne and Bourri{\'{e}}, Guilhem and Grauby, Olivier and Branscomb, Elbert and Russell, Michael J. and Nitschke, Wolfgang},
+ number = {6},
+ month = {12},
+ volume = {9},
+ publisher = {Interface Focus},
+ url = {https://pubmed.ncbi.nlm.nih.gov/31641434/},
+ doi = {10.1098/RSFS.2019.0063},
+ issn = {2042-8898},
+ pmid = {31641434},
+ keywords = {Frauke Baymann, MEDLINE, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, PMC6802129, PubMed Abstract, Review, Simon Duval, Wolfgang Nitschke, doi:10.1098/rsfs.2019.0063, pmid:31641434}
+}
+
+@book{Petit2013FourierSpectroscopy,
+ title = {{Fourier Transform Infrared Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Petit, S. and Madejova, J.},
+ edition = {2},
+ number = {C},
+ pages = {213--231},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00009-3},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00009-3},
+ issn = {15724352},
+ keywords = {Characterization, Clay mineral identification, Crystal-chemistry, Mid-infrared, Near-infrared, Structural changes}
+}
+
+@article{Branscomb2018FrankensteinBeginning,
+ title = {{Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?: Part 2: As life is now, so it must have been in the beginning}},
+ year = {2018},
+ journal = {BioEssays},
+ author = {Branscomb, Elbert and Russell, Michael J.},
+ number = {8},
+ month = {8},
+ volume = {40},
+ publisher = {John Wiley and Sons Inc.},
+ doi = {10.1002/bies.201700182},
+ issn = {15211878},
+ pmid = {29974482},
+ keywords = {alkaline vent, emergence of life, green rust}
+}
+
+@article{Simonson2007FreeMacromolecules,
+ title = {{Free energy calculations: Approximate methods for biological macromolecules}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Simonson, Thomas},
+ pages = {423--461},
+ volume = {86},
+ publisher = {Springer New York},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}12},
+ issn = {01726218}
+}
+
+@article{Chipot2007FreePhysics,
+ title = {{Free Energy Calculations: Theory and Applications in Chemistry and Biology (Springer Series in Chemical Physics)}},
+ year = {2007},
+ journal = {Journal of the American Chemical Society, 2007},
+ author = {Chipot, Christophe and Pohorille, Andrew},
+ isbn = {978-3-540-38447-2}
+}
+
+@article{Pohorille2007FreeForeword,
+ title = {{Free Energy Calculations: Theory and Applications in Chemistry and Biology - Foreword}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Pohorille, Andrew and Chipot, Christophe},
+ pages = {517},
+ volume = {86},
+ publisher = {Springer},
+ isbn = {9783540736172},
+ issn = {01726218}
+}
+
+@misc{Catterall2000FromChannels,
+ title = {{From ionic currents to molecular mechanisms: The structure and function of voltage-gated sodium channels}},
+ year = {2000},
+ booktitle = {Neuron},
+ author = {Catterall, William A.},
+ number = {1},
+ pages = {13--25},
+ volume = {26},
+ publisher = {Cell Press},
+ doi = {10.1016/S0896-6273(00)81133-2},
+ issn = {08966273},
+ pmid = {10798388}
+}
+
+@article{Eck2009FromAge,
+ title = {{From Prospecting to Product - Industrial Metagenomics Is Coming of Age}},
+ year = {2009},
+ journal = {Protein Engineering Handbook},
+ author = {Eck, Jürgen Juergen and Gabor, Esther and Liebeton, Klaus and Meurer, Guido and Niehaus, Frank and Garbor, Esther and Liebeton, Klaus and Meurer, Guido and Niehaus, Frank},
+ pages = {295--323},
+ url = {http://doi.wiley.com/10.1002/9783527634026.ch11},
+ isbn = {978-3-527-31850-6},
+ doi = {10.1002/9783527634026.ch11}
+}
+
+@incollection{2005FrontMatter,
+ title = {{Front Matter}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {i-xxiii},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.fmatter},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.fmatter}
+}
+
+@article{2015FrontMatter,
+ title = {{Front Matter}},
+ year = {2015},
+ month = {10},
+ pages = {i-xvii},
+ isbn = {9780891188469},
+ doi = {10.2136/SSSABOOKSER5.5.FRONTMATTER}
+}
+
+@book{Emmerich2013FullSmectites,
+ title = {{Full Characterization of Smectites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Emmerich, K.},
+ edition = {2},
+ number = {C},
+ pages = {381--404},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00015-9},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00015-9},
+ issn = {15724352},
+ keywords = {2:1 layer silicates, Classification, Montmorillonite, Smectite}
+}
+
+@article{Emmerich2013FullSmectitesb,
+ title = {{Full Characterization of Smectites}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {Emmerich, K.},
+ number = {C},
+ month = {1},
+ pages = {381--404},
+ volume = {5},
+ publisher = {Elsevier},
+ doi = {10.1016/B978-0-08-098259-5.00015-9},
+ issn = {1572-4352},
+ keywords = {2:1 layer silicates, Classification, Montmorillonite, Smectite}
+}
+
+@article{Full-text,
+ title = {{full-text}}
+}
+
+@article{Protein2013GIn,
+ title = {{G Glycine (alternative to Gly). G-less cassette A sequence of DNA which, when transcribed, yields RNA containing no guanosine residues; such a G-less cassette is often used in}},
+ year = {2013},
+ author = {Protein, G and Dna, Quadruplex and Dna, Quadruplex and Antibiotic, Glycoside},
+ doi = {10.1093/nar/gkr}
+}
+
+@article{ResG-lessCassette,
+ title = {{G-less cassette}},
+ author = {Res, Nucleic Acids and One, Plos and Biol, Plos and Natl, Proc and Sci, Acad and Ca, Carlsbad}
+}
+
+@article{Doucet2011GainingMotions,
+ title = {{Gaining Insight into Enzyme Function through Correlation with Protein Motions}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Doucet, Nicolas and Pelletier, Joelle N.},
+ pages = {187--211},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch7},
+ keywords = {Computational modeling, Conformational exchange, Enzyme catalysis, Kinetic crystallography, Nuclear spin relaxation, Protein dynamics, Protein motions}
+}
+
+@article{OMaille2004GeneEngineering,
+ title = {{Gene library synthesis by structure-based combinatorial protein engineering}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {O'Maille, Paul E. and Tsai, Ming Daw and Greenhagen, Bryan T. and Chappell, Joseph and Noel, Joseph P.},
+ number = {2002},
+ pages = {75--91},
+ volume = {388},
+ isbn = {0076-6879 (Print){\textbackslash}r0076-6879 (Linking)},
+ doi = {10.1016/S0076-6879(04)88008-X},
+ issn = {00766879},
+ pmid = {15289063}
+}
+
+@article{Goraczniak2009GeneAdaptors,
+ title = {{Gene silencing by synthetic U1 Adaptors}},
+ year = {2009},
+ journal = {Nature Biotechnology},
+ author = {Goraczniak, Rafal and Behlke, Mark A. and Gunderson, Samuel I.},
+ number = {3},
+ pages = {257--263},
+ volume = {27},
+ isbn = {1546-1696 (Electronic){\textbackslash}n1087-0156 (Linking)},
+ doi = {10.1038/nbt.1525},
+ issn = {10870156},
+ pmid = {19219028}
+}
+
+@article{Kretz2004GeneApproach,
+ title = {{Gene site saturation mutagenesis: A comprehensive mutagenesis approach}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Kretz, Keith A. and Richardson, Toby H. and Gray, Kevin A. and Robertson, Dan E. and Tan, Xuqiu and Short, Jay M.},
+ number = {1996},
+ pages = {3--11},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88001-7},
+ issn = {00766879},
+ pmid = {15289056}
+}
+
+@misc{Kahkasshan.ZGeneralAREA,
+ title = {{General Chapters: <846> SPECIFIC SURFACE AREA}},
+ booktitle = {Pharmacopeial Forum},
+ author = {{Kahkasshan.Z}},
+ url = {http://pharmacopeia.cn/v29240/usp29nf24s0_c846.html}
+}
+
+@article{Bergaya2017GeneralIntroduction,
+ title = {{General Introduction}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Bergaya, F. and Gates, W. P. and Madejov{\'{a}}, J. and Kloprogge, J. T. and Bain, D.},
+ pages = {1--5},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00001-1},
+ issn = {15724352},
+ keywords = {IR, IR spectroscopy, Raman, Raman Spectroscopy, clay mineral}
+}
+
+@book{Galan2013GenesisMinerals,
+ title = {{Genesis of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Gal{\'{a}}n, E. and Ferrell, R. E.},
+ pages = {83--126},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00003-1},
+ issn = {15724352},
+ keywords = {Clay minerals, Geological environments, Isotopic geochemistry, Martian clays, Statistical analysis}
+}
+
+@article{Roux2013GenomeAtypical,
+ title = {{Genome Sequences of Three Atypical}},
+ year = {2013},
+ author = {Roux, Brice and Jiang, Bo-le and Tang, Ji-liang and Arlat, Matthieu},
+ number = {4},
+ pages = {13--14},
+ volume = {1},
+ doi = {10.1093/nar/gkq}
+}
+
+@article{Lafferty2004GigaMatrix:Platform,
+ title = {{GigaMatrix: A novel ultrahigh throughput protein optimization and discovery platform}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Lafferty, Mike and Dycaico, Mark J.},
+ number = {1996},
+ pages = {119--134},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88011-X},
+ issn = {00766879},
+ pmid = {15289066}
+}
+
+@article{Russell2018GreenLife,
+ title = {{Green Rust: The Simple Organizing ‘Seed’ of All Life?}},
+ year = {2018},
+ journal = {Life 2018, Vol. 8, Page 35},
+ author = {Russell, Michael J.},
+ number = {3},
+ month = {8},
+ pages = {35},
+ volume = {8},
+ publisher = {Multidisciplinary Digital Publishing Institute},
+ url = {https://www.mdpi.com/2075-1729/8/3/35/htm https://www.mdpi.com/2075-1729/8/3/35},
+ doi = {10.3390/LIFE8030035},
+ issn = {20751729},
+ keywords = {Hadean, banded iron formation, carbonic ocean, emergence of life, green rust, mantle plumes, submarine alkaline vents}
+}
+
+@article{GRUNDBEGRIFFEMATHEMATIK,
+ title = {{GRUNDBEGRIFFE DER MATHEMATIK}},
+ url = {http://imsc.uni-graz.at/propst/Grundbegriffe_Skript_Jan11.pdf}
+}
+
+@article{Edmondson2011GuidelinesEnzymes,
+ title = {{Guidelines for the Functional Analysis of Engineered and Mutant Enzymes}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Edmondson, Dale E. and Gadda, Giovanni},
+ pages = {1--13},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch1},
+ keywords = {Coupled enzyme assays, Functional active sites, Initial velocity measurements, Kcat, Km and kcat/Km, Michaelis-Menten equation, Steady-state enzyme kinetic properties, Two-substrate enzymes}
+}
+
+@article{HoweverH-dna,
+ title = {{H ′ -dna}},
+ author = {However, V and Gc, The and Natl, Proc and Sci, Acad},
+ number = {1},
+ pages = {111--117}
+}
+
+@article{Engkvist2000HeyrovskyInstituteHeyrovskyHeyrovskyInstitute8,
+ title = {{Heyrovsky´InstituteHeyrovsky´Heyrovsky´Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolej{\v{s}}kova 3, 182 23 Prague 8}},
+ year = {2000},
+ author = {Engkvist, Ola and Karlstr{\"{o}}m, Gunnar},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/cr9900477}
+}
+
+@article{Berezovsky2004HierarchyStructure,
+ title = {{Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure}},
+ year = {2004},
+ journal = {https://home.liebertpub.com/cmb},
+ author = {Berezovsky, Igor N. and Esipova, Natalia G. and Tumanyan, Vladimir G.},
+ number = {1-2},
+ month = {7},
+ pages = {183--192},
+ volume = {7},
+ publisher = { Mary Ann Liebert, Inc. },
+ url = {https://www.liebertpub.com/doi/epdf/10.1089/10665270050081450},
+ doi = {10.1089/10665270050081450},
+ issn = {10665277},
+ pmid = {10890395},
+ keywords = {HIERARCHY OF DOMAIN STRUCTURE, INTERACTION ENERGY, PROTEIN FOLDING, PROTEIN SPATIAL STRUCTURE, SEQUENCE ALIGNMENT}
+}
+
+@article{Berezovsky2000HierarchyStructure,
+ title = {{Hierarchy of regions of amino acid sequence with respect to their role in the protein spatial structure}},
+ year = {2000},
+ journal = {Journal of Computational Biology},
+ author = {Berezovsky, Igor N. and Esipova, Natalia G. and Tumanyan, Vladimir G.},
+ number = {1-2},
+ pages = {183--192},
+ volume = {7},
+ doi = {10.1089/10665270050081450},
+ issn = {10665277},
+ pmid = {10890395},
+ keywords = {Hierarchy of domain structure, Interaction energy, Protein folding, Protein spatial structure, Sequence alignment}
+}
+@article{Matyska1996a,
+ title = {{High performance computing - The computational chemistry perspective}},
+ year = {1996},
+ journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
+ author = {Matyska, Luděk},
+ pages = {197--216},
+ volume = {1175},
+ isbn = {3540619941},
+ doi = {10.1007/BFb0037405},
+ issn = {16113349}
+}
+
+@article{Harvey2012,
+ title = {{High-throughput molecular dynamics: the powerful new tool for drug discovery}},
+ year = {2012},
+ journal = {Drug Discovery Today},
+ author = {Harvey, Matthew J. and De Fabritiis, Gianni},
+ number = {19-20},
+ month = {10},
+ pages = {1059--1062},
+ volume = {17},
+ url = {https://www.sciencedirect.com/science/article/pii/S1359644612001213 https://linkinghub.elsevier.com/retrieve/pii/S1359644612001213},
+ doi = {10.1016/j.drudis.2012.03.017},
+ issn = {13596446}
+}
+
+@article{Allaire2012,
+ title = {{Homogenization of reactive flows in porous media and competition between bulk and surface diffusion}},
+ year = {2012},
+ journal = {IMA Journal of Applied Mathematics (Institute of Mathematics and Its Applications)},
+ author = {Allaire, G. and Hutridurga, H.},
+ number = {6},
+ month = {12},
+ pages = {788--815},
+ volume = {77},
+ doi = {10.1093/imamat/hxs049},
+ issn = {02724960},
+ keywords = {effective dispersion, reactive flows, two-scale convergence}
+}
+
+@article{Pedreira-Segade2018,
+ title = {{How do Nucleotides Adsorb Onto Clays?}},
+ year = {2018},
+ journal = {Life},
+ author = {Pedreira-Segade, Ulysse and Hao, Jihua and Razafitianamaharavo, Angelina and Pelletier, Manuel and Marry, Virginie and Le Crom, Sébastien and Michot, Laurent and Daniel, Isabelle},
+ number = {4},
+ month = {11},
+ pages = {59},
+ volume = {8},
+ url = {http://www.mdpi.com/2075-1729/8/4/59},
+ doi = {10.3390/life8040059},
+ issn = {2075-1729},
+ keywords = {adsorption, geochemistry, origins of life, phyllosilicates, surface chemistry}
+}
+
+@article{Zhang2014,
+ title = {{Hydration and Mobility of Interlayer Ions of (Na x , Ca y )-Montmorillonite: A Molecular Dynamics Study}},
+ year = {2014},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Zhang, Lihu and Lu, Xiancai and Liu, Xiandong and Zhou, Jinhong and Zhou, Huiqun},
+ number = {51},
+ month = {12},
+ pages = {29811--29821},
+ volume = {118},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/jp508427c},
+ doi = {10.1021/jp508427c},
+ issn = {1932-7447}
+}
+
+@article{Ferrage2010,
+ title = {{Hydration properties and interlayer organization of water and ions in synthetic na-smectite with tetrahedral layer charge. Part 1. Results from X-ray diffraction profile modeling}},
+ year = {2010},
+ journal = {Journal of Physical Chemistry C},
+ author = {Ferrage, Eric and Lanson, Bruno and Michot, Laurent J. and Robert, Jean Louis},
+ number = {10},
+ month = {3},
+ pages = {4515--4526},
+ volume = {114},
+ publisher = { American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/jp909860p},
+ issn = {19327447}
+}
+
+@article{Ferrage2011,
+ title = {{Hydration Properties and Interlayer Organization of Water and Ions in Synthetic Na-Smectite with Tetrahedral Layer Charge. Part 2. Toward a Precise Coupling between Molecular Simulations and Diffraction Data}},
+ year = {2011},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Ferrage, Eric and Sakharov, Boris A. and Michot, Laurent J. and Delville, Alfred and Bauer, Allan and Lanson, Bruno and Grangeon, Sylvain and Frapper, Gilles and Jim{\'{e}}nez-Ruiz, Mónica and Cuello, Gabriel J.},
+ number = {5},
+ month = {2},
+ pages = {1867--1881},
+ volume = {115},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/jp105128r},
+ doi = {10.1021/jp105128r},
+ issn = {1932-7447}
+}
+
+@article{Arulanandan1969,
+ title = {{Hydraulic and electrical flows in clays}},
+ year = {1969},
+ journal = {Clays and Clay Minerals},
+ author = {Arulanandan, Kandiah},
+ number = {2},
+ pages = {63--76},
+ volume = {17},
+ doi = {10.1346/CCMN.1969.0170204},
+ issn = {00098604}
+}
+
+@article{Reading2012,
+ title = {{Hydraulic conductivity increases in a sodic clay soil in response to gypsum applications: Impacts of bulk density and cation exchange}},
+ year = {2012},
+ journal = {Soil Science},
+ author = {Reading, Lucy P. and Baumgartl, Thomas and Bristow, Keith L. and Lockington, David A.},
+ number = {3},
+ month = {3},
+ pages = {165--171},
+ volume = {177},
+ doi = {10.1097/SS.0b013e3182408f4f},
+ issn = {0038075X},
+ keywords = {Gypsum, amelioration, cation exchange, hydraulic conductivity, sodic soils}
+}
+
+@misc{Botan2011,
+ title = {{Hydrodynamics in clay nanopores}},
+ year = {2011},
+ booktitle = {Journal of Physical Chemistry C},
+ author = {Boţan, Alexandru and Rotenberg, Benjamin and Marry, Virginie and Turq, Pierre and Noetinger, Benoît},
+ number = {32},
+ month = {8},
+ pages = {16109--16115},
+ volume = {115},
+ doi = {10.1021/jp204772c},
+ issn = {19327447}
+}
+
+@article{Busto2010,
+ title = {{Hydrolases: catalytically promiscuous enzymes for non-conventional reactions in organic synthesis}},
+ year = {2010},
+ journal = {Chemical Society Reviews},
+ author = {Busto, Eduardo and Gotor-Fern{\'{a}}ndez, Vicente and Gotor, Vicente},
+ number = {11},
+ pages = {4504},
+ volume = {39},
+ url = {http://xlink.rsc.org/?DOI=c003811c},
+ isbn = {10.1039/C003811C},
+ doi = {10.1039/c003811c},
+ issn = {0306-0012},
+ pmid = {20877864}
+}
+
+@article{Tambach2006,
+ title = {{Hysteresis in Clay Swelling Induced by Hydrogen Bonding: Accurate Prediction of Swelling States}},
+ year = {2006},
+ journal = {Langmuir},
+ author = {Tambach, Tim J. and Bolhuis, Peter G. and Hensen, Emiel J. M. and Smit, Berend},
+ number = {3},
+ month = {1},
+ pages = {1223--1234},
+ volume = {22},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/la051367q https://pubs.acs.org/doi/10.1021/la051367q},
+ doi = {10.1021/la051367q},
+ issn = {0743-7463}
+}
+
+@article{Laird1995,
+ title = {{Hysteresis in crystalline swelling of smectites}},
+ year = {1995},
+ journal = {Journal of Colloid And Interface Science},
+ author = {Laird, David A. and Shang, Chao and Thompson, Michael L.},
+ number = {1},
+ pages = {240--245},
+ volume = {171}
+}
+
+@article{Verburg1994,
+ title = {{Hysteresis in the binary exchange of cations on 2:1 clay minerals: A critical review}},
+ year = {1994},
+ journal = {Clays and Clay Minerals},
+ author = {Verburg, Kirsten and Baveye, Philippe},
+ number = {2},
+ pages = {207--220},
+ volume = {42},
+ publisher = {Clay Minerals Society},
+ doi = {10.1346/CCMN.1994.0420211},
+ issn = {15528367},
+ keywords = {Cation exchange, Crystalline swelling, Hysteresis, Kinetics, Quasi-crystal, Smectites}
+}
+
+@article{Kumar2020,
+ title = {{Identification and evaluation of potent Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL Pro inhibitors}},
+ year = {2017},
+ journal = {Antiviral Research},
+ author = {Kumar, Vathan and Shin, Jin Soo and Shie, Jiun-jie and Ku, Keun Bon and Kim, Chonsaeng and Go, Yun Young and Huang, Kai-Fa and Kim, Meehyein and Liang, Po-Huang},
+ number = {January},
+ month = {5},
+ pages = {101--106},
+ volume = {141},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0166354216305083},
+ doi = {10.1016/j.antiviral.2017.02.007},
+ issn = {01663542}
+}
+
+@article{Kumar2017,
+ title = {{Identification and evaluation of potent Middle East respiratory syndrome coronavirus (MERS-CoV) 3CLPro inhibitors}},
+ year = {2017},
+ journal = {Antiviral Research},
+ author = {Kumar, Vathan and Shin, Jin Soo and Shie, Jiun Jie and Ku, Keun Bon and Kim, Chonsaeng and Go, Yun Young and Huang, Kai Fa and Kim, Meehyein and Liang, Po Huang},
+ month = {5},
+ pages = {101--106},
+ volume = {141},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.antiviral.2017.02.007},
+ issn = {18729096},
+ keywords = {3C-like protease, Coronavirus, MERS-CoV, Peptidomimetic inhibitor, Picornavirus, SARS-CoV}
+}
+
+@incollection{Srodon2013,
+ title = {{Identification and Quantitative Analysis of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {{\'{S}}rodo{\'{n}}, J.},
+ number = {C},
+ month = {1},
+ pages = {25--49},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00004-4},
+ issn = {15724352},
+ keywords = {Clay mineral identification, Clay mineral quantification, Clay sample preparation, Clay separation, Crystal thickness, Mixed-layer clay minerals}
+}
+
+@article{Kumar2016,
+ title = {{Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors}},
+ year = {2016},
+ journal = {Bioorganic and Medicinal Chemistry},
+ author = {Kumar, Vathan and Tan, Kian Pin and Wang, Ying Ming and Lin, Sheng Wei and Liang, Po Huang},
+ number = {13},
+ month = {7},
+ pages = {3035--3042},
+ volume = {24},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.bmc.2016.05.013},
+ issn = {14643391},
+ keywords = {3CLpro, Coronavirus, MERS-CoV, Pyrazolone, SARS-Cov}
+}
+
+@article{Zhong2019,
+ title = {{Imaging the Pore Structure in Geomaterials Using Rhodamine B Covalently Decorated Magnetic Nanoparticles}},
+ year = {2019},
+ journal = {ACS Earth and Space Chemistry},
+ author = {Zhong, Ting and Liao, Peng and Chen, Qian Xia and Li, Na and Deng, Hu Cheng and Liu, Qi Jun and Luo, Yu Lan and Lan, Hao Xiang and Li, Chong Ying},
+ number = {11},
+ month = {11},
+ pages = {2482--2489},
+ volume = {3},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acsearthspacechem.9b00071},
+ issn = {24723452},
+ keywords = {bifunctional nanomarker, covalently decorate, fluorescence imaging, geomaterials, nanoparticles, pore structure}
+}
+
+@article{Schnetzer2017,
+ title = {{Impact of Intrinsic Structural Properties on the Hydration of 2:1 Layer Silicates}},
+ year = {2017},
+ journal = {ACS Earth and Space Chemistry},
+ author = {Schnetzer, Florian and Johnston, Cliff T. and Premachandra, Gnanasiri S. and Giraudo, Nicolas and Schuhmann, Rainer and Thissen, Peter and Emmerich, Katja},
+ number = {10},
+ month = {12},
+ pages = {608--620},
+ volume = {1},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/acsearthspacechem.7b00091},
+ doi = {10.1021/acsearthspacechem.7b00091},
+ issn = {2472-3452},
+ keywords = {clay, hectorite, infrared spectroscopy, montmorillonite, smectite, vermiculite, water}
+}
+
+@article{Greathouse2009,
+ title = {{Implementation of a Morse potential to model hydroxyl behavior in phyllosilicates}},
+ year = {2009},
+ journal = {The Journal of Chemical Physics},
+ author = {Greathouse, Jeffery A. and Durkin, Justin S. and Larentzos, James P. and Cygan, Randall T.},
+ number = {13},
+ month = {4},
+ pages = {134713},
+ volume = {130},
+ publisher = {American Institute of PhysicsAIP},
+ url = {http://aip.scitation.org/doi/10.1063/1.3103886 https://doi.org/10.1063/1.3103886},
+ doi = {10.1063/1.3103886},
+ issn = {0021-9606},
+ pmid = {19355770},
+ keywords = {Morse potential, ab initio calculations, aluminium compounds, clay, crystal structure, density functional theory, magnesium compounds, minerals, molecular dynamics method, sodium compounds, vibrational modes}
+}
+
+@article{Dunderdale2012,
+ title = {{Importance of Particle Tracking and Calculating the Mean-Squared Displacement in Distinguishing Nanopropulsion from Other Processes}},
+ year = {2012},
+ journal = {Langmuir},
+ author = {Dunderdale, Gary and Ebbens, Stephen and Fairclough, Patrick and Howse, Jonathan},
+ number = {30},
+ month = {7},
+ pages = {10997--11006},
+ volume = {28},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/pdf/10.1021/la301370y https://pubs.acs.org/doi/10.1021/la301370y https://pubs.acs.org/doi/full/10.1021/la301370y},
+ doi = {10.1021/la301370y},
+ issn = {0743-7463}
+}
+
+@article{Pick2014,
+ title = {{Improving the NADH-cofactor specificity of the highly active AdhZ3 and AdhZ2 from Escherichia coli K-12}},
+ year = {2014},
+ journal = {Journal of Biotechnology},
+ author = {Pick, André and Ott, Wolfgang and Howe, Thomas and Schmid, Jochen and Sieber, Volker},
+ month = {11},
+ pages = {157--165},
+ volume = {189},
+ publisher = {Elsevier},
+ url = {https://www.sciencedirect.com/science/article/pii/S016816561400296X?via%3Dihub},
+ isbn = {0168-1656},
+ doi = {10.1016/j.jbiotec.2014.06.015},
+ issn = {18734863},
+ pmid = {24992211},
+ keywords = {AdhZ2, AdhZ3, Alcohol dehydrogenase, Cofactor, Enzyme engineering}
+}
+
+@article{Pick2014b,
+ title = {{Improving the NADH-cofactor specificity of the highly active AdhZ3 and AdhZ2 from Escherichia coli K-12}},
+ year = {2014},
+ journal = {Journal of Biotechnology},
+ author = {Pick, André and Ott, Wolfgang and Howe, Thomas and Schmid, Jochen and Sieber, Volker},
+ month = {11},
+ pages = {157--165},
+ volume = {189},
+ publisher = {Elsevier},
+ url = {https://www.sciencedirect.com/science/article/pii/S016816561400296X?via%3Dihub},
+ isbn = {0168-1656},
+ doi = {10.1016/j.jbiotec.2014.06.015},
+ issn = {18734863},
+ pmid = {24992211},
+ keywords = {AdhZ2, AdhZ3, Alcohol dehydrogenase, Cofactor, Enzyme engineering}
+}
+
+@article{Shah2020,
+ title = {{In silico studies on therapeutic agents for COVID-19: Drug repurposing approach}},
+ year = {2020},
+ journal = {Life Sciences},
+ author = {Shah, Bhumi and Modi, Palmi and Sagar, Sneha R.},
+ number = {March},
+ pages = {117652},
+ volume = {252},
+ publisher = {Elsevier},
+ url = {https://doi.org/10.1016/j.lfs.2020.117652},
+ doi = {10.1016/j.lfs.2020.117652},
+ issn = {18790631},
+ pmid = {32278693},
+ keywords = {Antiviral drugs, COVID-19, Corona virus, Docking studies, MERS-CoV, SARS-CoV-2}
+}
+
+@incollection{Harvey2013,
+ title = {{Industrial Applications}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Harvey, C. C. and Lagaly, G.},
+ number = {C},
+ month = {1},
+ pages = {451--490},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00018-4},
+ issn = {15724352},
+ keywords = {Acid activation, Alkylammonium clay, Anti-caking, Bentonite, Binding agent, Bleaching earth, Carrier, Catalyst, Categorization of clays, Ceramics, Common clay, Cosmetics, Diluents, Drilling, Engineering, Filler, Foundry, Ion exchange, Kaolin, Liquefaction, Modification, Organoclay, Paint, Palygorskite, Paper, Pelletizing, Pharmaceutics, Polymer, Processing of clay, Resource evaluation, Resources, Rheology, Sepiolite, Soda-activation, Thickener, Thixotropy}
+}
+
+@article{Baron,
+ title = {{INFLUENCE OF AQUEOUS Si AND Fe SPECIATION ON TETRAHEDRAL Fe(III) SUBSTITUTIONS IN NONTRONITES: A CLAY SYNTHESIS APPROACH}},
+ author = {Baron, Fabien and Petit, Sabine and Ertre, Emmanuel T and Decarreau, Alain},
+ doi = {10.1346/CCMN.2016.0640309},
+ keywords = {AQUEOUS SPECIATION, CLAY MINERALS, CLAY SYNTHESIS, FE(III), INFRARED SPECTROSCOPY, IRON, NONTRONITE, PERMANENT CHARGE, SMECTITE, TETRAHEDRAL SUBSTITUTION}
+}
+
+@article{Christidis2006,
+ title = {{Influence of layer charge and charge distribution of smectites on the flow behaviour and swelling of bentonites}},
+ year = {2006},
+ journal = {Applied Clay Science},
+ author = {Christidis, George E. and Blum, Alex E. and Eberl, D. D.},
+ number = {1-4},
+ month = {10},
+ pages = {125--138},
+ volume = {34},
+ keywords = {Flocculation, Intermediate charge smectites, Layer charge, Low charge layers, Rheological properties, Smectite}
+}
+
+@article{Sun2016,
+ title = {{Influence of layer charge and charge location on the swelling pressure of dioctahedral smectites}},
+ year = {2016},
+ journal = {Chemical Physics},
+ author = {Sun, Linlin and Ling, Chian Ye and Lavikainen, Lasse P. and Hirvi, Janne T. and Kasa, Seppo and Pakkanen, Tapani A.},
+ pages = {40--45},
+ volume = {473},
+ publisher = {Elsevier B.V.},
+ url = {http://dx.doi.org/10.1016/j.chemphys.2016.05.002},
+ doi = {10.1016/j.chemphys.2016.05.002},
+ issn = {03010104},
+ keywords = {Beidellite, Molecular dynamics, Montmorillonite, Simulations, Smectite, Swelling pressure}
+}
+
+@article{Laird2006,
+ title = {{Influence of layer charge on swelling of smectites}},
+ year = {2006},
+ journal = {Applied Clay Science},
+ author = {Laird, David A.},
+ number = {1-4},
+ month = {10},
+ pages = {74--87},
+ volume = {34},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0169131706001207},
+ doi = {10.1016/j.clay.2006.01.009},
+ issn = {01691317},
+ keywords = {Cation demixing, Co-volume swelling, Crystalline swelling, Double-layer swelling, Layer charge, Smectite}
+}
+
+@article{DosSantos2016a,
+ title = {{Influence of mineralogy on the preservation of amino acids under simulated Mars conditions}},
+ year = {2016},
+ journal = {Icarus},
+ author = {dos Santos, Renato and Patel, Manish and Cuadros, Javier and Martins, Zita},
+ month = {10},
+ volume = {277},
+ doi = {10.1016/j.icarus.2016.05.029},
+ issn = {00191035}
+}
+
+@article{DosSantos2016,
+ title = {{Influence of mineralogy on the preservation of amino acids under simulated Mars conditions}},
+ year = {2016},
+ journal = {Icarus},
+ author = {dos Santos, Renato and Patel, Manish and Cuadros, Javier and Martins, Zita},
+ month = {10},
+ pages = {342--353},
+ volume = {277},
+ publisher = {Academic Press Inc.},
+ doi = {10.1016/j.icarus.2016.05.029},
+ issn = {10902643},
+ keywords = {Mars, Mineralogy, Solar radiation}
+}
+
+@article{LeCrom2020,
+ title = {{Influence of Polarizability on the Prediction of the Electrical Double Layer Structure in a Clay Mesopore: A Molecular Dynamics Study}},
+ year = {2020},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Le Crom, Sébastien and Tournassat, Christophe and Robinet, Jean-Charles and Marry, Virginie},
+ number = {11},
+ month = {3},
+ pages = {6221--6232},
+ volume = {124},
+ publisher = {American Chemical Society (ACS)},
+ url = {https://dx.doi.org/10.1021/acs.jpcc.0c00190},
+ doi = {10.1021/acs.jpcc.0c00190},
+ issn = {1932-7447}
+}
+
+@article{Denis1991,
+ title = {{Influence of potassium concentration on the swelling and compaction of mixed (Na,K) ion-exchanged montmorillonite}},
+ year = {1991},
+ journal = {Clay Minerals},
+ author = {Denis, J. H. and Keall, M. J. and Hall, P. L. and Meeten, G. H.},
+ number = {2},
+ month = {6},
+ pages = {255--268},
+ volume = {26},
+ publisher = {Mineralogical Society},
+ url = {https://www.cambridge.org/core/journals/clay-minerals/article/abs/influence-of-potassium-concentration-on-the-swelling-and-compaction-of-mixed-nak-ionexchanged-montmorillonite/CBA609EF62D742F4A174E0BDEFFE6619 https://www.cambridge.org/core/product/identif},
+ doi = {10.1180/claymin.1991.026.2.09},
+ issn = {0009-8558}
+}
+
+@article{Dzene2017,
+ title = {{Influence of Tetrahedral Layer Charge on the Fixation of Cesium in Synthetic Smectite}},
+ year = {2017},
+ journal = {Journal of Physical Chemistry C},
+ author = {Dzene, Liva and Verron, Heloïse and Delville, Alfred and Michot, Laurent J. and Robert, Jean Louis and Tertre, Emmanuel and Hubert, Fabien and Ferrage, Eric},
+ number = {42},
+ month = {10},
+ pages = {23422--23435},
+ volume = {121},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.7b06308},
+ issn = {19327455}
+}
+
+@article{Martinez-Gonzalez2020,
+ title = {{Infrared spectra and density of states at the interface between water and protein: Insights from classical molecular dynamics}},
+ year = {2020},
+ journal = {Chemical Physics Letters},
+ author = {Mart{\'{i}}nez-Gonz{\'{a}}lez, José A. and Nandi, Prithwish K. and English, Niall J. and Gowen, Aoife A.},
+ month = {10},
+ pages = {137867},
+ volume = {757},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.cplett.2020.137867},
+ issn = {00092614}
+}
+
+@article{Jo2020,
+ title = {{Inhibition of SARS-CoV 3CL protease by flavonoids}},
+ year = {2020},
+ journal = {Journal of Enzyme Inhibition and Medicinal Chemistry},
+ author = {Jo, Seri and Kim, Suwon and Shin, Dong Hae and Kim, Mi-Sun},
+ number = {1},
+ month = {1},
+ pages = {145--151},
+ volume = {35},
+ publisher = {Taylor and Francis Ltd},
+ url = {https://www.tandfonline.com/doi/full/10.1080/14756366.2019.1690480},
+ doi = {10.1080/14756366.2019.1690480},
+ issn = {1475-6366},
+ keywords = {FRET, SARS-CoV, SARS-CoV 3CLpro, flavonoid, inhibitory compounds}
+}
+
+@article{Macchiagodena2020,
+ title = {{Inhibition of the Main Protease 3CL-pro of the Coronavirus Disease 19 via Structure-Based Ligand Design and Molecular Modeling}},
+ year = {2020},
+ author = {Macchiagodena, Marina and Pagliai, Marco and Procacci, Piero},
+ month = {2},
+ url = {http://arxiv.org/abs/2002.09937},
+ arxivId = {2002.09937}
+}
+
+@article{Srinivasamurthy,
+ title = {{INITIAL SWELLING MECHANISM OF EXPANSIVE CLAYS-A MOLECULAR DYNAMICS STUDY}},
+ author = {Srinivasamurthy, Lakshmikanth and Gajan, Sivapalan and Saini-Eidukat, Bernhardt and Dinesh, Katti}
+}
+
+@article{Sang2020,
+ title = {{Insight Derived from Molecular Docking and Molecular Dynamics Simulations into the Binding Interactions Between HIV-1 Protease Inhibitors and SARS-CoV-2 3CLpro}},
+ year = {2020},
+ author = {Sang, Peng and Tian, Shuhui and Meng, Zhaohui and Yang, Liquan},
+ number = {PG -},
+ month = {3},
+ publisher = {ChemRxiv},
+ url = {NS -},
+ doi = {10.26434/CHEMRXIV.11932995.V1},
+ keywords = {computational biology/molecular dynamics}
+}
+
+@article{Alexandrov2013b,
+ title = {{Insights into the mechanism of Fe(II) adsorption and oxidation at Fe-clay mineral surfaces from first-principles calculations}},
+ year = {2013},
+ journal = {Journal of Physical Chemistry C},
+ author = {Alexandrov, Vitaly and Rosso, Kevin M.},
+ number = {44},
+ month = {11},
+ pages = {22880--22886},
+ volume = {117},
+ issn = {19327447}
+}
+
+@misc{EMBLEuropeanBioinformaticsInstitute,
+ title = {{IntEnz - EC 4.2}},
+ author = {{EMBL European Bioinformatics Institute}},
+ url = {http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=4.2},
+ keywords = {bioinformatics, europe, institute}
+}
+
+@incollection{Berendsen1981,
+ title = {{Interaction Models for Water in Relation to Protein Hydration}},
+ year = {1981},
+ author = {Berendsen, H. J. C. and Postma, J. P. M. and van Gunsteren, W. F. and Hermans, J.},
+ pages = {331--342},
+ publisher = {Springer, Dordrecht},
+ url = {https://link.springer.com/chapter/10.1007/978-94-015-7658-1_21 http://link.springer.com/10.1007/978-94-015-7658-1_21},
+ doi = {10.1007/978-94-015-7658-1{\_}21}
+}
+
+@misc{Greathouse2014,
+ title = {{Interaction of natural organic matter with layered minerals: Recent developments in computational methods at the nanoscale}},
+ year = {2014},
+ booktitle = {Minerals},
+ author = {Greathouse, Jeffery A. and Johnson, Karen L. and Greenwell, H. Christopher},
+ number = {2},
+ month = {7},
+ pages = {519--540},
+ volume = {4},
+ publisher = {MDPI AG},
+ doi = {10.3390/min4020519},
+ issn = {2075163X},
+ keywords = {Density functional theory, Fulvic acid, Humic acid, Layered mineral, Manganese, Manganese oxides, Mineral, Molecular dynamics, Molecular modeling, Natural organic matter, Simulation, Surface}
+}
+
+@article{Knight2020,
+ title = {{Interfacial reactions of Cu(ii) adsorption and hydrolysis driven by nano-scale confinement}},
+ year = {2020},
+ journal = {Environmental Science: Nano},
+ author = {Knight, Andrew W. and Ilani-Kashkouli, Poorandokht and Harvey, Jacob A. and Greathouse, Jeffery A. and Ho, Tuan A. and Kabengi, Nadine and Ilgen, Anastasia G.},
+ number = {1},
+ month = {1},
+ pages = {68--80},
+ volume = {7},
+ publisher = {Royal Society of Chemistry},
+ doi = {10.1039/c9en00855a},
+ issn = {20518161}
+}
+
+@article{Greenwell2005,
+ title = {{Interlayer Structure and Bonding in Nonswelling Primary Amine Intercalated Clays}},
+ year = {2005},
+ journal = {Macromolecules},
+ author = {Greenwell, H. Chris. and Harvey, Matthew J. and Boulet, Pascal and Bowden, Allen A. and Coveney, Peter V. and Whiting, Andy},
+ number = {14},
+ month = {7},
+ pages = {6189--6200},
+ volume = {38},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/ma0503817},
+ doi = {10.1021/ma0503817},
+ issn = {0024-9297}
+}
+
+@article{Zhou2012,
+ title = {{Interlayer structure and dynamics of HDTMA +-intercalated rectorite with and without water: A molecular dynamics study}},
+ year = {2012},
+ journal = {Journal of Physical Chemistry C},
+ author = {Zhou, Jinhong and Lu, Xiancai and Zhu, Jianxi and Liu, Xiandong and Wei, Jingming and Zhou, Qing and Yuan, Peng and He, Hongping},
+ number = {24},
+ month = {6},
+ pages = {13071--13078},
+ volume = {116},
+ doi = {10.1021/jp303856n},
+ issn = {19327447}
+}
+
+@article{Slade1985,
+ title = {{Interlayer structures of the two-layer hydrates of Na- and Ca- vermiculites.}},
+ year = {1985},
+ journal = {Clays {\&} Clay Minerals},
+ author = {Slade, P. G. and Stone, P. A. and Radoslovich, E. W.},
+ number = {1},
+ pages = {51--61},
+ volume = {33},
+ doi = {10.1346/CCMN.1985.0330106},
+ issn = {0009-8604}
+}
+
+@article{Bohm1984,
+ title = {{Intermolecular potentials for CH4, CH3F, CHF 3, CH3Cl, CH2Cl2, CH3CN and CO2}},
+ year = {1984},
+ journal = {The Journal of Chemical Physics},
+ author = {B{\"{o}}hm, H. J. and Ahlrichs, R. and Scharf, P. and Schiffer, H.},
+ number = {3},
+ pages = {1389--1395},
+ volume = {81},
+ doi = {10.1063/1.447773},
+ issn = {00219606}
+}
+
+@article{Dainyak2006,
+ title = {{Interpretation of the nontronite-dehydroxylate Mossbauer spectrum using EFG calculations}},
+ year = {2006},
+ journal = {European Journal of Mineralogy},
+ author = {Dainyak, Lidia G. and Zviagina, Bella B. and Rusakov, Viacheslav S. and Drits, Victor A.},
+ number = {6},
+ month = {12},
+ pages = {753--764},
+ volume = {18},
+ publisher = {Schweizerbart},
+ url = {http://www.schweizerbart.de/papers/ejm/detail/18/57353/Interpretation_of_the_nontronite_dehydroxylate_Mos?af=crossref},
+ doi = {10.1127/0935-1221/2006/0018-0753},
+ issn = {0935-1221}
+}
+
+@article{Nadeau1984,
+ title = {{Interstratified clays as fundamental particles}},
+ year = {1984},
+ journal = {Science},
+ author = {Nadeau, P. H. and Wilson, M. J. and McHardy, W. J. and Tait, J. M.},
+ number = {4665},
+ pages = {923--925},
+ volume = {225},
+ doi = {10.1126/science.225.4665.923},
+ issn = {00368075}
+}
+
+@incollection{Bergaya2013h,
+ title = {{Introduction on modified clays and clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ pages = {383},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00012-2},
+ issn = {15724352}
+}
+
+@incollection{Bornscheuer2005,
+ title = {{Introduction to Biocatalysis}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ author = {Bommarius, Andreas Sebastian and Riebel, Bettina R.},
+ month = {1},
+ pages = {1--18},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch1},
+ address = {Weinheim, FRG},
+ isbn = {3527303448},
+ doi = {10.1002/3527602364.ch1},
+ issn = {01677799}
+}
+
+@incollection{Bergaya2013,
+ title = {{Introduction to Clay Science}},
+ year = {2013},
+ booktitle = {Handbook of Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {2},
+ pages = {1--7},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00001-9 https://linkinghub.elsevier.com/retrieve/pii/B9780080982595000019},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00001-9},
+ issn = {15724352},
+ keywords = {Aggregate, Anionic clay, Associated mineral, Associated phase, Clay minerals, Clay science, Clays, Delamination, Exfoliation, Hydrotalcite, LDH, Particle, Tactoid}
+}
+
+@incollection{Bergaya2013g,
+ title = {{Introduction to Clay Science: Techniques and Applications}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ month = {1},
+ pages = {1--7},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-098259-5.00001-9},
+ issn = {15724352},
+ keywords = {Aggregate, Anionic clay, Associated mineral, Associated phase, Clay minerals, Clay science, Clays, Delamination, Exfoliation, Hydrotalcite, LDH, Particle, Tactoid}
+}
+
+@incollection{Bergaya2013b,
+ title = {{Introduction to clay-polymer nanocomposites (CPN)}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Detellier, C. and Lambert, J. F. and Lagaly, G.},
+ pages = {655--677},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00020-1},
+ issn = {15724352},
+ keywords = {Clay polymer nanocomposites, Delamination, Exfoliation, Intercalation, Microcomposites, Polymer nomenclature}
+}
+
+@incollection{Bergaya2013a,
+ title = {{Introduction to Pure Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ pages = {211},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588000079},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00007-9},
+ issn = {15724352}
+}
+
+@article{Ferrage2007,
+ title = {{Investigation of dioctahedral smectite hydration properties by modeling of X-ray diffraction profiles: Influence of layer charge and charge location}},
+ year = {2007},
+ journal = {American Mineralogist},
+ author = {Ferrage, Eric and Lanson, Bruno and Sakharov, Boris A. and Geoffroy, Nicolas and Jacquot, Emmanuel and Drits, Victor A.},
+ number = {10},
+ month = {10},
+ pages = {1731--1743},
+ volume = {92},
+ url = {https://www.degruyter.com/document/doi/10.2138/am.2007.2273/html},
+ doi = {10.2138/am.2007.2273},
+ issn = {0003-004X},
+ keywords = {Beidellite, Hydration, Interstratification, Layer charge, Montmorillonite, Phyllosilicate, Smectite, XRD data}
+}
+
+@article{Ferrage2005,
+ title = {{Investigation of smectite hydration properties by modeling experimental X-ray diffraction patterns: Part I. Montmorillonite hydration properties}},
+ year = {2005},
+ journal = {American Mineralogist},
+ author = {Ferrage, Eric},
+ number = {8-9},
+ month = {8},
+ pages = {1358--1374},
+ volume = {90},
+ publisher = {Mineralogical Society of America},
+ url = {https://www.degruyter.com/document/doi/10.2138/am.2005.1776/html},
+ doi = {10.2138/am.2005.1776},
+ issn = {0003-004X}
+}
+
+@article{Vogt2002,
+ title = {{Investigation of the clay fraction (<2 {$\mu$}m) of the clay minerals society reference clays}},
+ year = {2002},
+ journal = {Clays and Clay Minerals},
+ author = {Vogt, Christoph and Lauterjung, Jörn and Fischer, Reinhard X.},
+ number = {3},
+ month = {6},
+ pages = {388--400},
+ volume = {50},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1346/000986002760833765},
+ doi = {10.1346/000986002760833765},
+ issn = {00098604},
+ keywords = {Arctic Ocean, Clay Minerals Society (CMS), Marine geology, Quantitative phase analysis, Reference clays, Source clays repository, XRD, XRF}
+}
+
+@article{Underwood2016,
+ title = {{Ion adsorption at Clay-Mineral surfaces: The hofmeister series for hydrated smectite minerals}},
+ year = {2016},
+ journal = {Clays and Clay Minerals},
+ author = {Underwood, Thomas and Erastova, Valentina and Chris Greenwell, H.},
+ number = {4},
+ month = {8},
+ pages = {472--487},
+ volume = {64},
+ publisher = {Clay Minerals Society},
+ url = {https://link.springer.com/article/10.1346/CCMN.2016.0640310},
+ doi = {10.1346/CCMN.2016.0640310},
+ issn = {15528367},
+ keywords = {Binding affinity, Cation exchange, Molecular dynamics, Montmorillonite, Welltempered metadynamics}
+}
+
+@misc{Bagal2013,
+ title = {{Ion channels as therapeutic targets: A drug discovery perspective}},
+ year = {2013},
+ booktitle = {Journal of Medicinal Chemistry},
+ author = {Bagal, Sharan K. and Brown, Alan D. and Cox, Peter J. and Omoto, Kiyoyuki and Owen, Robert M. and Pryde, David C. and Sidders, Benjamin and Skerratt, Sarah E. and Stevens, Edward B. and Storer, R. Ian and Swain, Nigel A.},
+ number = {3},
+ month = {2},
+ pages = {593--624},
+ volume = {56},
+ doi = {10.1021/jm3011433},
+ issn = {00222623}
+}
+
+@book{Hille2001,
+ title = {{Ion Channels of Excitable Membranes}},
+ year = {2001},
+ author = {Hille, Bertil},
+ edition = {3},
+ publisher = {Sinauer Associates Inc.},
+ address = {Sunderland},
+ isbn = {0-87893-321-2},
+ keywords = {Hille1992}
+}
+
+@article{SooLee2021,
+ title = {{Ion correlations drive charge overscreening and heterogeneous nucleation at solid-aqueous electrolyte interfaces}},
+ year = {2021},
+ author = {Soo Lee, Sang and Koishi, Ayumi and Bourg, Ian C and Fenter, Paul},
+ pages = {2105154118},
+ volume = {118},
+ publisher = {PNAS},
+ doi = {10.1073/pnas.2105154118/-/DCSupplemental}
+}
+
+@article{Dudev2014,
+ title = {{Ion Selectivity Strategies of Sodium Channel Selectivity Filters}},
+ year = {2014},
+ journal = {Accounts of Chemical Research},
+ author = {Dudev, Todor and Lim, Carmay},
+ number = {12},
+ month = {12},
+ pages = {3580--3587},
+ volume = {47},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/ar5002878},
+ doi = {10.1021/ar5002878},
+ issn = {0001-4842}
+}
+
+@article{Furini2018,
+ title = {{Ion-triggered selectivity in bacterial sodium channels}},
+ year = {2018},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Furini, Simone and Domene, Carmen},
+ number = {21},
+ month = {5},
+ pages = {5450--5455},
+ volume = {115},
+ publisher = {National Academy of Sciences},
+ doi = {10.1073/pnas.1722516115},
+ issn = {10916490},
+ keywords = {Conduction, Ion channels, Markov state models, Membrane proteins, Molecular dynamics}
+}
+
+@inproceedings{10.1007/978-3-319-21407-8_26,
+ title = {{Ion-Water Cluster Molecular Dynamics Using a Semiempirical Intermolecular Potential}},
+ year = {2015},
+ booktitle = {Computational Science and Its Applications -- ICCSA 2015},
+ author = {Faginas-Lago, Noelia and Albert{\'{i}}, Margarita and Lagan{\`{a}}, Antonio and Lombardi, Andrea},
+ editor = {Gervasi, Osvaldo and Murgante, Beniamino and Misra, Sanjay and Gavrilova, Marina L and Rocha, Ana Maria Alves Coutinho and Torre, Carmelo and Taniar, David and Apduhan, Bernady O},
+ pages = {355--370},
+ publisher = {Springer International Publishing},
+ address = {Cham},
+ isbn = {978-3-319-21407-8}
+}
+
+@article{Eisenberg2013,
+ title = {{Ionic interactions in biological and physical systems: A variational treatment}},
+ year = {2013},
+ journal = {Faraday Discussions},
+ author = {Eisenberg, Bob},
+ pages = {279--296},
+ volume = {160},
+ doi = {10.1039/c2fd20066j},
+ issn = {13596640},
+ pmid = {23795506}
+}
+
+@article{Marcus1988,
+ title = {{Ionic radii in aqueous solutions}},
+ year = {1988},
+ journal = {Chemical Reviews},
+ author = {Marcus, Yizhak},
+ number = {8},
+ month = {12},
+ pages = {1475--1498},
+ volume = {88},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/abs/10.1021/cr00090a003},
+ doi = {10.1021/cr00090a003},
+ issn = {0009-2665}
+}
+
+@article{Hille1975,
+ title = {{Ionic selectivity, saturation, and block in sodium channels. A four-barrier model.}},
+ year = {1975},
+ journal = {The Journal of General Physiology},
+ author = {Hille, Bertil},
+ number = {5},
+ month = {11},
+ pages = {535--560},
+ volume = {66},
+ publisher = {J Gen Physiol},
+ url = {https://pubmed.ncbi.nlm.nih.gov/1194886/ https://rupress.org/jgp/article/66/5/535/26652/Ionic-selectivity-saturation-and-block-in-sodium},
+ doi = {10.1085/jgp.66.5.535},
+ issn = {0022-1295},
+ keywords = {Animals, Anura, B Hille, Binding Sites, Biological*, Cell Membrane Permeability, Chlorine / metabolism, Electrophysiology, MEDLINE, Membrane Potentials, Models, Myelinated / metabolism*, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Nerve Fibers, P.H.S., PMC2226224, Potassium / metabolism, PubMed Abstract, Research Support, Sodium / metabolism*, U.S. Gov't, doi:10.1085/jgp.66.5.535, pmid:1194886}
+}
+
+@article{Turq2014,
+ title = {{Ions in Clays}},
+ year = {2014},
+ journal = {Encyclopedia of Applied Electrochemistry},
+ author = {Turq, Pierre and Rotenberg, Benjamin and Marry, Virginie and Dufreche, Jean François},
+ pages = {1140--1144},
+ publisher = {Springer, New York, NY},
+ url = {https://link.springer.com/referenceworkentry/10.1007/978-1-4419-6996-5_20},
+ doi = {10.1007/978-1-4419-6996-5{\_}20}
+}
+
+@article{Keri2020,
+ title = {{Iron Adsorption on Clays Inferred from Atomistic Simulations and X-ray Absorption Spectroscopy}},
+ year = {2020},
+ journal = {Environmental Science and Technology},
+ author = {K{\'{e}}ri, Annamária and D{\"{a}}hn, Rainer and Marques Fernandes, Maria and Scheinost, Andreas C. and Krack, Matthias and Churakov, Sergey V.},
+ number = {19},
+ month = {10},
+ pages = {11886--11893},
+ volume = {54},
+ publisher = {American Chemical Society},
+ doi = {10.1021/ACS.EST.9B07962},
+ issn = {15205851},
+ pmid = {32343570}
+}
+
+@article{Beinert1997,
+ title = {{Iron-sulfur clusters: Nature's modular, multipurpose structures}},
+ year = {1997},
+ journal = {Science},
+ author = {Beinert, Helmut and Holm, Richard H. and M{\"{u}}nck, Eckard},
+ number = {5326},
+ month = {8},
+ pages = {653--659},
+ volume = {277},
+ publisher = {American Association for the Advancement of Science},
+ url = {https://www.science.org/doi/abs/10.1126/science.277.5326.653},
+ doi = {10.1126/SCIENCE.277.5326.653/ASSET/A3A7A00E-61CC-4EBE-8244-86C497FA458F/ASSETS/GRAPHIC/SE3175524006.JPEG},
+ issn = {00368075},
+ pmid = {9235882}
+}
+
+@article{ERICSSON1973,
+ title = {{Isolation of Fractions rich in Human Y Sperm}},
+ year = {1973},
+ journal = {Nature},
+ author = {ERICSSON, R. J. and LANGEVIN, C. N. and NISHINO, M.},
+ number = {5433},
+ month = {12},
+ pages = {421--424},
+ volume = {246},
+ url = {http://www.nature.com/articles/246421a0},
+ isbn = {1059-1524},
+ doi = {10.1038/246421a0},
+ issn = {0028-0836},
+ pmid = {3507349}
+}
+
+@article{Wang2017,
+ title = {{Isomorphic Substitutions in Clay Materials and Adsorption of Metal Ions onto External Surfaces: A DFT Investigation}},
+ year = {2017},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Wang, Qian and Zhu, Chang and Yun, Jiena and Yang, Gang},
+ number = {48},
+ month = {12},
+ pages = {26722--26732},
+ volume = {121},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acs.jpcc.7b03488},
+ doi = {10.1021/acs.jpcc.7b03488},
+ issn = {1932-7447}
+}
+
+@article{Kim2014,
+ title = {{Issues on the choice of a proper time step in molecular dynamics}},
+ year = {2014},
+ journal = {Physics Procedia},
+ author = {Kim, Sangrak},
+ pages = {60--62},
+ volume = {53},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S1875389214000388},
+ doi = {10.1016/j.phpro.2014.06.027},
+ issn = {18753892},
+ keywords = {Molecular dynamics, Roundoff error, Time step, Truncation error}
+}
+
+@incollection{Bjorck2015a,
+ title = {{Iterative Methods}},
+ year = {2015},
+ booktitle = {Numerical Methods in Matrix Computations},
+ author = {Bj{\"{o}}rck, Åke},
+ chapter = {Iterative},
+ pages = {613--781},
+ publisher = {Springer International Publishing},
+ url = {http://link.springer.com/10.1007/978-3-319-05089-8_4},
+ address = {Cham},
+ doi = {10.1007/978-3-319-05089-8{\_}4},
+ keywords = {akechap}
+}
+
+@article{doi:10.1063/1.1390175,
+ title = {{Jacob’s ladder of density functional approximations for the exchange-correlation energy}},
+ year = {2003},
+ journal = {AIP Conference Proceedings},
+ author = {Perdew, John P.},
+ number = {1},
+ pages = {1--20},
+ volume = {577},
+ url = {https://aip.scitation.org/doi/abs/10.1063/1.1390175},
+ doi = {10.1063/1.1390175}
+}
+
+@incollection{Detellier2013,
+ title = {{Kaolinite-polymer nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Detellier, C. and Letaief, S.},
+ pages = {707--719},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00022-5},
+ issn = {15724352},
+ keywords = {Delamination, Dickite, Exfoliation, Grafting, Halloysite, Intercalation, Kaolin group, Kaolinite, Kaolinite polymer nanocomposite, Nanohybrid material}
+}
+
+@article{Underwood2020,
+ title = {{Large-scale molecular dynamics simulation of the dehydration of a suspension of smectite clay nanoparticles}},
+ year = {2020},
+ journal = {Journal of Physical Chemistry C},
+ author = {Underwood, Thomas R. and Bourg, Ian C.},
+ number = {6},
+ month = {2},
+ pages = {3702--3714},
+ volume = {124},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.9b11197},
+ issn = {19327455}
+}
+
+@article{Suter2007,
+ title = {{Large-scale molecular dynamics study of montmorillonite clay: Emergence of undulatory fluctuations and determination of material properties}},
+ year = {2007},
+ journal = {Journal of Physical Chemistry C},
+ author = {Suter, James L. and Coveney, Peter V. and Greenwell, H. Chris and Thyveetil, Mary Ann},
+ number = {23},
+ month = {6},
+ pages = {8248--8259},
+ volume = {111},
+ doi = {10.1021/jp070294b},
+ issn = {19327447}
+}
+
+@techreport{AlanLaird,
+ title = {{Layer charge and crystalline swelling of expanding 2:1 phyllosilicates Recommended Citation}},
+ author = {Alan Laird, David and Alan, David},
+ url = {https://lib.dr.iastate.edu/rtd/8554}
+}
+
+@incollection{Forano2013,
+ title = {{Layered double hydroxides (LDH)}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Forano, C. and Costantino, U. and Pr{\'{e}}vot, V. and Gueho, C. Taviot},
+ pages = {745--782},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00025-0},
+ issn = {15724352},
+ keywords = {Hydrotalcite, LDH, Layered double hydroxides}
+}
+
+@incollection{Costantino2013,
+ title = {{LDH in Physical, Chemical, Biochemical, and Life Sciences}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Costantino, U. and Leroux, F. and Nocchetti, M. and Mousty, C.},
+ number = {C},
+ month = {1},
+ pages = {765--791},
+ volume = {5},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982595000263},
+ doi = {10.1016/B978-0-08-098259-5.00026-3},
+ keywords = {Agriculture, Biotechnology, Catalysts, Environment application, Intercalation of dyes, Layered double hydroxides, Modified LDH, Pharmaceutical technology and cosmetics, Polymers fillers}
+}
+
+@article{Morse2020,
+ title = {{Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019‐nCoV}},
+ year = {2020},
+ journal = {ChemBioChem},
+ author = {Morse, Jared S. and Lalonde, Tyler and Xu, Shiqing and Liu, Wenshe Ray},
+ number = {5},
+ month = {3},
+ pages = {730--738},
+ volume = {21},
+ publisher = {NLM (Medline)},
+ url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.202000047},
+ doi = {10.1002/cbic.202000047},
+ issn = {1439-4227},
+ keywords = {2019-nCoV, 3CLpro, RdRp, SARS, antiviral agents, coronavirus, spike proteins}
+}
+
+@book{hollemann,
+ title = {{Lehrbuch der Anorganischen Chemie}},
+ year = {2007},
+ author = {Holleman, A. F. and Wiberg, Nils and Wiberg, Egon and Fischer, Gerd},
+ edition = {102},
+ publisher = {Walter de Gruyter},
+ url = {https://www.degruyter.com/view/product/19732 https://www.degruyter.com/view/books/9783110177701/9783110177701/9783110177701.xml},
+ address = {Berlin • New York},
+ isbn = {9783110206845},
+ doi = {10.1515/9783110177701}
+}
+
+@article{Viennet2021,
+ title = {{Martian Magmatic Clay Minerals Forming Vesicles: Perfect Niches for Emerging Life?}},
+ year = {2021},
+ journal = {Astrobiology},
+ author = {Viennet, Jean-Christophe and Bernard, Sylvain and Le Guillou, Corentin and Sautter, Violaine and Gr{\'{e}}goire, Brian and Jambon, Albert and Pont, Sylvain and Beyssac, Olivier and Zanda, Brigitte and Hewins, Roger and Remusat, Laurent},
+ number = {5},
+ month = {5},
+ volume = {21},
+ doi = {10.1089/ast.2020.2345},
+ issn = {1531-1074}
+}
+
+@inproceedings{Gowers2016,
+ title = {{MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations}},
+ year = {2016},
+ author = {Gowers, Richard and Linke, Max and Barnoud, Jonathan and Reddy, Tyler and Melo, Manuel and Seyler, Sean and Doma{\'{n}}ski, Jan and Dotson, David and Buchoux, Sébastien and Kenney, Ian and Beckstein, Oliver},
+ pages = {98--105},
+ url = {https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html},
+ doi = {10.25080/Majora-629e541a-00e}
+}
+
+@inproceedings{Gowers2016b,
+ title = {{MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations}},
+ year = {2016},
+ booktitle = {Proceedings of the 15th Python in Science Conference},
+ author = {Gowers, Richard and Linke, Max and Barnoud, Jonathan and Reddy, Tyler and Melo, Manuel and Seyler, Sean and Doma{\'{n}}ski, Jan and Dotson, David and Buchoux, Sébastien and Kenney, Ian and Beckstein, Oliver},
+ pages = {98--105},
+ publisher = {SciPy},
+ url = {https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html},
+ doi = {10.25080/Majora-629e541a-00e},
+ keywords = {Index Terms-molecular dynamics simulations, biology, chemistry, physics, science}
+}
+
+@article{Michaud-Agrawal2011,
+ title = {{MDAnalysis: A toolkit for the analysis of molecular dynamics simulations}},
+ year = {2011},
+ journal = {Journal of Computational Chemistry},
+ author = {Michaud-Agrawal, Naveen and Denning, Elizabeth J. and Woolf, Thomas B. and Beckstein, Oliver},
+ number = {10},
+ month = {7},
+ pages = {2319--2327},
+ volume = {32},
+ url = {http://doi.wiley.com/10.1002/jcc.21787},
+ doi = {10.1002/jcc.21787},
+ issn = {01928651}
+}
+
+@incollection{Wagner2013,
+ title = {{Mechanical properties of clays and clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Wagner, J. F.},
+ pages = {347--381},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00011-0},
+ issn = {15724352},
+ keywords = {Black shales, Cohesive soils, Compressibility, Expansive soils, Permeability, Plasticity, Quick clays, Settlement, Shear strength, Shrinkage, Soils}
+}
+
+@incollection{Jonas2011,
+ title = {{Mechanism and Catalytic Promiscuity: Emerging Mechanistic Principles for Identification and Manipulation of Catalytically Promiscuous Enzymes}},
+ year = {2011},
+ booktitle = {Protein Engineering Handbook},
+ author = {Jonas, Stefanie and Hollfelder, Florian},
+ chapter = {3},
+ month = {3},
+ pages = {47--79},
+ volume = {1},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/9783527634026.ch3},
+ address = {Weinheim, Germany},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch3},
+ keywords = {Active site, Catalytic promiscuity, Enzyme mechanism, Protein superfamily, Rate acceleration}
+}
+
+@article{Cases1992,
+ title = {{Mechanism of Adsorption and Desorption of Water Vapor by Homoionic Montmorillonite. 1. The Sodium-Exchanged Form}},
+ year = {1992},
+ journal = {Langmuir},
+ author = {Cases, J. M. and B{\'{e}}rend, I. and Besson, G. and Francois, M. and Uriot, J. P. and Thomas, F. and Poirier, J. E.},
+ number = {11},
+ month = {11},
+ pages = {2730--2739},
+ volume = {8},
+ doi = {10.1021/LA00047A025}
+}
+
+@article{Corry2012,
+ title = {{Mechanism of ion permeation and selectivity in a voltage gated sodium channel}},
+ year = {2012},
+ journal = {Journal of the American Chemical Society},
+ author = {Corry, Ben and Thomas, Michael},
+ number = {3},
+ month = {1},
+ pages = {1840--1846},
+ volume = {134},
+ doi = {10.1021/ja210020h},
+ issn = {00027863}
+}
+
+@article{Corry2012b,
+ title = {{Mechanism of ion permeation and selectivity in a voltage gated sodium channel}},
+ year = {2012},
+ journal = {Journal of the American Chemical Society},
+ author = {Corry, Ben and Thomas, Michael},
+ number = {3},
+ month = {1},
+ pages = {1840--1846},
+ volume = {134},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/ja210020h},
+ issn = {00027863},
+ pmid = {22191670}
+}
+
+@article{Yuan2018,
+ title = {{Mechanisms of electron transfer from structrual Fe(II) in reduced nontronite to oxygen for production of hydroxyl radicals}},
+ year = {2018},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Yuan, Songhu and Liu, Xixiang and Liao, Wenjuan and Zhang, Peng and Wang, Xiaoming and Tong, Man},
+ month = {2},
+ pages = {422--436},
+ volume = {223},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/J.GCA.2017.12.025},
+ issn = {00167037},
+ keywords = {Clay minerals, Electron transfer, Ferrous iron, Oxygen, Reactive oxygen species}
+}
+
+@book{Maskill2011,
+ title = {{Mechanisms of Organic Reactions}},
+ year = {2011},
+ author = {Maskill, Howard},
+ publisher = {Oxford University Press},
+ address = {New York},
+ keywords = {orgmech}
+}
+
+@article{ABarducci2011,
+ title = {{Metadynamics}},
+ year = {2011},
+ journal = {Wiley Interdiscip. Rev. Comput. Mol. Sci.},
+ author = {A Barducci, M Bonomi, M Parrinello},
+ pages = {826--843},
+ volume = {1}
+}
+
+@article{ALaio2008,
+ title = {{Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science}},
+ year = {2008},
+ journal = {Rep. Prog. Phys.},
+ author = {A Laio, FL Gervasio},
+ pages = {126601},
+ volume = {71}
+}
+
+@article{NatRev,
+ title = {{Methods for the directed evolution of proteins}},
+ year = {2015},
+ journal = {Nature Reviews Genetics},
+ author = {Packer, Michael S. and Liu, David R.},
+ number = {7},
+ month = {7},
+ pages = {379--394},
+ volume = {16},
+ url = {http://www.nature.com/articles/nrg3927},
+ isbn = {1471-0056},
+ doi = {10.1038/nrg3927},
+ issn = {1471-0056},
+ pmid = {26055155},
+ arxivId = {arXiv:1011.1669v3}
+}
+
+@article{Azerad1999,
+ title = {{Microbial models for drug metabolism.}},
+ year = {1999},
+ journal = {Advances in biochemical engineering/biotechnology},
+ author = {Azerad, R},
+ pages = {169--218},
+ volume = {63},
+ isbn = {0724-6145 (Print){\textbackslash}n0724-6145 (Linking)},
+ doi = {10.1016/S0968-0896(99)00179-0},
+ issn = {0724-6145},
+ pmid = {9933985},
+ keywords = {biotransformation, fungi, glycoconjugates, hydroxylation, metabolites, microorganisms, pharmacology, phase i, phase ii, screening, toxicology}
+}
+
+@article{Erastova2017,
+ title = {{Mineral surface chemistry control for origin of prebiotic peptides}},
+ year = {2017},
+ journal = {Nature Communications},
+ author = {Erastova, Valentina and Degiacomi, Matteo T. and G. Fraser, Donald and Greenwell, H. Chris},
+ number = {1},
+ month = {12},
+ pages = {2033},
+ volume = {8},
+ url = {http://www.nature.com/articles/s41467-017-02248-y},
+ doi = {10.1038/s41467-017-02248-y},
+ issn = {2041-1723},
+ pmid = {29229963}
+}
+
+@article{Simonnin2018,
+ title = {{Mineral- and Ion-Specific Effects at Clay–Water Interfaces: Structure, Diffusion, and Hydrodynamics}},
+ year = {2018},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Simonnin, Pauline and Marry, Virginie and Noetinger, Benoit and Nieto-Draghi, Carlos and Rotenberg, Benjamin},
+ number = {32},
+ month = {8},
+ pages = {18484--18492},
+ volume = {122},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/acs.jpcc.8b04259 https://pubs.acs.org/doi/10.1021/acs.jpcc.8b04259}
+}
+
+@misc{Geckeis2013,
+ title = {{Mineral-water interface reactions of actinides}},
+ year = {2013},
+ booktitle = {Chemical Reviews},
+ author = {Geckeis, Horst and L{\"{u}}tzenkirchen, Johannes and Polly, Robert and Rabung, Thomas and Schmidt, Moritz},
+ number = {2},
+ month = {2},
+ pages = {1016--1062},
+ volume = {113},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/cr300370h},
+ issn = {00092665}
+}
+
+@article{Koster1999,
+ title = {{Mineralogical and chemical characteristics of five nontronites and Fe-rich smectites}},
+ year = {1999},
+ journal = {Clay Minerals},
+ author = {K{\"{o}}ster, H. M. and Ehrlicher, U. and Gilg, H. A. and Jordan, R. and Murad, E. and Onnich, K.},
+ number = {4},
+ month = {12},
+ pages = {579--599},
+ volume = {34},
+ publisher = {Mineralogical Society},
+ url = {https://www.cambridge.org/core/product/identifier/S0009855800003599/type/journal_article},
+ doi = {10.1180/000985599546460},
+ issn = {0009-8558}
+}
+
+@article{Bouna2012,
+ title = {{Mineralogical and physico-chemical characterizations of ferruginous beidellite-rich clay from Agadir basin (Morocco)}},
+ year = {2012},
+ journal = {Clays and Clay Minerals},
+ author = {Bouna, L. and Rhouta, B. and Daoudi, L. and Maury, F. and Amjoud, M. and Senocq, F. and Lafont, M. C. and Jada, A. and A{\"{i}}t Aghzzaf, A.},
+ number = {3},
+ month = {6},
+ pages = {278--290},
+ volume = {60},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1346/CCMN.2012.0600305},
+ doi = {10.1346/CCMN.2012.0600305},
+ issn = {00098604},
+ keywords = {Agadir basin, Beidellite, Clay, Dioctahedral, Ferruginous, Greene-Kelly test, Hofmann-Klemen effect, Tetrahedral-octahedral charge magnitude}
+}
+
+@article{Avena1996,
+ title = {{Modeling the interfacial properties of an amorphous aluminosilicate dispersed in aqueous NaCl solutions}},
+ year = {1996},
+ journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
+ author = {Avena, Marcelo J. and De Pauli, Carlos P.},
+ number = {1-2},
+ month = {11},
+ pages = {75--87},
+ volume = {118},
+ publisher = {Elsevier Science B.V.},
+ doi = {10.1016/0927-7757(96)03668-0},
+ issn = {09277757},
+ keywords = {amorphous aluminosilicate, cation exchange, double layer, electrophoresis, ion adsorption, structural charge, surface charge}
+}
+
+@article{Bacle2016,
+ title = {{Modeling the transport of water and ionic tracers in a micrometric clay sample}},
+ year = {2016},
+ journal = {Applied Clay Science},
+ author = {Bacle, Pauline and Dufr{\^{e}}che, Jean François and Rotenberg, Benjamin and Bourg, Ian C. and Marry, Virginie},
+ month = {4},
+ pages = {18--28},
+ volume = {123},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.clay.2015.12.014},
+ issn = {01691317},
+ keywords = {Brownian dynamics, Diffusion, Modeling, Molecular dynamics, Montmorillonite}
+}
+
+@article{Agbaogun2021,
+ title = {{Modelling of the adsorption of urea herbicides by tropical soils with an Adaptive‐Neural‐based Fuzzy Inference System}},
+ year = {2021},
+ journal = {Journal of Chemometrics},
+ author = {Agbaogun, Babatunde K. and Alonso, Jose M. and Buddenbaum, Henning and Fischer, Klaus},
+ month = {2},
+ pages = {e3335},
+ publisher = {John Wiley and Sons Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/10.1002/cem.3335},
+ doi = {10.1002/cem.3335},
+ issn = {0886-9383},
+ keywords = {Adaptive Neural-based Fuzzy Inference System, modelling, multiple linear regression, phenylurea herbicides, sorption, tropical soils}
+}
+
+@misc{Rotenberg2007a,
+ title = {{Modelling water and ion diffusion in clays: A multiscale approach}},
+ year = {2007},
+ booktitle = {Comptes Rendus Chimie},
+ author = {Rotenberg, Benjamin and Marry, Virginie and Dufr{\^{e}}che, Jean François and Malikova, Natalie and Giffaut, Eric and Turq, Pierre},
+ number = {10-11},
+ month = {10},
+ pages = {1108--1116},
+ volume = {10},
+ doi = {10.1016/j.crci.2007.02.009},
+ issn = {16310748},
+ keywords = {Ion transport, Montmorillonite clay, Multiscale, Nuclear waste}
+}
+
+@article{Lott2016,
+ title = {{Modern Python Cookbook The latest in modern Python recipes for the busy modern programmer}},
+ year = {2016},
+ author = {Lott, Steven F},
+ url = {www.packtpub.com},
+ isbn = {9781786469250}
+}
+
+@article{molden2,
+ title = {{Molden 2.0: quantum chemistry meets proteins}},
+ year = {2017},
+ journal = {Journal of Computer-Aided Molecular Design},
+ author = {Schaftenaar, Gijs and Vlieg, Elias and Vriend, Gert},
+ number = {9},
+ month = {9},
+ pages = {789--800},
+ volume = {31},
+ url = {https://doi.org/10.1007/s10822-017-0042-5},
+ doi = {10.1007/s10822-017-0042-5},
+ issn = {15734951},
+ keywords = {Electron density, Electrostatic potential, Molecular modelling, Molecular visualisation, Protein manipulation, Quantum mechanics}
+}
+
+@article{molden1,
+ title = {{Molden: A pre- and post-processing program for molecular and electronic structures}},
+ year = {2000},
+ journal = {Journal of Computer-Aided Molecular Design},
+ author = {Schaftenaar, G. and Noordik, J. H.},
+ number = {2},
+ month = {2},
+ pages = {123--134},
+ volume = {14},
+ url = {https://doi.org/10.1023/A:1008193805436},
+ doi = {10.1023/A:1008193805436},
+ issn = {0920654X},
+ pmid = {10721501},
+ keywords = {Animation, Charge distribution, Electrostatic potential, Molecular density, Visualization}
+}
+
+@article{Smith1998,
+ title = {{Molecular Computer Simulations of the Swelling Properties and Interlayer Structure of Cesium Montmorillonite}},
+ year = {1998},
+ journal = {Langmuir},
+ author = {Smith, David E.},
+ number = {20},
+ month = {9},
+ pages = {5959--5967},
+ volume = {14},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/la980015z},
+ doi = {10.1021/la980015z},
+ issn = {0743-7463}
+}
+
+@article{Levesque2013,
+ title = {{Molecular diffusion between walls with adsorption and desorption}},
+ year = {2013},
+ journal = {The Journal of Chemical Physics},
+ author = {Levesque, Maximilien and B{\'{e}}nichou, Olivier and Rotenberg, Benjamin},
+ number = {3},
+ month = {1},
+ pages = {034107},
+ volume = {138},
+ url = {http://aip.scitation.org/doi/10.1063/1.4775742},
+ doi = {10.1063/1.4775742},
+ issn = {0021-9606}
+}
+
+@article{Nukoolkarn2008,
+ title = {{Molecular dynamic simulations analysis of ritronavir and lopinavir as SARS-CoV 3CLpro inhibitors}},
+ year = {2008},
+ journal = {Journal of Theoretical Biology},
+ author = {Nukoolkarn, Veena and Lee, Vannajan Sanghiran and Malaisree, Maturos and Aruksakulwong, Ornjira and Hannongbua, Supot},
+ number = {4},
+ month = {10},
+ pages = {861--867},
+ volume = {254},
+ publisher = {Elsevier},
+ doi = {10.1016/j.jtbi.2008.07.030},
+ issn = {00225193},
+ keywords = {Lopinavir, MD simulations, Proteinase, Ritonavir, SARS}
+}
+
+@techreport{Blyverket2015,
+ title = {{MOLECULAR DYNAMICS MODELING OF CLAY-FLUID INTERFACES}},
+ year = {2015},
+ author = {Blyverket, Jostein}
+}
+
+@article{Callahan2018a,
+ title = {{Molecular Dynamics of Ion Conduction through the Selectivity Filter of the Na V Ab Sodium Channel}},
+ year = {2018},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Callahan, Karen M. and Roux, Benoît},
+ number = {44},
+ month = {11},
+ pages = {10126--10142},
+ volume = {122},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.8b09678},
+ doi = {10.1021/acs.jpcb.8b09678},
+ issn = {1520-6106}
+}
+
+@article{Callahan2018,
+ title = {{Molecular Dynamics of Ion Conduction through the Selectivity Filter of the Na V Ab Sodium Channel}},
+ year = {2018},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Callahan, Karen M. and Roux, Benoît},
+ number = {44},
+ month = {11},
+ pages = {10126--10142},
+ volume = {122},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.8b09678},
+ doi = {10.1021/acs.jpcb.8b09678},
+ issn = {1520-6106}
+}
+
+@article{Ulmschneider2013,
+ title = {{Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel}},
+ year = {2013},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Ulmschneider, Martin B. and Bagn{\'{e}}ris, Claire and McCusker, Emily C. and DeCaen, Paul G. and Delling, Markus and Clapham, David E. and Ulmschneider, Jakob P. and Wallace, B. A.},
+ number = {16},
+ month = {4},
+ pages = {6364--6369},
+ volume = {110},
+ doi = {10.1073/pnas.1214667110},
+ issn = {00278424}
+}
+
+@article{Rahromostaqim2018,
+ title = {{Molecular Dynamics Simulation of Hydration and Swelling of Mixed-Layer Clays}},
+ year = {2018},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Rahromostaqim, Mahsa and Sahimi, Muhammad},
+ number = {26},
+ month = {7},
+ pages = {14631--14639},
+ volume = {122},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.8b03693},
+ doi = {10.1021/acs.jpcc.8b03693},
+ issn = {1932-7447}
+}
+
+@article{Zeng2004,
+ title = {{Molecular Dynamics Simulation of the Structural and Dynamic Properties of Dioctadecyldimethyl Ammoniums in Organoclays}},
+ year = {2004},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Zeng, Q. H. and Yu, A. B. and Lu, G. Q. and Standish, R. K.},
+ number = {28},
+ month = {7},
+ pages = {10025--10033},
+ volume = {108},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/jp037245t},
+ doi = {10.1021/jp037245t},
+ issn = {1520-6106}
+}
+
+@article{Andersen1980,
+ title = {{Molecular dynamics simulations at constant pressure and/or temperature}},
+ year = {1980},
+ journal = {The Journal of Chemical Physics},
+ author = {Andersen, Hans C.},
+ number = {4},
+ month = {2},
+ pages = {2384--2393},
+ volume = {72},
+ url = {http://aip.scitation.org/doi/10.1063/1.439486},
+ doi = {10.1063/1.439486},
+ issn = {0021-9606}
+}
+
+@article{Newton2015,
+ title = {{Molecular Dynamics Simulations of Pyrophyllite Edge Surfaces: Structure, Surface Energies, and Solvent Accessibility}},
+ year = {2015},
+ journal = {Clays and Clay Minerals},
+ author = {Newton, Aric G and Sposito, Garrison},
+ number = {4},
+ month = {8},
+ pages = {277--289},
+ volume = {63},
+ url = {http://link.springer.com/10.1346/CCMN.2015.0630403},
+ doi = {10.1346/CCMN.2015.0630403},
+ issn = {00098604},
+ keywords = {CLAY MINERAL EDGE SURFACES, MOLECULAR MECHANICS, PYROPHYLLITE, SURFACE ENERGIES, SURFACE STRUCTURE}
+}
+
+@article{Newton2015a,
+ title = {{Molecular Dynamics Simulations of Pyrophyllite Edge Surfaces: Structure, Surface Energies, and Solvent Accessibility}},
+ year = {2015},
+ journal = {Clays and Clay Minerals},
+ author = {Newton, Aric G and Sposito, Garrison},
+ number = {4},
+ month = {8},
+ pages = {277--289},
+ volume = {63},
+ url = {http://link.springer.com/10.1346/CCMN.2015.0630403},
+ doi = {10.1346/CCMN.2015.0630403},
+ issn = {00098604},
+ keywords = {CLAY MINERAL EDGE SURFACES, MOLECULAR MECHANICS, PYROPHYLLITE, SURFACE ENERGIES, SURFACE STRUCTURE}
+}
+
+@inproceedings{Jost2002,
+ title = {{Molecular dynamics simulations of static and dynamic properties of water adsorbed in chabazite}},
+ year = {2002},
+ booktitle = {Studies in Surface Science and Catalysis},
+ author = {Jost, S. and Fritzsche, S. and Haberlandt, R.},
+ month = {1},
+ pages = {1947--1954},
+ volume = {142 B},
+ publisher = {Elsevier Inc.},
+ doi = {10.1016/s0167-2991(02)80373-1},
+ issn = {01672991}
+}
+
+@article{Willemsen2019,
+ title = {{Molecular Dynamics Simulations of the Adsorption of Phthalate Esters on Smectite Clay Surfaces}},
+ year = {2019},
+ journal = {Journal of Physical Chemistry C},
+ author = {Willemsen, Jennifer A.R. and Myneni, Satish C.B. and Bourg, Ian C.},
+ number = {22},
+ month = {6},
+ pages = {13624--13636},
+ volume = {123},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/acs.jpcc.9b01864},
+ issn = {19327455}
+}
+
+@article{Shen2021,
+ title = {{Molecular dynamics simulations of the colloidal interaction between smectite clay nanoparticles in liquid water}},
+ year = {2021},
+ journal = {Journal of Colloid and Interface Science},
+ author = {Shen, Xinyi and Bourg, Ian C.},
+ month = {2},
+ pages = {610--621},
+ volume = {584},
+ publisher = {Academic Press},
+ doi = {10.1016/J.JCIS.2020.10.029},
+ issn = {0021-9797},
+ keywords = {Adsorption, Clay swelling, Colloidal aggregation, DLVO theory, Disjoining pressure, Electrical double layer, Molecular dynamics simulation}
+}
+
+@article{Bourg2011,
+ title = {{Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl2) solutions}},
+ year = {2011},
+ journal = {Journal of Colloid and Interface Science},
+ author = {Bourg, Ian C. and Sposito, Garrison},
+ number = {2},
+ month = {8},
+ pages = {701--715},
+ volume = {360},
+ publisher = {Academic Press},
+ doi = {10.1016/j.jcis.2011.04.063},
+ issn = {00219797},
+ keywords = {Adsorption, Clay mineral, Diffusion, Electrical double layer, Molecular dynamics simulation, Montmorillonite, Smectite, Surface complex, Surface complexation model, Triple layer model}
+}
+
+@article{Holmboe2014,
+ title = {{Molecular Dynamics Simulations of Water and Sodium Diffusion in Smectite Interlayer Nanopores as a Function of Pore Size and Temperature}},
+ year = {2014},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Holmboe, Michael and Bourg, Ian C.},
+ number = {2},
+ month = {1},
+ pages = {1001--1013},
+ volume = {118},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/jp408884g},
+ doi = {10.1021/jp408884g},
+ issn = {1932-7447}
+}
+
+@article{Collin2018,
+ title = {{Molecular Dynamics Simulations of Water Structure and Diffusion in a 1 nm Diameter Silica Nanopore as a Function of Surface Charge and Alkali Metal Counterion Identity}},
+ year = {2018},
+ journal = {Journal of Physical Chemistry C},
+ author = {Collin, Marie and Gin, Stéphane and Dazas, Baptiste and Mahadevan, Thiruvillamalai and Du, Jincheng and Bourg, Ian C.},
+ number = {31},
+ month = {8},
+ pages = {17764--17776},
+ volume = {122},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.8b03902},
+ issn = {19327455}
+}
+
+@article{Bourg2012,
+ title = {{Molecular dynamics simulations of water structure and diffusion in silica nanopores}},
+ year = {2012},
+ journal = {Journal of Physical Chemistry C},
+ author = {Bourg, Ian C. and Steefel, Carl I.},
+ number = {21},
+ month = {5},
+ pages = {11556--11564},
+ volume = {116},
+ publisher = {UTC},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/jp301299a},
+ issn = {19327447}
+}
+
+@misc{handson,
+ title = {{Molecular Dynamics Simulations: Hands On}},
+ year = {2019},
+ author = {Huarte-Larranaga, Fermin},
+ publisher = {14th International Intensive Course},
+ institution = {Universidad Autonoma de Madrid},
+ address = {Madrid}
+}
+
+@article{Marchand1998,
+ title = {{Molecular dynamics study of calbindin D(9k) in the Apo and singly and doubly calcium-loaded states}},
+ year = {1998},
+ journal = {Proteins: Structure, Function and Genetics},
+ author = {Marchand, Sylvie and Roux, Benoît},
+ number = {2},
+ month = {11},
+ pages = {265--284},
+ volume = {33},
+ doi = {10.1002/(SICI)1097-0134(19981101)33:2<265::AID-PROT10>3.0.CO;2-I},
+ issn = {08873585},
+ pmid = {9779793},
+ keywords = {B-factors, Cooperativity, EF-hands, Hydration, Hydrogen bonds, NMR, Order parameters}
+}
+
+@article{Berendsen1984,
+ title = {{Molecular dynamics with coupling to an external bath}},
+ year = {1984},
+ journal = {The Journal of Chemical Physics},
+ author = {Berendsen, H. J.C. and Postma, J. P.M. and Van Gunsteren, W. F. and Dinola, A. and Haak, J. R.},
+ number = {8},
+ pages = {3684--3690},
+ volume = {81},
+ doi = {10.1063/1.448118},
+ issn = {00219606}
+}
+
+@article{Rotenberg2011,
+ title = {{Molecular explanation for why talc surfaces can be both hydrophilic and hydrophobic}},
+ year = {2011},
+ journal = {Journal of the American Chemical Society},
+ author = {Rotenberg, Benjamin and Patel, Amish J. and Chandler, David},
+ number = {50},
+ month = {12},
+ pages = {20521--20527},
+ volume = {133},
+ doi = {10.1021/ja208687a},
+ issn = {00027863},
+ pmid = {22035164},
+ arxivId = {1109.4284}
+}
+
+@article{Wang2001,
+ title = {{Molecular modeling of the structure and energetics of hydrotalcite hydration}},
+ year = {2001},
+ journal = {Chemistry of Materials},
+ author = {Wang, J. and Kalinichev, A. G. and Kirkpatrick, R. J. and Hou, X.},
+ number = {1},
+ pages = {145--150},
+ volume = {13},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/cm000441h},
+ issn = {08974756}
+}
+
+@article{Bains2001,
+ title = {{Molecular modelling of the mechanism of action of organic clay-swelling inhibitors}},
+ year = {2001},
+ journal = {Molecular Simulation},
+ author = {Bains, A. S. and Boek, E. S. and Coveney, P. V. and Williams, S. J. and Akbar, M. V.},
+ number = {2},
+ pages = {101--145},
+ volume = {26},
+ publisher = {Taylor and Francis Inc.},
+ doi = {10.1080/08927020108023012}
+}
+
+@article{Cygan2009,
+ title = {{Molecular models and simulations of layered materials}},
+ year = {2009},
+ journal = {Journal of Materials Chemistry},
+ author = {Cygan, Randall T. and Greathouse, Jeffery A. and Heinz, Hendrik and Kalinichev, Andrey G.},
+ number = {17},
+ month = {4},
+ pages = {2470},
+ volume = {19},
+ publisher = {The Royal Society of Chemistry},
+ url = {www.iupac2009.org http://xlink.rsc.org/?DOI=b819076c},
+ doi = {10.1039/b819076c},
+ issn = {0959-9428}
+}
+
+@article{Cygan2004,
+ title = {{Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry B},
+ author = {Cygan, Randall T. and Liang, Jian Jie and Kalinichev, Andrey G.},
+ number = {4},
+ month = {1},
+ pages = {1255--1266},
+ volume = {108},
+ publisher = {American Chemical Society},
+ doi = {10.1021/JP0363287},
+ issn = {15206106}
+}
+
+@article{Marry2010a,
+ title = {{Molecular simulation of aqueous solutions at clay surfaces}},
+ year = {2010},
+ journal = {Journal of Physics: Condensed Matter},
+ author = {Marry, Virginie and Malikova, Natalie and Turq, Pierre},
+ number = {28},
+ pages = {284114},
+ publisher = {IOP Publishing},
+ url = {https://hal.archives-ouvertes.fr/hal-00531718},
+ doi = {10.1088/0953-8984/22/28/284114{\"{i}}}
+}
+
+@article{Marry2010,
+ title = {{Molecular simulation of aqueous solutions at clay surfaces}},
+ year = {2010},
+ journal = {Journal of Physics: Condensed Matter},
+ author = {Marry, Virginie and Malikova, Natalie and Turq, Pierre},
+ number = {28},
+ pages = {284114},
+ publisher = {IOP Publishing},
+ url = {https://hal.archives-ouvertes.fr/hal-00531718},
+ doi = {10.1088/0953-8984/22/28/284114{\"{i}}}
+}
+
+@article{Rotenberg2010,
+ title = {{Molecular simulation of aqueous solutions at clay surfaces}},
+ year = {2010},
+ journal = {Journal of Physics: Condensed Matter},
+ author = {Rotenberg, B. and Marry, V. and Malikova, N. and Turq, P.},
+ number = {28},
+ month = {7},
+ pages = {284114},
+ volume = {22},
+ url = {https://iopscience.iop.org/article/10.1088/0953-8984/22/28/284114},
+ doi = {10.1088/0953-8984/22/28/284114},
+ issn = {0953-8984},
+ pmid = {21399286}
+}
+
+@incollection{Greathouse2013,
+ title = {{Molecular Simulation of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Greathouse, J. A. and Cygan, R. T.},
+ number = {C},
+ month = {1},
+ pages = {405--423},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00016-0},
+ issn = {15724352},
+ keywords = {Clay mineral, Layered mineral, Monte Carlo, Simulation molecular dynamics}
+}
+
+@article{Tambach2004,
+ title = {{Molecular Simulations of Swelling Clay Minerals}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry B},
+ author = {Tambach, Tim J. and Hensen, Emiel J.M. M. and Smit, Berend},
+ number = {23},
+ month = {6},
+ pages = {7586--7596},
+ volume = {108},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/jp049799h},
+ doi = {10.1021/jp049799h},
+ issn = {15206106}
+}
+
+@article{Chang1998,
+ title = {{Monte Carlo and Molecular Dynamics Simulations of Electrical Double-Layer Structure in Potassium−Montmorillonite Hydrates}},
+ year = {1998},
+ journal = {Langmuir},
+ author = {Chang, Fang-Ru Chou and Skipper, N. T. and Sposito, Garrison},
+ number = {5},
+ month = {3},
+ pages = {1201--1207},
+ volume = {14},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/la9704720},
+ doi = {10.1021/la9704720},
+ issn = {0743-7463}
+}
+
+@article{Warren2001,
+ title = {{Monte Carlo methods for the study of cation ordering in minerals}},
+ year = {2001},
+ journal = {Mineralogical Magazine},
+ author = {Warren, M. C. and Dove, M. T. and Myers, E. R. and Bosenick, A. and Palin, E. J. and Sainz-Diaz, C. I. and Guiton, B. S. and Redfern, S. A. T.},
+ number = {2},
+ month = {4},
+ pages = {221--248},
+ volume = {65},
+ publisher = {Cambridge University Press},
+ url = {https://www.cambridge.org/core/journals/mineralogical-magazine/article/abs/monte-carlo-methods-for-the-study-of-cation-ordering-in-minerals/2DA112CE9C3C6C936DB266B4FAD59A7C},
+ doi = {10.1180/002646101550235},
+ issn = {0026-461X},
+ keywords = {Monte Carlo simulation, NMR, aluminosilicates, cation ordering, phase transitions}
+}
+
+@article{Boek1995,
+ title = {{Monte Carlo Molecular Modeling Studies of Hydrated Li-, Na-, and K-Smectites: Understanding the Role of Potassium as a Clay Swelling Inhibitor}},
+ year = {1995},
+ journal = {Journal of the American Chemical Society},
+ author = {Boek, E. S. and Coveney, P. V. and Skipper, N. T.},
+ number = {50},
+ month = {12},
+ pages = {12608--12617},
+ volume = {117},
+ url = {https://pubs.acs.org/doi/abs/10.1021/ja00155a025},
+ doi = {10.1021/ja00155a025},
+ issn = {0002-7863}
+}
+
+@article{Skipper1995a,
+ title = {{Monte Carlo Simulation of Interlayer Molecular Structure in Swelling Clay Minerals. 2. Monolayer Hydrates}},
+ year = {1995},
+ journal = {Clays and Clay Minerals},
+ author = {Skipper, N. T.},
+ number = {3},
+ pages = {294--303},
+ volume = {43},
+ publisher = {Clay Minerals Society},
+ url = {http://link.springer.com/10.1346/CCMN.1995.0430304},
+ doi = {10.1346/CCMN.1995.0430304},
+ issn = {0009-8604},
+ keywords = {Clay water systems, Monte Carlo simulation, Swelling clays}
+}
+
+@book{Wagner1997,
+ title = {{M{\"{o}}{\ss}bauerspektroskopie/ Untersuchungsmethoden in der Chemie (Einf{\"{u}}hrung in die moderne Analytik)}},
+ year = {1997},
+ booktitle = {Untersuchungsmethoden in der Chemie},
+ author = {Wagner, H},
+ pages = {334--345},
+ volume = {22},
+ publisher = {Thieme},
+ isbn = {3136814037}
+}
+
+@incollection{Murad2013,
+ title = {{M{\"{o}}ssbauer Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Murad, E.},
+ number = {C},
+ month = {1},
+ pages = {11--24},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00003-2},
+ issn = {15724352},
+ keywords = {Clay firing, Fe (hydr)oxides, Magnetism, Mars, M{\"{o}}ssbauer spectroscopy, gamma rays}
+}
+
+@article{Briggs2017,
+ title = {{Multi-dimensional transport modelling of corrosive agents through a bentonite buffer in a Canadian deep geological repository}},
+ year = {2017},
+ journal = {Science of the Total Environment},
+ author = {Briggs, Scott and McKelvie, Jennifer and Sleep, Brent and Krol, Magdalena},
+ month = {12},
+ pages = {348--354},
+ volume = {599-600},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.scitotenv.2017.04.242},
+ issn = {18791026},
+ pmid = {28478364},
+ keywords = {Bentonite, Diffusion modelling, Finite-element}
+}
+
+@article{Rotenberg2014a,
+ title = {{Multiscale modelling of transport in clays from the molecular to the sample scale}},
+ year = {2014},
+ journal = {Comptes Rendus - Geoscience},
+ author = {Rotenberg, Benjamin and Marry, Virginie and Salanne, Mathieu and Jardat, Marie and Turq, Pierre},
+ number = {11-12},
+ month = {11},
+ pages = {298--306},
+ volume = {346},
+ publisher = {Elsevier Masson SAS},
+ doi = {10.1016/j.crte.2014.07.002},
+ issn = {16310713},
+ keywords = {Acidity, Clay minerals, Electrokinetic effects, Ion exchange, Multiscale simulation, Sorption}
+}
+
+@article{Newton2017,
+ title = {{Na-Montmorillonite Edge Structure and Surface Complexes: An Atomistic Perspective}},
+ year = {2017},
+ journal = {Minerals},
+ author = {Newton, Aric G and Lee, Jin-Yong and Kwon, Kideok D},
+ number = {5},
+ month = {5},
+ pages = {78},
+ volume = {7},
+ url = {www.mdpi.com/journal/minerals http://www.mdpi.com/2075-163X/7/5/78},
+ doi = {10.3390/min7050078},
+ issn = {2075-163X},
+ keywords = {Na-montmorillonite, clay edge, computational geochemistry, density functional theory, mineral surface, molecular dynamics, nanoporous minerals}
+}
+
+@misc{Bernardi2018,
+ title = {{NAMD User's Guide NAMD Version 2.13 NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License}},
+ year = {2018},
+ author = {Bernardi, R and Bhandarkar, M and Bhatele, A and Bohm, E and Brunner, R and Buelens, F and Chipot, C and Dalke, A and Dixit, S and Fiorin, G and Freddolino, P and Fu, H and Grayson, P and Gullingsrud, J and Gursoy, A and Hardy, D and Harrison, C and H{\'{e}}nin, J and Humphrey, W and Hurwitz, D and Hynninen, A and Jain, N and Krawetz, N and Kumar, S and Kunzman, D and Lai, J and Lee, C and Maia, J and Mcgreevy, R and Mei, C and Melo, M and Nelson, M and Phillips, J and Radak, B and Rudack, T and Sarood, O and Shinozaki, A and Tanner, D and Wells, D and Zheng, G and Zhu, F},
+ url = {http://www.ks.uiuc.edu/Research/namd/.}
+}
+
+@book{Liu2006,
+ title = {{Nano Mechanics and Materials}},
+ year = {2006},
+ booktitle = {Nano Mechanics and Materials: Theory, Multiscale Methods and Applications},
+ author = {Liu, Wing Kam and Karpov, Eduard G. and Park, Harold S.},
+ month = {1},
+ pages = {1--320},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {http://doi.wiley.com/10.1002/0470034106},
+ address = {Chichester, UK},
+ isbn = {9780470034101},
+ doi = {10.1002/0470034106}
+}
+
+@article{Ockwig,
+ title = {{Nanoconfined Water in Magnesium-Rich 2:1 Phyllosilicates}},
+ author = {Ockwig, Nathan W and Greathouse, Jeffery A and Durkin, Justin S and Cygan, Randall T and Daemen, Luke L and Nenoff, Tina M and Lujan, Manuel and Neutron, Jr},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/ja900812m}
+}
+
+@book{Brechigniac2006,
+ title = {{Nanomaterials and Nanochemistry}},
+ year = {2006},
+ author = {Br{\'{e}}chigniac, Catherine and Houdy, Philippe and Lahmani, Marcel},
+ editor = {Br{\'{e}}chigniac, Catherine and Houdy, Philippe and Lahmani, Marcel},
+ publisher = {Springer Berlin Heidelberg},
+ address = {Belin},
+ isbn = {9783540729921}
+}
+
+@book{GouzhongCao2004,
+ title = {{Nanostructures and Nanomaterials Synthesis, Properties and Applications}},
+ year = {2004},
+ author = {{Gouzhong Cao}},
+ publisher = {Imperial College Press},
+ isbn = {1860944159}
+}
+
+@misc{Wang2010,
+ title = {{Natural zeolites as effective adsorbents in water and wastewater treatment}},
+ year = {2010},
+ booktitle = {Chemical Engineering Journal},
+ author = {Wang, Shaobin and Peng, Yuelian},
+ number = {1},
+ month = {1},
+ pages = {11--24},
+ volume = {156},
+ doi = {10.1016/j.cej.2009.10.029},
+ issn = {13858947},
+ keywords = {Adsorption, Inorganic ions, Natural zeolite, Organics, Water treatment}
+}
+
+@article{LSutto2012,
+ title = {{New advances in metadynamics}},
+ year = {2012},
+ journal = {Wiley Interdiscip. Rev. Comput. Mol. Sci.},
+ author = {L Sutto, S Marsili, FL Gervasio},
+ pages = {771--779},
+ volume = {2}
+}
+
+@article{Ferrage2005a,
+ title = {{New insights on the distribution of interlayer water in bi-hydrated smectite from X-ray diffraction profile modeling of 00l reflections}},
+ year = {2005},
+ journal = {Chemistry of Materials},
+ author = {Ferrage, Eric and Lanson, Bruno and Malikova, Natalie and Plan{\c{c}}on, Alain and Sakharov, Boris A. and Drits, Victor A.},
+ number = {13},
+ month = {6},
+ pages = {3499--3512},
+ volume = {17},
+ publisher = {Prague},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/cm047995v},
+ issn = {08974756}
+}
+
+@article{Pong2007,
+ title = {{New Insights on the Nanoparticle Growth Mechanism in the Citrate Reduction of Gold(III) Salt: Formation of the Au Nanowire Intermediate and Its Nonlinear Optical Properties}},
+ year = {2007},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Pong, Boon-Kin and Elim, Hendry I. and Chong, Jian-Xiong and Ji, Wei and Trout, Bernhardt L. and Lee, Jim-Yang},
+ number = {17},
+ month = {5},
+ pages = {6281--6287},
+ volume = {111},
+ url = {http://pubs.acs.org/doi/abs/10.1021/jp068666o},
+ isbn = {1932-7447},
+ doi = {10.1021/jp068666o},
+ issn = {1932-7447}
+}
+
+@article{Manuscript2008a,
+ title = {{Nihms19489}},
+ year = {2008},
+ author = {Manuscript, Author},
+ number = {3},
+ pages = {1--20},
+ volume = {157},
+ url = {papers://c33b182f-cf88-47e8-a9c5-ad67b5626483/Paper/p435},
+ keywords = {high performance computing, molecular dynamics simulation, ribosome, rna}
+}
+
+@misc{nist,
+ title = {{NIST Standard Reference Database 78: NIST Atomic Spectra Database}},
+ year = {2016},
+ booktitle = {National Institute of Standards and Technology, Gaithersburg},
+ author = {Kramida, A. and Ralchenko, Yu. and Reader, J. and Team, NIST ASD},
+ url = {http://www.nist.gov/pml/data/asd.cfm},
+ address = {Gaithersburg, MD},
+ doi = {10.18434/T4W30F}
+}
+
+@article{Stebbins2014,
+ title = {{NMR Spectroscopy of Inorganic Earth Materials}},
+ year = {2014},
+ journal = {Reviews in Mineralogy and Geochemistry},
+ author = {Stebbins, Jonathan F. and Xue, Xianyu},
+ number = {1},
+ month = {1},
+ pages = {605--653},
+ volume = {78},
+ publisher = {GeoScienceWorld},
+ url = {http://dx.doi.org/10.2138/rmg.2014.78.15},
+ isbn = {9780939950935},
+ doi = {10.2138/RMG.2014.78.15},
+ issn = {1529-6466}
+}
+
+@misc{top500,
+ title = {{No TitleNovember 2013 | TOP500 Supercomputer Sites}},
+ url = {https://www.top500.org/lists/2013/11/}
+}
+
+@article{Williams1967,
+ title = {{Nonbonded potential parameters derived from crystalline hydrocarbons}},
+ year = {1967},
+ journal = {The Journal of Chemical Physics},
+ author = {Williams, Donald E.},
+ number = {11},
+ pages = {4680--4684},
+ volume = {47},
+ doi = {10.1063/1.1701684},
+ issn = {00219606}
+}
+
+@article{Muchowska2020,
+ title = {{Nonenzymatic Metabolic Reactions and Life’s Origins}},
+ year = {2020},
+ journal = {Chemical Reviews},
+ author = {Muchowska, Kamila B. and Varma, Sreejith J. and Moran, Joseph},
+ number = {15},
+ month = {8},
+ pages = {7708--7744},
+ volume = {120},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/acs.chemrev.0c00191 https://pubs.acs.org/doi/10.1021/acs.chemrev.0c00191},
+ doi = {10.1021/acs.chemrev.0c00191},
+ issn = {0009-2665},
+ pmid = {32687326}
+}
+
+@techreport{Eggleton1977,
+ title = {{NONTRONITE: CHEMISTRY AND DIFFRACTION}},
+ year = {1977},
+ booktitle = {Clay Minerals},
+ author = {Eggleton, R A},
+ pages = {181}
+}
+
+@article{Abnormalities,
+ title = {{Note: Page numbers followed by f refer to figures; page numbers followed by}},
+ author = {Abnormalities, The and Test, Wakefulness and Council, Accreditation and Adrenocomcomphic, See},
+ pages = {25--28},
+ doi = {10.1016/B0-7216-0797-7/50007-0}
+}
+
+@misc{Top500b,
+ title = {{November 2013 | TOP500 Supercomputer Sites}},
+ url = {https://www.top500.org/lists/2013/11/}
+}
+
+@incollection{Sanz2013,
+ title = {{Nuclear Magnetic Resonance Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Sanz, J. and Massiot, D.},
+ number = {C},
+ month = {1},
+ pages = {233--274},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00010-X},
+ issn = {15724352},
+ keywords = {Acid and alkaline activation, Adsorption, Catalysis, Magic-angle spinning technique, Nuclear magnetic resonance, Thermal reactions}
+}
+
+@article{SHAKE,
+ title = {{Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes}},
+ year = {1977},
+ journal = {Journal of Computational Physics},
+ author = {Ryckaert, Jean-Paul and Ciccotti, Giovanni and Berendsen, Herman J.C.},
+ number = {3},
+ month = {3},
+ pages = {327--341},
+ volume = {23},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/0021999177900985},
+ doi = {10.1016/0021-9991(77)90098-5},
+ issn = {00219991}
+}
+
+@book{Bjorck2015,
+ title = {{Numerical Methods in Matrix Computations}},
+ year = {2015},
+ author = {Bj{\"{o}}rck, Åke},
+ series = {Texts in Applied Mathematics},
+ volume = {59},
+ publisher = {Springer International Publishing},
+ url = {http://link.springer.com/10.1007/978-3-319-05089-8},
+ address = {Cham},
+ isbn = {978-3-319-05088-1},
+ doi = {10.1007/978-3-319-05089-8},
+ keywords = {ake}
+}
+
+@phdthesis{Berglez2017,
+ title = {{Numerisches Rechnen und Lineare Algebra}},
+ year = {2017},
+ author = {Berglez, P.},
+ school = {Technische Universit{\"{a}}t Graz},
+ address = {Graz},
+ keywords = {Skript}
+}
+
+@article{Rotenberg2009,
+ title = {{On the driving force of cation exchange in clays: Insights from combined microcalorimetry experiments and molecular simulation}},
+ year = {2009},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Rotenberg, Benjamin and Morel, Jean Pierre and Marry, Virginie and Turq, Pierre and Morel-Desrosiers, Nicole},
+ number = {14},
+ month = {7},
+ pages = {4034--4044},
+ volume = {73},
+ doi = {10.1016/j.gca.2009.04.012},
+ issn = {00167037}
+}
+
+@article{Favre1996,
+ title = {{On the structural basis for ionic selectivity among Na+, K+, and Ca2+ in the voltage-gated sodium channel}},
+ year = {1996},
+ journal = {Biophysical Journal},
+ author = {Favre, Isabelle and Moczydlowski, Edward and Schild, Laurent},
+ number = {6},
+ pages = {3110--3125},
+ volume = {71},
+ publisher = {Biophysical Society},
+ doi = {10.1016/S0006-3495(96)79505-X},
+ issn = {00063495}
+}
+
+@article{Garcia-Romero2021,
+ title = {{On the structural formula of smectites: a review and new data on the influence of exchangeable cations}},
+ year = {2021},
+ journal = {Journal of Applied Crystallography},
+ author = {Garc{\'{i}}a-Romero, Emilia and Lorenzo, Adrián and Garc{\'{i}}a-Vicente, Andrea and Morales, Juan and Garc{\'{i}}a-Rivas, Javier and Su{\'{a}}rez, Mercedes},
+ number = {Pt 1},
+ month = {2},
+ pages = {251},
+ volume = {54},
+ publisher = {International Union of Crystallography},
+ url = {/pmc/articles/PMC7941322/ /pmc/articles/PMC7941322/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7941322/},
+ doi = {10.1107/S1600576720016040},
+ pmid = {33833651},
+ keywords = {beidellite, homoionization, kerolite., montmorillonite, saponite, smectite, stevensite, structural formula}
+}
+
+@article{10.1371/journal.pcbi.1005659,
+ title = {{OpenMM 7: Rapid development of high performance algorithms for molecular dynamics}},
+ year = {2017},
+ journal = {PLoS Computational Biology},
+ author = {Eastman, Peter and Swails, Jason and Chodera, John D. and McGibbon, Robert T. and Zhao, Yutong and Beauchamp, Kyle A. and Wang, Lee Ping and Simmonett, Andrew C. and Harrigan, Matthew P. and Stern, Chaya D. and Wiewiora, Rafal P. and Brooks, Bernard R. and Pande, Vijay S.},
+ number = {7},
+ pages = {1--17},
+ volume = {13},
+ publisher = {Public Library of Science},
+ url = {https://doi.org/10.1371/journal.pcbi.1005659},
+ doi = {10.1371/journal.pcbi.1005659},
+ issn = {15537358}
+}
+
+@article{Lomize2012,
+ title = {{OPM database and PPM web server: resources for positioning of proteins in membranes}},
+ year = {2012},
+ journal = {Nucleic Acids Research},
+ author = {Lomize, Mikhail A. and Pogozheva, Irina D. and Joo, Hyeon and Mosberg, Henry I. and Lomize, Andrei L.},
+ number = {D1},
+ month = {1},
+ pages = {D370-D376},
+ volume = {40},
+ url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkr703},
+ doi = {10.1093/nar/gkr703},
+ issn = {1362-4962}
+}
+
+@book{JinZhongZhang2009,
+ title = {{Optical Properties and Spectroscopy of Nanomaterials}},
+ year = {2009},
+ author = {{Jin Zhong Zhang}},
+ publisher = {World Scientific Publishing Co. Pte. Ltd.},
+ isbn = {9789812836649}
+}
+
+@book{Quinten2011,
+ title = {{Optical Properties of Nanoparticle Systems Mie and Beyond}},
+ year = {2011},
+ author = {Quinten, Michael},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ isbn = {9783527325894}
+}
+
+@article{Best2012,
+ title = {{Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, {$\psi$} and Side-Chain {$\chi$} 1 and {$\chi$} 2 Dihedral Angles}},
+ year = {2012},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Best, Robert B. and Zhu, Xiao and Shim, Jihyun and Lopes, Pedro E. M. and Mittal, Jeetain and Feig, Michael and MacKerell, Alexander D.},
+ number = {9},
+ month = {9},
+ pages = {3257--3273},
+ volume = {8},
+ url = {https://pubs.acs.org/doi/10.1021/ct300400x},
+ doi = {10.1021/ct300400x},
+ issn = {1549-9618}
+}
+
+@book{Clayden2001,
+ title = {{Organic Chemistry}},
+ year = {2012},
+ booktitle = {The American Naturalist},
+ author = {Clayden, Jonathan Jonanthan and Greeves, Nick and Warren, Stuart and Wothers, Peter},
+ edition = {2},
+ month = {6},
+ pages = {492--496},
+ publisher = {Oxford University Press},
+ address = {Heidelberg},
+ isbn = {9780199270293}
+}
+
+@book{Becker2009,
+ title = {{Organikum}},
+ year = {2009},
+ booktitle = {Angewandte Chemie},
+ author = {Becker, Heinz G O and Berger, Werner},
+ volume = {77},
+ url = {http://doi.wiley.com/10.1002/ange.19650772420},
+ isbn = {3527299858},
+ doi = {10.1002/ange.19650772420},
+ issn = {00448249}
+}
+
+@book{Schwetlick2015,
+ title = {{Organikum: Organisch-chemisches Grundpraktikum}},
+ year = {2009},
+ author = {Schwetlick, Klaus},
+ edition = {23},
+ pages = {883},
+ publisher = {Wiley VCH Verlag GmbH, 2015},
+ isbn = {3527322922}
+}
+
+@misc{Stone2018,
+ title = {{Orient: a program for studying interactions betweenmolecules}},
+ year = {2018},
+ author = {Stone, A. J. and Dullweber, A. and Engkvist, O. and Fraschini, E. and Hodges, M. P. and Meredith, A. W. and Nutt, D. R. and Popelier, P. L. A. and Wales, D. J.},
+ url = {http://www-stone.ch.cam.ac.uk/programs.html#Orient}
+}
+
+@article{Manceau2000,
+ title = {{Oxidation-reduction mechanism of iron in dioctahedral smectites: I. Crystal chemistry of oxidized reference nontronites}},
+ year = {2000},
+ journal = {American Mineralogist},
+ author = {Manceau, A. and Lanson, B. and Drits, V.A. and Chateigner, D. and Gates, W.P. and Wu, J. and Huo, D. and Stucki, J.W.},
+ number = {1},
+ month = {1},
+ pages = {133--152},
+ volume = {85},
+ publisher = {Mineralogical Society of America},
+ url = {https://www.degruyter.com/document/doi/10.2138/am-2000-0114/html},
+ doi = {10.2138/am-2000-0114},
+ issn = {0003-004X}
+}
+
+@article{Manceau2000a,
+ title = {{Oxidation-reduction mechanism of iron in dioctahedral smectites: I. Crystal chemistry of oxidized reference nontronites}},
+ year = {2000},
+ journal = {American Mineralogist},
+ author = {Manceau, A. and Lanson, B. and Drits, V.A. and Chateigner, D. and Gates, W.P. and Wu, J. and Huo, D. and Stucki, J.W.},
+ number = {1},
+ month = {1},
+ pages = {133--152},
+ volume = {85},
+ publisher = {De Gruyter},
+ url = {https://www.degruyter.com/document/doi/10.2138/am-2000-0114/html},
+ doi = {10.2138/AM-2000-0114},
+ issn = {1945-3027}
+}
+
+@article{Chemtob2017,
+ title = {{Oxidative Alteration of Ferrous Smectites and Implications for the Redox Evolution of Early Mars}},
+ year = {2017},
+ journal = {Journal of Geophysical Research: Planets},
+ author = {Chemtob, Steven M. and Nickerson, Ryan D. and Morris, Richard V. and Agresti, David G. and Catalano, Jeffrey G.},
+ number = {12},
+ month = {12},
+ pages = {2469--2488},
+ volume = {122},
+ publisher = {Blackwell Publishing Ltd},
+ doi = {10.1002/2017JE005331},
+ keywords = {Gale Crater, Mars, alteration and weathering processes, clay mineralogy, experimental mineralogy}
+}
+
+@incollection{Bish2013,
+ title = {{Parallels and distinctions between clay minerals and zeolites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bish, D. L.},
+ pages = {783--800},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00026-2},
+ issn = {15724352},
+ keywords = {Adsorption, Chabazite, Clinoptilolite, Dehydration, Enthalpy, Hydration, Laumontite, Nontronite, Phase transition, Smectite, Zeolite}
+}
+
+@article{SoterasGutierrez2016,
+ title = {{Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions}},
+ year = {2016},
+ journal = {Bioorganic {\&} Medicinal Chemistry},
+ author = {Soteras Guti{\'{e}}rrez, Ignacio and Lin, Fang-Yu and Vanommeslaeghe, Kenno and Lemkul, Justin A. and Armacost, Kira A. and Brooks, Charles L. and MacKerell, Alexander D.},
+ number = {20},
+ month = {10},
+ pages = {4812--4825},
+ volume = {24},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0968089616304576},
+ doi = {10.1016/j.bmc.2016.06.034},
+ issn = {09680896}
+}
+
+@article{Darden1993,
+ title = {{Particle mesh Ewald: An N{\textperiodcentered}log(N) method for Ewald sums in large systems}},
+ year = {1993},
+ journal = {The Journal of Chemical Physics},
+ author = {Darden, Tom and York, Darrin and Pedersen, Lee},
+ number = {12},
+ pages = {10089--10092},
+ volume = {98},
+ doi = {10.1063/1.464397},
+ issn = {00219606}
+}
+
+@misc{PDB4uu3,
+ title = {{PDB 4uu3 structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI}},
+ year = {2015},
+ author = {in Europe, Protein Data Bank and Europe, Protein Data Bank in},
+ url = {https://www.ebi.ac.uk/pdbe/entry/pdb/4UU3}
+}
+
+@book{DictDNA,
+ title = {{Perinuclear P granules are the principal sites of mRNA export in adult C. elegans germ cells}},
+ year = {2010},
+ booktitle = {Development},
+ author = {Sheth, U. and Pitt, J. and Dennis, S. and Priess, J. R.},
+ number = {8},
+ pages = {1305--1314},
+ volume = {137},
+ url = {http://dev.biologists.org/cgi/doi/10.1242/dev.044255},
+ isbn = {1477-9129 (Electronic) 0950-1991 (Linking)},
+ doi = {10.1242/dev.044255},
+ issn = {0950-1991},
+ pmid = {20223759}
+}
+
+@article{Krylov2018,
+ title = {{Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science}},
+ year = {2018},
+ journal = {The Journal of Chemical Physics},
+ author = {Krylov, Anna and Windus, Theresa L. and Barnes, Taylor and Marin-Rimoldi, Eliseo and Nash, Jessica A. and Pritchard, Benjamin and Smith, Daniel G. A. and Altarawy, Doaa and Saxe, Paul and Clementi, Cecilia and Crawford, T. Daniel and Harrison, Robert J. and Jha, Shantenu and Pande, Vijay S. and Head-Gordon, Teresa},
+ number = {18},
+ month = {11},
+ pages = {180901},
+ volume = {149},
+ url = {http://aip.scitation.org/doi/10.1063/1.5052551},
+ doi = {10.1063/1.5052551},
+ issn = {0021-9606}
+}
+
+@article{Cherian2020,
+ title = {{Perspectives for repurposing drugs for the coronavirus disease 2019}},
+ year = {2020},
+ journal = {Indian Journal of Medical Research},
+ author = {Cherian, Sarah S and Agrawa, Megha and Basu, Atanu and Abraham, Priya and Gangakhedkar, Raman R and Bhargava, Balram},
+ number = {2},
+ pages = {160--171},
+ volume = {151},
+ publisher = {Medknow},
+ doi = {10.4103/ijmr.ijmr{\_}585{\_}20},
+ issn = {0971-5916},
+ pmid = {32317408}
+}
+
+@article{Poulet2005,
+ title = {{Phyllosilicates on Mars and implications for early martian climate}},
+ year = {2005},
+ journal = {Nature},
+ author = {Poulet, F. and Bibring, J.-P. and Mustard, J. F. and Gendrin, A. and Mangold, N. and Langevin, Y. and Arvidson, R. E. and Gondet, B. and Gomez, C.},
+ number = {7068},
+ month = {12},
+ pages = {623--627},
+ volume = {438},
+ publisher = {Nature Publishing Group},
+ url = {http://www.nature.com/articles/nature04274},
+ doi = {10.1038/nature04274},
+ issn = {0028-0836}
+}
+
+@incollection{Vicente2013,
+ title = {{Pillared Clays and Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Vicente, M.A. and Gil, A. and Bergaya, F.},
+ pages = {523--557},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588000171},
+ doi = {10.1016/B978-0-08-098258-8.00017-1},
+ keywords = {PILC properties, Pillared clays, Pillaring methods, Pillaring species}
+}
+
+@article{Gapsys2015,
+ title = {{pmx: Automated protein structure and topology generation for alchemical perturbations}},
+ year = {2015},
+ journal = {Journal of Computational Chemistry},
+ author = {Gapsys, Vytautas and Michielssens, Servaas and Seeliger, Daniel and De Groot, Bert L.},
+ number = {5},
+ month = {2},
+ pages = {348--354},
+ volume = {36},
+ publisher = {John Wiley and Sons Inc.},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23804 https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23804 https://onlinelibrary.wiley.com/doi/10.1002/jcc.23804},
+ doi = {10.1002/jcc.23804},
+ issn = {1096987X},
+ pmid = {25487359},
+ keywords = {Alchemy, Free energy calculations, Molecular dynamics, Mutations, Thermostability}
+}
+
+@article{Jing2019,
+ title = {{Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications}},
+ year = {2019},
+ author = {Jing, Zhifeng and Liu, Chengwen and Cheng, Sara Y and Qi, Rui and Walker, Brandon D and Piquemal, Jean-Philip and Ren, Pengyu},
+ url = {https://doi.org/10.1146/annurev-biophys-070317-},
+ doi = {10.1146/annurev-biophys-070317},
+ keywords = {QM/MM, molecular dynamics simulation, nucleic acid, polarizable force field, protein}
+}
+
+@article{Baker2015,
+ title = {{Polarizable force fields for molecular dynamics simulations of biomolecules}},
+ year = {2015},
+ journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
+ author = {Baker, Christopher M.},
+ number = {2},
+ month = {3},
+ pages = {241--254},
+ volume = {5},
+ publisher = {Blackwell Publishing Inc.},
+ url = {http://doi.wiley.com/10.1002/wcms.1215},
+ doi = {10.1002/wcms.1215},
+ issn = {17590876}
+}
+
+@article{Luque2011,
+ title = {{Polarization effects in molecular interactions}},
+ year = {2011},
+ journal = {WIREs Computational Molecular Science},
+ author = {Luque, F. Javier and Dehez, François and Chipot, Christophe and Orozco, Modesto},
+ number = {5},
+ month = {9},
+ pages = {844--854},
+ volume = {1},
+ url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/wcms.32},
+ doi = {10.1002/wcms.32},
+ issn = {1759-0876}
+}
+
+@article{Allen1999,
+ title = {{Polyamino Acids as Man-Made Catalysts}},
+ year = {1999},
+ journal = {Biotransformations},
+ author = {Allen, Joanne and Roberts, Stanley and Williamson, Natalie},
+ pages = {125--144},
+ volume = {63},
+ url = {http://dx.doi.org/10.1007/3-540-69791-8_6},
+ isbn = {0724-6145 (Print){\textbackslash}n0724-6145 (Linking)},
+ doi = {10.1007/3-540-49811-7{\_}4},
+ issn = {0724-6145},
+ pmid = {9933984},
+ arxivId = {arXiv:1011.1669v3},
+ keywords = {asymmetric oxidation, optically active epoxyketones, polyamino acids, side-chain, synthesis of diltiazem and, taxol}
+}
+
+@article{Berry2015a,
+ title = {{Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study}},
+ year = {2015},
+ journal = {Viruses},
+ author = {Berry, Michael and Fielding, Burtram C. and Gamieldien, Junaid},
+ number = {12},
+ month = {12},
+ pages = {6642--6660},
+ volume = {7},
+ publisher = {MDPI AG},
+ url = {http://www.mdpi.com/1999-4915/7/12/2963 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690886/ http://www.ncbi.nlm.nih.gov/pubmed/26694449 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4690886},
+ doi = {10.3390/v7122963},
+ issn = {1999-4915},
+ pmid = {26694449},
+ keywords = {3CLpro, Human coronaviruses, Molecular docking, Molecular dynamics, Structure-based drug design, Virtual screening, human coronaviruses, molecular docking, molecular dynamics, structure-based drug design, virtual screening}
+}
+
+@article{Berry2015ab,
+ title = {{Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study}},
+ year = {2015},
+ journal = {Viruses},
+ author = {Berry, Michael and Fielding, Burtram and Gamieldien, Junaid},
+ number = {12},
+ month = {12},
+ pages = {6642--6660},
+ volume = {7},
+ publisher = {MDPI AG},
+ url = {http://www.mdpi.com/1999-4915/7/12/2963 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690886/ http://www.ncbi.nlm.nih.gov/pubmed/26694449 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4690886},
+ doi = {10.3390/v7122963},
+ issn = {1999-4915},
+ pmid = {26694449},
+ keywords = {3CLpro, Human coronaviruses, Molecular docking, Molecular dynamics, Structure-based drug design, Virtual screening, human coronaviruses, molecular docking, molecular dynamics, structure-based drug design, virtual screening}
+}
+
+@article{Liu,
+ title = {{Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines}},
+ journal = {ncbi.nlm.nih.gov},
+ author = {Liu, X and Genomics, XJ Wang - Journal of Genetics and},
+ url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7128649/},
+ keywords = {Liu2020}
+}
+
+@article{Liu2020,
+ title = {{Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines}},
+ year = {2020},
+ journal = {Journal of Genetics and Genomics},
+ author = {Liu, Xin and Wang, Xiu Jie},
+ number = {2},
+ month = {2},
+ pages = {119--121},
+ volume = {47},
+ publisher = {Institute of Genetics and Developmental Biology},
+ doi = {10.1016/j.jgg.2020.02.001},
+ issn = {18735533},
+ pmid = {32173287}
+}
+
+@article{liu2020potential,
+ title = {{Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines}},
+ year = {2020},
+ journal = {bioRxiv},
+ author = {Liu, Xin and Wang, Xiu-Jie},
+ publisher = {Cold Spring Harbor Laboratory},
+ url = {https://doi.org/10.1101/2020.01.29.924100 https://www.biorxiv.org/content/10.1101/2020.01.29.924100v1.abstract},
+ doi = {doi.org/10.1101/2020.01.29.924100}
+}
+
+@article{Chang2020,
+ title = {{Potential therapeutic agents for COVID-19 based on the analysis of protease and RNA polymerase docking}},
+ year = {2020},
+ journal = {Virology Journal},
+ author = {Chang, Yu-chuan and Tung, Yi-an and Lee, Ko-han and Chen, Ting-fu and Hsiao, Yu-chun and Chang, Ching and Hsieh, Tsung-ting and Su, Chan-hung and Wang, Su-shia and Yu, Jheng-ying and Lin, Yu-hsiang and Lin, Yin-hung and Tu, Yi-chin Ethan and Tung, Chun-wei},
+ number = {February},
+ month = {2},
+ pages = {1--7},
+ publisher = {Preprints},
+ doi = {10.20944/preprints202002.0242.v1},
+ keywords = {COVID-19, HIV protease inhibitor, molecular docking, nucleotide analogues}
+}
+
+@article{Scarlett2011,
+ title = {{Powder X-Ray Diffraction Study of the Hydration and Leaching Behavior of Nontronite}},
+ year = {2011},
+ journal = {Clays and Clay Minerals},
+ author = {Scarlett, Nicola V. Y. and Raven, Mark and Madsen, Ian},
+ number = {6},
+ month = {12},
+ pages = {560--567},
+ volume = {59},
+ publisher = {GeoScienceWorld},
+ url = {http://link.springer.com/10.1346/CCMN.2011.0590602},
+ doi = {10.1346/CCMN.2011.0590602},
+ issn = {00098604},
+ keywords = {High-pressure acid leaching, Nontronite, Powder XRD, Synchrotron, Time-resolved XRD}
+}
+
+@article{GholamalizadehAhangar2014,
+ title = {{Predicting Soil Sorption Coefficients of an Environmental Pollutant Herbicide (Diuron) Using a Neural Network Model}},
+ year = {2014},
+ journal = {Health Scope},
+ author = {Gholamalizadeh Ahangar, Ahmad and Shabani, Asma},
+ number = {2},
+ month = {5},
+ volume = {3},
+ publisher = {Kowsar Medical Institute},
+ doi = {10.17795/jhealthscope-14974},
+ issn = {2251-8959}
+}
+
+@article{Seybold2006,
+ title = {{PREDICTION OF EFFECTIVE CATION EXCHANGE CAPACITY IN LOW pH SOILS}},
+ year = {2006},
+ journal = {Soil Science},
+ author = {Seybold, C. A. and Grossman, R. B.},
+ number = {1},
+ month = {1},
+ pages = {3--12},
+ volume = {171},
+ url = {https://journals.lww.com/00010694-200601000-00002},
+ doi = {10.1097/01.ss.0000187360.92976.b2},
+ issn = {0038-075X},
+ keywords = {Effective cation exchange capacity, General linear models, Prediction, Soil taxonomy}
+}
+
+@misc{Kuhnel2013,
+ title = {{Preface to the First Edition}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {K{\"{u}}hnel, Radko A.},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.09986-7},
+ issn = {15724352}
+}
+
+@misc{Bergaya2013l,
+ title = {{Preface to the Second Edition}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, Faïza and Lagaly, Gerhard},
+ month = {1},
+ pages = {xxvii},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ issn = {15724352}
+}
+
+@article{Zeng2019,
+ title = {{Preservation of organic matters in nontronite against microbial iron reduction under high temperature}},
+ year = {2019},
+ journal = {Yanshi Xuebao/Acta Petrologica Sinica},
+ author = {Zeng, Qiang and Dong, Hai Liang and Wang, Dan},
+ number = {1},
+ pages = {193--203},
+ volume = {35},
+ publisher = {Science Press},
+ doi = {10.18654/1000-0569/2019.01.15},
+ issn = {20958927},
+ keywords = {High temperature, Microbial iron reduction, Nontronite, Organic matter preservation}
+}
+
+@article{Desdouits2015,
+ title = {{Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins}},
+ year = {2015},
+ journal = {Journal of Molecular Graphics and Modelling},
+ author = {Desdouits, Nathan and Nilges, Michael and Blondel, Arnaud},
+ month = {2},
+ pages = {13--24},
+ volume = {55},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/j.jmgm.2014.10.011},
+ doi = {10.1016/j.jmgm.2014.10.011},
+ issn = {18734243},
+ pmid = {25424655},
+ keywords = {Cavity geometry evolution, Drug design, Functional analysis, Molecular dynamics, Principal component analysis, Protein cavities}
+}
+
+@book{his,
+ title = {{Principles of Biochemistry: Life at the Molecular Level}},
+ year = {2008},
+ author = {Voet, Donald and Pratt, Charlotte W. and Voet, Judith G.},
+ edition = {3},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ address = {London}
+}
+
+@article{Shimizu1999,
+ title = {{Production of chiral C3- and C4-units by microbial enzymes.}},
+ year = {1999},
+ journal = {Advances in biochemical engineering/biotechnology},
+ author = {Shimizu, Sakayu and Kataoka, Michihiko},
+ pages = {109--123},
+ volume = {63},
+ issn = {0724-6145},
+ pmid = {9933983},
+ keywords = {chiral building blocks, chiral synthon, degradation, microbial transformation, stereoselective, stereospecific synthesis}
+}
+
+@article{Jroundi2020,
+ title = {{Profiling native aquifer bacteria in a uranium roll-front deposit and their role in biogeochemical cycle dynamics: Insights regarding in situ recovery mining}},
+ year = {2020},
+ journal = {Science of the Total Environment},
+ author = {Jroundi, Fadwa and Descostes, Michael and Povedano-Priego, Cristina and S{\'{a}}nchez-Castro, Iván and Suvannagan, Vitthavat and Grizard, Pierre and Merroun, Mohamed L.},
+ month = {6},
+ volume = {721},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.scitotenv.2020.137758},
+ issn = {18791026},
+ pmid = {32179349},
+ keywords = {Bacterial diversity, Bioremediation, In-situ recovery, Natural attenuation, Network analysis, Uranium}
+}
+
+@article{Galan1996,
+ title = {{Properties and applications of palygorskite-sepiolite clays}},
+ year = {1996},
+ journal = {Clay Minerals},
+ author = {Galan, E},
+ pages = {443--453},
+ volume = {31}
+}
+
+@incollection{Stucki2013,
+ title = {{Properties and Behaviour of Iron in Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Stucki, J.W.},
+ pages = {559--611},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588000183},
+ doi = {10.1016/B978-0-08-098258-8.00018-3},
+ keywords = {Alkylammonium ions, Bacteria, Chlorinated aliphatics, Colour, Dithionite, EXAFS, Electron microscopy, Ferric ions, Ferrous ions, Infrared, Intervalence transfer, Iron, Microorganisms, M{\"{o}}ssbauer, Nitroaromatics, Organo-clay interactions, Oxidation, Pesticides, Redox, Redox-active metals, Reduction, Synchrotron methods, UV-visible spectroscopy}
+}
+
+@incollection{HPII65_1,
+ title = {{Protection for Phenols and Catechols}},
+ year = {2006},
+ booktitle = {Greene's Protective Groups in Organic Synthesis},
+ author = {Wuts, Peter G.M. and Greene, Theodora W.},
+ chapter = {3},
+ edition = {4},
+ pages = {367--430},
+ publisher = {John Wiley {\&} Sons, Inc.},
+ url = {http://doi.wiley.com/10.1002/9780470053485.ch3},
+ address = {Hoboken, NJ, USA},
+ doi = {10.1002/9780470053485.ch3}
+}
+
+@incollection{BommariusProteinEng,
+ title = {{Protein Engineering}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ author = {Bommarius, Andreas Sebastian and Riebel, Bettina R},
+ month = {1},
+ pages = {281--308},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch10 http://dx.doi.org/10.1002/3527602364.ch10},
+ address = {Weinheim, FRG},
+ isbn = {9783527602360},
+ doi = {10.1002/3527602364.ch10},
+ keywords = {Kunkel method, QuikChange kit, combined chain reaction (CCR), enantioselectivity, fusion PCR, glucose isomerase (GI), glycoamylase, lactate dehydrogenase, oxidation stability, oxygenases, protein engineering, subtilisin, synthetic peroxidases, thermostability}
+}
+
+@article{Studier2005,
+ title = {{Protein production by auto-induction in high-density shaking cultures}},
+ year = {2005},
+ journal = {Protein Expression and Purification},
+ author = {Studier, F. William},
+ number = {1},
+ month = {5},
+ pages = {207--234},
+ volume = {41},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/S1046592805000264},
+ isbn = {1046-5928 (Print){\textbackslash}n1046-5928 (Linking)},
+ doi = {10.1016/j.pep.2005.01.016},
+ issn = {10465928},
+ pmid = {15915565},
+ arxivId = {NIHMS150003},
+ keywords = {arabinose, auto-induction, background and introduction, control of ph, dna sequencing projects have, high-density batch cultures, isotopic labeling, lactose, metabolic, pbad promoter, protein production, provided coding se-, selenomethionine labeling, t7 expression system}
+}
+
+@article{imidazole,
+ title = {{Proton Transfer Properties of Imidazole}},
+ year = {1996},
+ journal = {The Journal of Physical Chemistry},
+ author = {Scheiner, Steve and Yi, Manyin},
+ number = {22},
+ month = {1},
+ pages = {9235--9241},
+ volume = {100},
+ url = {http://pubs.acs.org/doi/abs/10.1021/jp9600571},
+ isbn = {00223654},
+ doi = {10.1021/jp9600571},
+ issn = {0022-3654}
+}
+
+@incollection{Bergaya2013e,
+ title = {{Purification of natural clays}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ pages = {213--221},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00008-0},
+ issn = {15724352},
+ keywords = {Decomposition of carbonates, Dialysis, Dissolution of (hydr)oxides, Dissolution of silica, Fractionation, Oxidation of organic material, Particle size, Purification, Washing}
+}
+
+@article{Wang2008,
+ title = {{Quantum algorithm for obtaining the energy spectrum of molecular systems}},
+ year = {2008},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Wang, Hefeng and Kais, Sabre and Aspuru-Guzik, Alán and Hoffmann, Mark R.},
+ number = {35},
+ pages = {5388--5393},
+ volume = {10},
+ url = {http://xlink.rsc.org/?DOI=b804804e},
+ doi = {10.1039/b804804e},
+ issn = {14639076}
+}
+
+@article{Cao2019,
+ title = {{Quantum Chemistry in the Age of Quantum Computing}},
+ year = {2019},
+ journal = {Chemical Reviews},
+ author = {Cao, Yudong and Romero, Jonathan and Olson, Jonathan P. and Degroote, Matthias and Johnson, Peter D. and Kieferov{\'{a}}, Mária and Kivlichan, Ian D. and Menke, Tim and Peropadre, Borja and Sawaya, Nicolas P. D. and Sim, Sukin and Veis, Libor and Aspuru-Guzik, Alán},
+ number = {19},
+ month = {10},
+ pages = {10856--10915},
+ volume = {119},
+ url = {https://pubs.acs.org/doi/10.1021/acs.chemrev.8b00803},
+ doi = {10.1021/acs.chemrev.8b00803},
+ issn = {0009-2665},
+ arxivId = {1812.09976}
+}
+
+@article{Sugisaki2019a,
+ title = {{Quantum Chemistry on Quantum Computers: A Method for Preparation of Multiconfigurational Wave Functions on Quantum Computers without Performing Post-Hartree-Fock Calculations}},
+ year = {2019},
+ journal = {ACS Central Science},
+ author = {Sugisaki, Kenji and Nakazawa, Shigeaki and Toyota, Kazuo and Sato, Kazunobu and Shiomi, Daisuke and Takui, Takeji},
+ number = {1},
+ month = {1},
+ pages = {167--175},
+ volume = {5},
+ url = {https://pubs.acs.org/doi/10.1021/acscentsci.8b00788},
+ doi = {10.1021/acscentsci.8b00788},
+ issn = {23747951}
+}
+
+@article{Lu2012,
+ title = {{Quantum chemistry simulation on quantum computers: Theories and experiments}},
+ year = {2012},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Lu, Dawei and Xu, Boruo and Xu, Nanyang and Li, Zhaokai and Chen, Hongwei and Peng, Xinhua and Xu, Ruixue and Du, Jiangfeng},
+ number = {26},
+ pages = {9411--9420},
+ volume = {14},
+ url = {http://xlink.rsc.org/?DOI=c2cp23700h},
+ doi = {10.1039/c2cp23700h},
+ issn = {14639076}
+}
+
+@incollection{Churakov2018,
+ title = {{Quantum-chemical modelling of clay mineral surfaces and clay mineral–surface–adsorbate interactions}},
+ year = {2018},
+ booktitle = {Developments in Clay Science},
+ author = {Churakov, Sergey V. and Liu, Xiandong},
+ month = {1},
+ pages = {49--87},
+ volume = {9},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780081024324000032},
+ doi = {10.1016/B978-0-08-102432-4.00003-2},
+ issn = {15724352},
+ keywords = {Acid–base equilibria, Cation exchange, Density functional theory, Molecular dynamics simulations, Swelling}
+}
+
+@misc{Stratagene2009,
+ title = {{QuikChange XL Site-Directed Mutagenesis Kit}},
+ year = {2009},
+ booktitle = {Stratagene},
+ author = {{Stratagene}},
+ pages = {1--24},
+ volume = {200516},
+ pmid = {1000231370}
+}
+
+@article{Stratagene2009b,
+ title = {{QuikChange {\textregistered} II Site-Directed Mutagenesis Kit}},
+ author = {Site-directed, Quikchange I I and Kit, Mutagenesis},
+ volume = {200523},
+ isbn = {1617379530},
+ doi = {10.1093/protein/11.3.199},
+ issn = {15322661},
+ pmid = {1000231370}
+}
+
+@incollection{Allard2013,
+ title = {{Radiation Effects on Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Allard, T. and Balan, E. and Calas, G.},
+ pages = {127--138},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00004-3},
+ issn = {15724352},
+ keywords = {Amorphization, Dating, Dosimetry, EPR, Irradiation, Point defect, Uranium transfer}
+}
+
+@article{Pagonabarraga2010,
+ title = {{Recent advances in the modelling and simulation of electrokinetic effects: Bridging the gap between atomistic and macroscopic descriptions}},
+ year = {2010},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Pagonabarraga, I. and Rotenberg, B. and Frenkel, D.},
+ number = {33},
+ pages = {9566--9580},
+ volume = {12},
+ doi = {10.1039/c004012f},
+ issn = {14639076}
+}
+
+@misc{Bauer2012,
+ title = {{Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations}},
+ year = {2012},
+ booktitle = {Theoretical Chemistry Accounts},
+ author = {Bauer, Brad A. and Patel, Sandeep},
+ number = {3},
+ month = {3},
+ pages = {1--15},
+ volume = {131},
+ publisher = {Springer New York LLC},
+ url = {https://link.springer.com/article/10.1007/s00214-012-1153-7},
+ doi = {10.1007/s00214-012-1153-7},
+ issn = {1432881X},
+ keywords = {Charge equilibration, Force field, Molecular dynamics simulations, Polarizable, Quantum mechanics}
+}
+
+@article{Orinakova2011,
+ title = {{Recent applications of carbon nanotubes in hydrogen production and storage}},
+ year = {2011},
+ journal = {Fuel},
+ author = {Oriň{\'{a}}kov{\'{a}}, Renáta and Oriň{\'{a}}k, Andrej},
+ number = {11},
+ month = {11},
+ pages = {3123--3140},
+ volume = {90},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0016236111003693},
+ doi = {10.1016/j.fuel.2011.06.051},
+ issn = {00162361}
+}
+
+@article{Pillaiyar2020,
+ title = {{Recent discovery and development of inhibitors targeting coronaviruses}},
+ year = {2020},
+ journal = {Drug Discovery Today},
+ author = {Pillaiyar, Thanigaimalai and Meenakshisundaram, Sangeetha and Manickam, Manoj},
+ number = {4},
+ month = {4},
+ pages = {668--688},
+ volume = {25},
+ publisher = {Elsevier Ltd},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S1359644620300416},
+ doi = {10.1016/j.drudis.2020.01.015},
+ issn = {13596446},
+ pmid = {32006468}
+}
+
+@article{Bishop2014,
+ title = {{Reduction and immobilization of hexavalent chromium by microbially reduced Fe-bearing clay minerals}},
+ year = {2014},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Bishop, Michael E. and Glasser, Paul and Dong, Hailiang and Arey, Bruce and Kovarik, Libor},
+ month = {5},
+ pages = {186--203},
+ volume = {133},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.gca.2014.02.040},
+ issn = {00167037}
+}
+
+@article{Kaplan,
+ title = {{REFLECTANCE SPECTROSCOPY FOR ORGANIC DETECTION AND QUANTIFICATION IN CLAY-BEARING SAMPLES: EFFECTS OF ALBEDO, CLAY TYPE, AND WATER CONTENT}},
+ author = {Kaplan, Hannah H and Milliken, Ralph E},
+ doi = {10.1346/CCMN.2016.0640207},
+ keywords = {DETECTION LIMIT, ORGANIC DETECTION, ORGANO-CLAY, QUANTIFICATION, REFLECTANCE SPECTROSCOPY}
+}
+
+@article{Wuensch2015,
+ title = {{Regioselective Enzymatic {$\beta$}-Carboxylation of para -Hydroxy- styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases}},
+ year = {2015},
+ journal = {Advanced Synthesis {\&} Catalysis},
+ author = {Wuensch, Christiane and Pavkov-Keller, Tea and Steinkellner, Georg and Gross, Johannes and Fuchs, Michael and Hromic, Altijana and Lyskowski, Andrzej and Fauland, Kerstin and Gruber, Karl and Glueck, Silvia M. and Faber, Kurt},
+ number = {8},
+ month = {5},
+ pages = {1909--1918},
+ volume = {357},
+ url = {http://doi.wiley.com/10.1002/adsc.201401028},
+ doi = {10.1002/adsc.201401028},
+ issn = {16154150},
+ pmid = {26190963},
+ keywords = {biotransformations, enzyme catalysis, para-hydroxystyrenes, phenolic acid decarboxylases, reaction mechanism, regioselective carboxylation}
+}
+
+@article{DeBartolomeo2004,
+ title = {{Relationship among parameters of lake polluted sediments evaluated by multivariate statistical analysis}},
+ year = {2004},
+ journal = {Chemosphere},
+ author = {De Bartolomeo, A. and Poletti, L. and Sanchini, G. and Sebastiani, B. and Morozzi, G.},
+ number = {10},
+ month = {6},
+ pages = {1323--1329},
+ volume = {55},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/S0045653504000025},
+ doi = {10.1016/j.chemosphere.2003.12.005},
+ issn = {00456535},
+ pmid = {15081775},
+ keywords = {AVS, Heavy metals, LAS, Lake sediments, PAH, Principal component analysis}
+}
+
+@article{Chatterjee1996,
+ title = {{Relationship between infrared spectra and isomorphous substitution in smectites: A computer simulation study}},
+ year = {1996},
+ journal = {Journal of Molecular Graphics},
+ author = {Chatterjee, A. and Iwasaki, T. and Ebina, T. and Hayashi, H.},
+ number = {5},
+ month = {10},
+ pages = {302--305},
+ volume = {14},
+ publisher = {Elsevier},
+ doi = {10.1016/S0263-7855(96)00083-5},
+ issn = {0263-7855},
+ keywords = {IR, Isomorphous substitution, LDF calculation, Smectite, Vibrational frequency}
+}
+
+@article{Katti2006,
+ title = {{Relationship of Swelling and Swelling Pressure on Silica−Water Interactions in Montmorillonite}},
+ year = {2006},
+ journal = {Langmuir},
+ author = {Katti, Kalpana S. and Katti, Dinesh R.},
+ number = {2},
+ month = {1},
+ pages = {532--537},
+ volume = {22},
+ url = {https://pubs.acs.org/doi/10.1021/la051533u},
+ doi = {10.1021/la051533u},
+ issn = {0743-7463}
+}
+
+@article{Bishop2017,
+ title = {{Remote Detection of Clay Minerals}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Bishop, J. L. and Michalski, J. R. and Carter, J.},
+ pages = {482--514},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00014-X},
+ issn = {15724352},
+ keywords = {Ceres, Clay mineral, Clay minerals, Comets, Emission, IR, IR spectroscopy, Mars, Meteorites, Raman, Raman spectroscopy, Reflectance, Remote sensing, Spectroscopy, TIR, VNIR}
+}
+
+@article{Kubilay2007,
+ title = {{Removal of Cu(II), Zn(II) and Co(II) ions from aqueous solutions by adsorption onto natural bentonite}},
+ year = {2007},
+ journal = {Adsorption},
+ author = {Kubilay, Ş and G{\"{u}}rkan, R. and Savran, A. and {\c{S}}ahan, T.},
+ number = {1},
+ month = {2},
+ pages = {41--51},
+ volume = {13},
+ doi = {10.1007/s10450-007-9003-y},
+ issn = {09295607},
+ keywords = {Adsorption, Bentonite, Heavy metals, Removal, Wastewater}
+}
+
+@article{Vaduganathan2020,
+ title = {{Renin–Angiotensin–Aldosterone System Inhibitors in Patients with Covid-19}},
+ year = {2020},
+ journal = {New England Journal of Medicine},
+ author = {Vaduganathan, Muthiah and Vardeny, Orly and Michel, Thomas and McMurray, John J.V. and Pfeffer, Marc A. and Solomon, Scott D.},
+ number = {17},
+ month = {4},
+ pages = {1653--1659},
+ volume = {382},
+ publisher = {Massachusetts Medical Society},
+ url = {http://www.nejm.org/doi/10.1056/NEJMsr2005760},
+ doi = {10.1056/NEJMsr2005760},
+ issn = {0028-4793},
+ pmid = {32227760}
+}
+
+@article{Williams1965a,
+ title = {{Repulsion Center of a Bonded Hydrogen Atom}},
+ year = {1965},
+ journal = {The Journal of Chemical Physics},
+ author = {Williams, Donald E.},
+ number = {12},
+ month = {12},
+ pages = {4424--4426},
+ volume = {43},
+ publisher = {American Institute of Physics},
+ url = {https://doi.org/10.1063/1.1696710 http://aip.scitation.org/doi/10.1063/1.1696710},
+ doi = {10.1063/1.1696710},
+ issn = {0021-9606}
+}
+
+@article{Invernizzi2020,
+ title = {{Rethinking Metadynamics: From Bias Potentials to Probability Distributions}},
+ year = {2020},
+ journal = {Journal of Physical Chemistry Letters},
+ author = {Invernizzi, Michele and Parrinello, Michele},
+ number = {7},
+ month = {4},
+ pages = {2731--2736},
+ volume = {11},
+ publisher = {American Chemical Society},
+ url = {https://dx.doi.org/10.1021/acs.jpclett.0c00497},
+ doi = {10.1021/acs.jpclett.0c00497},
+ issn = {19487185},
+ pmid = {32191470},
+ arxivId = {1909.07250}
+}
+
+@article{Ho2019,
+ title = {{Revealing Transition States during the Hydration of Clay Minerals}},
+ year = {2019},
+ journal = {The Journal of Physical Chemistry Letters},
+ author = {Ho, Tuan A. and Criscenti, Louise J. and Greathouse, Jeffery A.},
+ number = {13},
+ month = {7},
+ pages = {3704--3709},
+ volume = {10},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.9b01565 https://pubs.acs.org/doi/10.1021/acs.jpclett.9b01565},
+ doi = {10.1021/acs.jpclett.9b01565},
+ issn = {1948-7185},
+ pmid = {31244275}
+}
+
+@article{Baron2017,
+ title = {{Revisiting the nontronite M{\"{o}}ssbauer spectra}},
+ year = {2017},
+ journal = {American Mineralogist},
+ author = {Baron, Fabien and Petit, Sabine and Pentr{\'{a}}k, Martin and Decarreau, Alain and Stucki, Joseph W.},
+ number = {7},
+ month = {7},
+ pages = {1501--1515},
+ volume = {102},
+ publisher = {Walter de Gruyter GmbH},
+ url = {https://www.degruyter.com/document/doi/10.2138/am-2017-1501x/html},
+ doi = {10.2138/am-2017-1501x},
+ issn = {0003-004X},
+ keywords = {Clay minerals, M{\"{o}}ssbauer spectroscopy, iron, nontronite, smectites, tetrahedral iron}
+}
+
+@article{Bergmann1998,
+ title = {{Rietveld analysis of disordered layer silicates}},
+ year = {1998},
+ journal = {Materials Science Forum},
+ author = {Bergmann, J. and Kleeberg, R.},
+ number = {PART 1},
+ pages = {300--305},
+ volume = {278-281},
+ publisher = {Trans Tech Publications Ltd},
+ doi = {10.4028/www.scientific.net/msf.278-281.300},
+ issn = {16629752},
+ keywords = {Disorder, Layer Silicates, Quantitative Analysis, Rietveld Analysis}
+}
+
+@article{Wang2018,
+ title = {{Rietveld structure refinement of Cu-trien exchanged nontronites}},
+ year = {2018},
+ journal = {Frontiers in Chemistry},
+ author = {Wang, Xiaoli and Liao, Libing},
+ number = {NOV},
+ month = {11},
+ pages = {558},
+ volume = {6},
+ publisher = {Frontiers Media S.A.},
+ url = {/pmc/articles/PMC6255908/ /pmc/articles/PMC6255908/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255908/},
+ doi = {10.3389/fchem.2018.00558},
+ issn = {22962646},
+ keywords = {Crystal structure, Cu-triethylenetetramine, Nontronites, Rietveld refinement, X-ray powder diffraction}
+}
+
+@article{Aldersley2013,
+ title = {{RNA dimer synthesis using montmorillonite as a catalyst: The role of surface layer charge}},
+ year = {2013},
+ journal = {Applied Clay Science},
+ author = {Aldersley, Michael F. and Joshi, Prakash C.},
+ month = {10},
+ pages = {77--82},
+ volume = {83-84},
+ publisher = {Elsevier},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0169131713002366},
+ doi = {10.1016/j.clay.2013.08.009},
+ issn = {01691317},
+ keywords = {Catalysis, Montmorillonite, Nucleoside, Nucleotide, Origin of life, RNA}
+}
+
+@incollection{Hashizume2012,
+ title = {{Role of Clay Minerals in Chemical Evolution and the Origins of Life}},
+ year = {2012},
+ booktitle = {Clay Minerals in Nature - Their Characterization, Modification and Application},
+ author = {Hashizume, Hideo},
+ month = {9},
+ publisher = {InTech},
+ url = {http://dx.doi.org/10.5772/50172},
+ doi = {10.5772/50172}
+}
+
+@article{Kim2004,
+ title = {{Role of Microbes in the Smectite-to-Illite Reaction}},
+ year = {2004},
+ journal = {Science},
+ author = {Kim, Jinwook and Dong, Hailiang and Seabaugh, Jennifer and Newell, Steven W. and Eberl, Dennis D.},
+ number = {5659},
+ month = {2},
+ pages = {830--832},
+ volume = {303},
+ doi = {10.1126/science.1093245},
+ issn = {00368075},
+ pmid = {14764877}
+}
+
+@article{VirginiaA.Colten-Bradley21987,
+ title = {{Role of Pressure in Smectite Dehydration--Effects on Geopressure and Smectite-to-Illite Transformation}},
+ year = {1987},
+ journal = {AAPG Bulletin},
+ author = {{Virginia A. Colten-Bradley (2)}},
+ number = {11},
+ month = {11},
+ pages = {1414--1427},
+ volume = {71},
+ publisher = {GeoScienceWorld},
+ url = {http://search.datapages.com/data/doi/10.1306/703C8092-1707-11D7-8645000102C1865D},
+ doi = {10.1306/703C8092-1707-11D7-8645000102C1865D},
+ issn = {0149-1423}
+}
+
+@article{Ilgen2012,
+ title = {{Role of structural Fe in nontronite NAu-1 and dissolved Fe(II) in redox transformations of arsenic and antimony}},
+ year = {2012},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Ilgen, Anastasia G. and Foster, Andrea L. and Trainor, Thomas P.},
+ month = {10},
+ pages = {128--145},
+ volume = {94},
+ doi = {10.1016/j.gca.2012.07.007},
+ issn = {00167037}
+}
+
+@article{Flynn,
+ title = {{Rolling your own Document Class: Using L A T E X to keep away from the Dark Side}},
+ author = {Flynn, Peter},
+ url = {http://silmaril.ie/cgi-bin/blog}
+}
+
+@article{Gotz2012,
+ title = {{Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born}},
+ year = {2012},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {G{\"{o}}tz, Andreas W and Williamson, Mark J and Xu, Dong and Poole, Duncan and Le Grand, Scott and Walker, Ross C},
+ number = {5},
+ month = {5},
+ pages = {1542--1555},
+ volume = {8},
+ publisher = {American Chemical Society},
+ url = {https://doi.org/10.1021/ct200909j},
+ doi = {10.1021/ct200909j},
+ issn = {1549-9618}
+}
+
+@article{Salomon-Ferrer2013,
+ title = {{Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald}},
+ year = {2013},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Salomon-Ferrer, Romelia and G{\"{o}}tz, Andreas W and Poole, Duncan and Le Grand, Scott and Walker, Ross C},
+ number = {9},
+ month = {9},
+ pages = {3878--3888},
+ volume = {9},
+ publisher = {American Chemical Society},
+ url = {https://doi.org/10.1021/ct400314y},
+ doi = {10.1021/ct400314y},
+ issn = {1549-9618}
+}
+
+@article{Villafane-Barajas2018,
+ title = {{Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment}},
+ year = {2018},
+ journal = {Origins of Life and Evolution of Biospheres},
+ author = {Villafa{\~{n}}e-Barajas, Saúl A. and Ba{\'{u}}, João Paulo T. and Col{\'{i}}n-Garc{\'{i}}a, María and Negr{\'{o}}n-Mendoza, Alicia and Heredia-Barbero, Alejandro and Pi-Puig, Teresa and Zaia, Dimas A.M.},
+ number = {2},
+ month = {6},
+ pages = {181--200},
+ volume = {48},
+ publisher = {Springer Netherlands},
+ doi = {10.1007/s11084-018-9554-9},
+ issn = {15730875},
+ pmid = {29392543},
+ keywords = {Adsorption, Montmorillonite, Nucleobases, Prebiotic chemistry, Primitive ocean model}
+}
+
+@article{Mangaud2020,
+ title = {{Sampling mobility profiles of confined fluids with equilibrium molecular dynamics simulations}},
+ year = {2020},
+ journal = {Journal of Chemical Physics},
+ author = {Mangaud, Etienne and Rotenberg, Benjamin},
+ number = {4},
+ month = {7},
+ volume = {153},
+ publisher = {American Institute of Physics Inc.},
+ doi = {10.1063/5.0013952},
+ issn = {10897690},
+ pmid = {32752721}
+}
+
+@article{Phillips2005,
+ title = {{Scalable molecular dynamics with NAMD}},
+ year = {2005},
+ journal = {Journal of Computational Chemistry},
+ author = {Phillips, James C. and Braun, Rosemary and Wang, Wei and Gumbart, James and Tajkhorshid, Emad and Villa, Elizabeth and Chipot, Christophe and Skeel, Robert D. and Kal{\'{e}}, Laxmikant and Schulten, Klaus},
+ number = {16},
+ month = {12},
+ pages = {1781--1802},
+ volume = {26},
+ url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20289 http://doi.wiley.com/10.1002/jcc.20289},
+ doi = {10.1002/jcc.20289},
+ issn = {0192-8651},
+ keywords = {biomolecular simulation, molecular dynamics, parallel computing}
+}
+
+@article{OMalley2016,
+ title = {{Scalable quantum simulation of molecular energies}},
+ year = {2016},
+ journal = {Physical Review X},
+ author = {O'Malley, P. J.J. and Babbush, R. and Kivlichan, I. D. and Romero, J. and McClean, J. R. and Barends, R. and Kelly, J. and Roushan, P. and Tranter, A. and Ding, N. and Campbell, B. and Chen, Y. and Chen, Z. and Chiaro, B. and Dunsworth, A. and Fowler, A. G. and Jeffrey, E. and Lucero, E. and Megrant, A. and Mutus, J. Y. and Neeley, M. and Neill, C. and Quintana, C. and Sank, D. and Vainsencher, A. and Wenner, J. and White, T. C. and Coveney, P. V. and Love, P. J. and Neven, H. and Aspuru-Guzik, A. and Martinis, J. M.},
+ number = {3},
+ month = {7},
+ pages = {031007},
+ volume = {6},
+ url = {https://journals.aps.org/prx/pdf/10.1103/PhysRevX.6.031007 https://link.aps.org/doi/10.1103/PhysRevX.6.031007},
+ doi = {10.1103/PhysRevX.6.031007},
+ issn = {21603308},
+ arxivId = {1512.06860}
+}
+
+@article{Jenkins2017,
+ title = {{Seed-Mediated Synthesis of Gold Nanoparticles of Controlled Sizes To Demonstrate the Impact of Size on Optical Properties}},
+ year = {2017},
+ journal = {Journal of Chemical Education},
+ author = {Jenkins, Julie A. and Wax, Terianna J. and Zhao, Jing},
+ number = {8},
+ month = {8},
+ pages = {1090--1093},
+ volume = {94},
+ url = {http://pubs.acs.org/doi/10.1021/acs.jchemed.6b00941},
+ doi = {10.1021/acs.jchemed.6b00941},
+ issn = {0021-9584},
+ pmid = {1986604},
+ keywords = {Colloids, Hands-On Learning/Manipulatives, High School/Introductory Chemistry, Nanotechnology, Public Understanding/Outreach, Synthesis, UV-Vis Spectroscopy}
+}
+
+@article{Ziegler2011,
+ title = {{Seeded Growth Synthesis of Uniform Gold Nanoparticles with Diameters of 15−300 nm}},
+ year = {2011},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Ziegler, Christoph and Eychm{\"{u}}ller, Alexander},
+ number = {11},
+ month = {3},
+ pages = {4502--4506},
+ volume = {115},
+ url = {http://pubs.acs.org/doi/10.1021/jp1106982},
+ isbn = {1932-7447},
+ doi = {10.1021/jp1106982},
+ issn = {1932-7447}
+}
+
+@article{Jana2001,
+ title = {{Seeding Growth for Size Control of 5−40 nm Diameter Gold Nanoparticles}},
+ year = {2001},
+ journal = {Langmuir},
+ author = {Jana, Nikhil R. and Gearheart, Latha and Murphy, Catherine J.},
+ number = {22},
+ month = {10},
+ pages = {6782--6786},
+ volume = {17},
+ url = {http://dx.doi.org/10.1021/la0104323 http://pubs.acs.org/doi/abs/10.1021/la0104323},
+ isbn = {0743-7463},
+ doi = {10.1021/la0104323},
+ issn = {0743-7463}
+}
+
+@article{Jaber2014,
+ title = {{Selectivities in Adsorption and Peptidic Condensation in the (Arginine and Glutamic Acid)/Montmorillonite Clay System}},
+ year = {2014},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Jaber, Maguy and Georgelin, Thomas and Bazzi, Houssein and Costa-Torro, France and Lambert, Jean-François and Bolbach, Gérard and Clodic, Gilles},
+ number = {44},
+ month = {11},
+ pages = {25447--25455},
+ volume = {118},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/jp507335e},
+ doi = {10.1021/jp507335e},
+ issn = {1932-7447}
+}
+
+@article{Ertem2017,
+ title = {{Shielding biomolecules from effects of radiation by Mars analogue minerals and soils}},
+ year = {2017},
+ journal = {International Journal of Astrobiology},
+ author = {Ertem, G. and Ertem, M. C. and McKay, C. P. and Hazen, R. M.},
+ number = {3},
+ month = {7},
+ pages = {280--285},
+ volume = {16},
+ publisher = {Cambridge University Press},
+ url = {https://doi.org/10.1017/S1473550416000331},
+ doi = {10.1017/S1473550416000331},
+ issn = {14753006},
+ keywords = {Mars, Mars analogue minerals, biomolecules, radiation}
+}
+
+@article{Ertem2021,
+ title = {{Shielding biomolecules from effects of radiation by Mars analogue minerals and soils}},
+ year = {2017},
+ journal = {International Journal of Astrobiology},
+ author = {Ertem, G. and Ertem, M C and McKay, C. P. and Hazen, R M},
+ number = {3},
+ month = {7},
+ pages = {280--285},
+ volume = {16},
+ url = {https://doi.org/10.1017/S1473550416000331 https://www.cambridge.org/core/product/identifier/S1473550416000331/type/journal_article},
+ doi = {10.1017/S1473550416000331},
+ issn = {1473-5504},
+ keywords = {Mars, Mars analogue minerals, biomolecules, radiation}
+}
+
+@article{Young2000,
+ title = {{Simulations of clay mineral swelling and hydration: Dependence upon interlayer ion size and charge}},
+ year = {2000},
+ journal = {Journal of Physical Chemistry B},
+ author = {Young, Daniel A. and Smith, David E.},
+ number = {39},
+ month = {10},
+ pages = {9163--9170},
+ volume = {104},
+ publisher = {American Chemical Society},
+ doi = {10.1021/jp000146k},
+ issn = {15206106}
+}
+
+@article{Gates2002,
+ title = {{Site Occupancies by Iron in Nontronites}},
+ year = {2002},
+ journal = {Clays and Clay Minerals},
+ author = {Gates, W. P. and Slade, P. G. and Manceau, A. and Lanson, B.},
+ number = {2},
+ month = {4},
+ pages = {223--239},
+ volume = {50},
+ url = {http://link.springer.com/10.1346/000986002760832829},
+ doi = {10.1346/000986002760832829},
+ issn = {00000000}
+}
+
+@article{D.,
+ title = {{Site occupancy of Fe3+ in Garfield nontronite: a spectroscopic study}},
+ journal = {Phys. Chem. Minerals},
+ author = {D., Bonnin and G., Calas and H., Suquet and H., Pezerat},
+ pages = {55--64},
+ volume = {12}
+}
+
+@article{Stratagene2007,
+ title = {{Site-directed mutagenesis in hemoglobin: attempts to control the oxygen affinity with cooperativity preserved}},
+ year = {1998},
+ journal = {Protein Engineering Design and Selection},
+ author = {Kono, M. and Miyazaki, G. and Nakamura, H. and Wada, Y. and Imai, K.},
+ number = {3},
+ pages = {199--204},
+ volume = {11},
+ url = {https://academic.oup.com/peds/article-lookup/doi/10.1093/protein/11.3.199},
+ isbn = {1617379530},
+ doi = {10.1093/protein/11.3.199},
+ issn = {1741-0126},
+ pmid = {22115331}
+}
+
+@article{Ji2007,
+ title = {{Size Control of Gold Nanocrystals in Citrate Reduction: The Third Role of Citrate}},
+ year = {2007},
+ journal = {Journal of the American Chemical Society},
+ author = {Ji, Xiaohui and Song, Xiangning and Li, Jun and Bai, Yubai and Yang, Wensheng and Peng, Xiaogang},
+ number = {45},
+ month = {11},
+ pages = {13939--13948},
+ volume = {129},
+ url = {http://pubs.acs.org/doi/abs/10.1021/ja074447k},
+ isbn = {0002-7863},
+ doi = {10.1021/ja074447k},
+ issn = {0002-7863},
+ pmid = {17948996},
+ arxivId = {arXiv:1408.1149}
+}
+
+@incollection{Cohaut2013,
+ title = {{Small-Angle Scattering Techniques}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Cohaut, N. and Tchoubar, D.},
+ number = {C},
+ month = {1},
+ pages = {177--211},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00008-1},
+ issn = {15724352},
+ keywords = {Clay–polymer nanocomposite, Light, Neutron, Small-angle scattering, Swelling clay mineral, X-ray}
+}
+
+@incollection{Lambert2013,
+ title = {{Smectite-polymer nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Lambert, J. F. and Bergaya, F.},
+ pages = {679--706},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00021-3},
+ issn = {15724352},
+ keywords = {Biopolymers, Clay-polymer nanocomposites, Preparation methods, Smectites}
+}
+
+@article{Siguin1994,
+ title = {{Smectites: the relationship between their properties and isomorphic substitution}},
+ year = {1994},
+ journal = {Journal of Materials Science},
+ author = {Sigu{\'{i}}n, D. and Ferreira, S. and Froufe, L. and Garc{\'{i}}a, F.},
+ number = {16},
+ month = {8},
+ pages = {4379--4384},
+ volume = {29},
+ publisher = {Kluwer Academic Publishers},
+ url = {http://link.springer.com/10.1007/BF00414225},
+ doi = {10.1007/BF00414225},
+ issn = {0022-2461}
+}
+
+@article{Aquilante2010,
+ title = {{Software news and update MOLCAS 7: The next generation}},
+ year = {2010},
+ journal = {Journal of Computational Chemistry},
+ author = {Aquilante, Francesco and De Vico, Luca and Ferr{\'{e}}, Nicolas and Ghigo, Giovanni and Malmqvist, Per Åke and Neogr{\'{a}}dy, Pavel and Pedersen, Thomas Bondo and Pitoň{\'{a}}k, Michal and Reiher, Markus and Roos, Björn O. and Serrano-Andr{\'{e}}s, Luis and Urban, Miroslav and Veryazov, Valera and Lindh, Roland},
+ number = {1},
+ month = {1},
+ pages = {224--247},
+ volume = {31},
+ url = {http://doi.wiley.com/10.1002/jcc.21318},
+ doi = {10.1002/jcc.21318},
+ issn = {01928651},
+ keywords = {ANO-RCC, Cholesky decomposition, Coupled cluster, Douglas-Kroll-Hess, ESPF, MOLCAS, Photo chemistry, RASPT2}
+}
+
+@article{Megyes2004,
+ title = {{Solvation of calcium ion in polar solvents: An x-ray diffraction and ab initio study}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry A},
+ author = {Megyes, Tünde and Gr{\'{o}}sz, Tamás and Radnai, Tamás and Bak{\'{o}}, Imre and P{\'{a}}link{\'{a}}s, Gábor},
+ number = {35},
+ month = {9},
+ pages = {7261--7271},
+ volume = {108},
+ doi = {10.1021/jp048838m},
+ issn = {10895639}
+}
+
+@article{Levesque2012,
+ title = {{Solvation of complex surfaces via molecular density functional theory}},
+ year = {2012},
+ journal = {Journal of Chemical Physics},
+ author = {Levesque, Maximilien and Marry, Virginie and Rotenberg, Benjamin and Jeanmairet, Guillaume and Vuilleumier, Rodolphe and Borgis, Daniel},
+ number = {22},
+ month = {12},
+ volume = {137},
+ doi = {10.1063/1.4769729},
+ issn = {00219606},
+ arxivId = {1211.4884}
+}
+
+@article{Perdew2009,
+ title = {{Some Fundamental Issues in Ground-State Density Functional Theory: A Guide for the Perplexed}},
+ year = {2009},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Perdew, John P. and Ruzsinszky, Adrienn and Constantin, Lucian A. and Sun, Jianwei and Csonka, Gábor I.},
+ number = {4},
+ month = {4},
+ pages = {902--908},
+ volume = {5},
+ url = {https://pubs.acs.org/doi/10.1021/ct800531s},
+ doi = {10.1021/ct800531s},
+ issn = {1549-9618}
+}
+
+@incollection{Bergaya2013j,
+ title = {{Some other materials related to clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ pages = {743},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00024-9},
+ issn = {15724352}
+}
+
+@article{Mcmurray2020,
+ title = {{Spe ci a l R e p or t Renin – Angiotensin – Aldosterone System Inhibitors in Patients with Covid-19}},
+ year = {2020},
+ author = {Mcmurray, John J V and Pfeffer, Marc A and Ph, D and Solomon, Scott D},
+ pages = {1653--1659}
+}
+
+@article{Jungwirth2006,
+ title = {{Specific Ion Effects at the Air/Water Interface}},
+ year = {2006},
+ journal = {Chemical Reviews},
+ author = {Jungwirth, Pavel and Tobias, Douglas J.},
+ number = {4},
+ month = {4},
+ pages = {1259--1281},
+ volume = {106},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/cr0403741 https://pubs.acs.org/doi/10.1021/cr0403741},
+ doi = {10.1021/cr0403741},
+ issn = {0009-2665},
+ pmid = {16608180}
+}
+
+@book{Silverstein2005,
+ title = {{Spectrometric Identification of Organic Compounds}},
+ year = {2005},
+ author = {Silverstein, Robert M and Webster, Francis X and Kiemle, David J},
+ edition = {7},
+ publisher = {John Wiley {\&} Sons, Inc.},
+ isbn = {0471393622}
+}
+
+@article{LeGrand2013,
+ title = {{SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations}},
+ year = {2013},
+ journal = {Computer Physics Communications},
+ author = {Le Grand, Scott and G{\"{o}}tz, Andreas W. and Walker, Ross C.},
+ number = {2},
+ month = {2},
+ pages = {374--380},
+ volume = {184},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0010465512003098},
+ doi = {10.1016/j.cpc.2012.09.022},
+ issn = {00104655}
+}
+
+@article{BAKER1993380,
+ title = {{Spin contamination in density functional theory}},
+ year = {1993},
+ journal = {Chemical Physics Letters},
+ author = {Baker, Jon and Scheiner, Andrew and Andzelm, Jan},
+ number = {3-6},
+ pages = {380--388},
+ volume = {216},
+ url = {http://www.sciencedirect.com/science/article/pii/000926149390113F},
+ doi = {10.1016/0009-2614(93)90113-F},
+ issn = {00092614}
+}
+
+@article{Jordan2021,
+ title = {{Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine}},
+ year = {2021},
+ journal = {Nature Communications},
+ author = {Jordan, Sean F. and Ioannou, Ioannis and Rammu, Hanadi and Halpern, Aaron and Bogart, Lara K. and Ahn, Minkoo and Vasiliadou, Rafaela and Christodoulou, John and Mar{\'{e}}chal, Amandine and Lane, Nick},
+ number = {1},
+ month = {12},
+ pages = {5925},
+ volume = {12},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s41467-021-26158-2},
+ doi = {10.1038/s41467-021-26158-2},
+ issn = {2041-1723},
+ pmid = {34635654},
+ keywords = {Biogeochemistry, Biophysical chemistry, Carbon cycle}
+}
+
+@article{Odriozola2005,
+ title = {{Stability of Ca-montmorillonite hydrates: A computer simulation study}},
+ year = {2005},
+ journal = {Journal of Chemical Physics},
+ author = {Odriozola, G. and Aguilar, J. F.},
+ number = {17},
+ month = {11},
+ volume = {123},
+ doi = {10.1063/1.2087447}
+}
+
+@techreport{Strattona,
+ title = {{STATE OF ILLINOIS DEPARTMENT OF REGISTRATION AND EDUCATION WATER-SORPTION CHARACTERISTICS OF CLAY MINERALS}},
+ author = {Stratton, William G and Binks, Vera M and White, W Arthur and Pichler, Ernesto and Frye, John C},
+ keywords = {http://archive.org/details/watersorptioncha266whit}
+}
+
+@techreport{Stratton,
+ title = {{STATE OF ILLINOIS DEPARTMENT OF REGISTRATION AND EDUCATION WATER-SORPTION CHARACTERISTICS OF CLAY MINERALS}},
+ author = {Stratton, William G and Binks, Vera M and White, W Arthur and Pichler, Ernesto and Frye, John C},
+ keywords = {http://archive.org/details/watersorptioncha266whit}
+}
+
+@article{MDijkstra1997,
+ title = {{Statistical model for the structure and gelation of smectite clay}},
+ year = {1997},
+ journal = {Physical Review E},
+ author = {M Dijkstra, JP Hansen, PA Madden},
+ pages = {3044--3053},
+ volume = {55}
+}
+
+@article{Geddie2004HighEvolution,
+ title = {{High throughput microplate screens for directed protein evolution}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Geddie, Melissa L. and Rowe, Lori A. and Alexander, Omar B. and Matsumura, Ichiro},
+ number = {2000},
+ pages = {134--145},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88012-1},
+ issn = {00766879},
+ pmid = {15289067}
+}
+
+@article{Cohen2001HowWorks,
+ title = {{How DNA Shuffling Works}},
+ year = {2001},
+ journal = {Science},
+ author = {Cohen, J},
+ number = {5528},
+ pages = {237},
+ volume = {293},
+ isbn = {0036-8075 (Print){\textbackslash}r0036-8075 (Linking)},
+ doi = {10.1126/science.293.5528.237},
+ issn = {0036-8075},
+ pmid = {11452110}
+}
+
+@article{Bishop2005HydratedMars,
+ title = {{Hydrated Minerals on Mars}},
+ year = {2005},
+ journal = {Adv. Astrobiol. Biogeophys},
+ author = {Bishop, Janice L},
+ pages = {65--96}
+}
+
+@article{Pietrucci2018HydrothermalCompounds,
+ title = {{Hydrothermal Decomposition of Amino Acids and Origins of Prebiotic Meteoritic Organic Compounds}},
+ year = {2018},
+ author = {Pietrucci, Fabio and Aponte, Joséc Joséc and Starr, Richard and Pérezpérez-Villa, Andrea and Elsila, Jamie E and Dworkin, Jason P and Saitta, A Marco},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/acsearthspacechem.8b00025},
+ keywords = {ab initio molecular dynamics, enhanced sampling, glycine, isovaline, meteoritic organics, parent body processes}
+}
+
+@article{Martin2008HydrothermalLife,
+ title = {{Hydrothermal vents and the origin of life}},
+ year = {2008},
+ journal = {Nature Reviews Microbiology},
+ author = {Martin, William and Baross, John and Kelley, Deborah and Russell, Michael J.},
+ number = {11},
+ month = {11},
+ pages = {805--814},
+ volume = {6},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/nrmicro1991 http://www.nature.com/articles/nrmicro1991},
+ doi = {10.1038/nrmicro1991},
+ issn = {1740-1526},
+ pmid = {18820700},
+ keywords = {Infectious Diseases, Life Sciences, Medical Microbiology, Microbiology, Parasitology, Virology, general}
+}
+
+@article{TheI-likePili,
+ title = {{I-like pili}},
+ author = {The, B and Dev, Genes and Res, Genome},
+ pages = {119--127}
+}
+
+@article{Srodon2013IdentificationMinerals,
+ title = {{Identification and Quantitative Analysis of Clay Minerals}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {{\'{S}}rodo{\'{n}}, J.},
+ number = {C},
+ pages = {25--49},
+ volume = {5},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00004-4},
+ issn = {15724352},
+ keywords = {Clay mineral identification, Clay mineral quantification, Clay sample preparation, Clay separation, Crystal thickness, Mixed-layer clay minerals}
+}
+
+@article{KhajehImplementation2.12,
+ title = {{Implementation of magnetic field force in molecular dynamics algorithm: NAMD source code version 2.12}},
+ author = {Khajeh, Kosar and Aminfar, Habib and Masuda, Yoshihiro and Mohammadpourfard, Mousa},
+ url = {https://doi.org/10.1007/s00894-020-4349-0},
+ doi = {10.1007/s00894-020-4349-0},
+ keywords = {Charged particle, Magnetic field, NAMD, Velocity Verlet algorithm, Water}
+}
+
+@misc{Noskov2007ImportanceChannels,
+ title = {{Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels}},
+ year = {2007},
+ booktitle = {Journal of General Physiology},
+ author = {Noskov, Sergei Yu and Roux, Benoît},
+ number = {2},
+ month = {2},
+ pages = {135--143},
+ volume = {129},
+ doi = {10.1085/jgp.200609633},
+ issn = {00221295}
+}
+
+@article{Pasternak2011ImprovedMonomer,
+ title = {{Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer}},
+ year = {2011},
+ journal = {Nucleic Acids Research},
+ author = {Pasternak, Anna and Hernandez, Frank J. and Rasmussen, Lars M. and Vester, Birte and Wengel, Jesper},
+ number = {3},
+ pages = {1155--1164},
+ volume = {39},
+ isbn = {1362-4962 (Electronic){\textbackslash}n0305-1048 (Linking)},
+ doi = {10.1093/nar/gkq823},
+ issn = {03051048},
+ pmid = {20870750}
+}
+
+@article{Park2004ImprovingSystem.,
+ title = {{Improving the functional expression of N-carbamoylase by directed evolution using the green fluorescent protein fusion reporter system.}},
+ year = {2004},
+ journal = {Methods in enzymology},
+ author = {Park, Hee-Sung and Oh, Ki-Hoon and Kim, Hak-Sung},
+ number = {1996},
+ pages = {187--95},
+ volume = {388},
+ url = {http://www.sciencedirect.com/science/article/pii/S0076687904880170},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88017-0},
+ issn = {0076-6879},
+ pmid = {15289072},
+ keywords = {Amidohydrolases, Amidohydrolases: chemistry, Amidohydrolases: genetics, Amidohydrolases: metabolism, Amino Acid Sequence, Amino Acid Substitution, Base Sequence, Directed Molecular Evolution, Directed Molecular Evolution: methods, Genes, Reporter, Mutagenesis, Site-Directed, Protein Engineering, Protein Engineering: methods, Recombinant Fusion Proteins, Recombinant Fusion Proteins: chemistry, Recombinant Fusion Proteins: metabolism}
+}
+
+@article{Aharoni2011InLibraries,
+ title = {{In Vitro Compartmentalization (IVC) and Other High-Throughput Screens of Enzyme Libraries}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Aharoni, Amir and Tawfik, Dan S.},
+ number = {i},
+ pages = {649--667},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch27},
+ keywords = {Directed evolution, Genotype-phenotype linkage, High-throughput screening, In vitro compartmentalization (IVC)}
+}
+
+@article{Herman2007IncorporatingLibraries,
+ title = {{Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): A versatile tool for generating targeted libraries}},
+ year = {2007},
+ journal = {Protein Engineering, Design and Selection},
+ author = {Herman, Asael and Tawfik, Dan S.},
+ number = {5},
+ pages = {219--226},
+ volume = {20},
+ isbn = {9783527318506},
+ doi = {10.1093/protein/gzm014},
+ issn = {17410126},
+ pmid = {17483523},
+ keywords = {DNA shuffling, Deletions, Directed evolution, Indels, Insertions, Methyltransferase, PON1, Rational design}
+}
+
+@incollection{2005Index,
+ title = {{Index}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {593--611},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.index},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.index}
+}
+
+@incollection{2013Index,
+ title = {{Index}},
+ year = {2013},
+ pages = {857--874},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588099843},
+ doi = {10.1016/B978-0-08-098258-8.09984-3}
+}
+
+@incollection{2013Indexb,
+ title = {{Index}},
+ year = {2013},
+ pages = {793--813},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982595099881},
+ doi = {10.1016/B978-0-08-098259-5.09988-1}
+}
+
+@article{2017Index,
+ title = {{Index}},
+ year = {2017},
+ pages = {592--604},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780081003558099926},
+ doi = {10.1016/B978-0-08-100355-8.09992-6}
+}
+
+@book{Harvey2013IndustrialApplications,
+ title = {{Industrial Applications}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Harvey, C. C. and Lagaly, G.},
+ edition = {2},
+ number = {C},
+ pages = {451--490},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00018-4},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00018-4},
+ issn = {15724352},
+ keywords = {Acid activation, Alkylammonium clay, Anti-caking, Bentonite, Binding agent, Bleaching earth, Carrier, Catalyst, Categorization of clays, Ceramics, Common clay, Cosmetics, Diluents, Drilling, Engineering, Filler, Foundry, Ion exchange, Kaolin, Liquefaction, Modification, Organoclay, Paint, Palygorskite, Paper, Pelletizing, Pharmaceutics, Polymer, Processing of clay, Resource evaluation, Resources, Rheology, Sepiolite, Soda-activation, Thickener, Thixotropy}
+}
+
+@article{Kloprogge2017InfraredClays,
+ title = {{Infrared and Raman Spectroscopies of Pillared Clays}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Kloprogge, J. T.},
+ pages = {411--446},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00012-6},
+ issn = {15724352},
+ keywords = {Al13PILC, Clay mineral, FePILC, IR, IR spectroscopy, Mixed PILC, Oligomers salts, Porous clay heterostructures, Raman, Raman spectroscopy, SiPILC, TiPILC, ZrPILC}
+}
+
+@article{Gaigeot2005InfraredSimulations,
+ title = {{Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations}},
+ year = {2005},
+ author = {Gaigeot, M P and Vuilleumier, † R and Sprik, M and Borgis, D},
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/ct050029z}
+}
+
+@incollection{Johnston2017InfraredInteractions,
+ title = {{Infrared Studies of Clay Mineral-Water Interactions}},
+ year = {2017},
+ booktitle = {Developments in Clay Science},
+ author = {Johnston, C.T.},
+ pages = {288--309},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780081003558000096},
+ doi = {10.1016/B978-0-08-100355-8.00009-6},
+ issn = {15724352},
+ keywords = {Basal spacing, Cation exchange capacity, Clay-water interactions, Hydration, Hydrophilic, Hydrophobic, IR, IR spectroscopy, Intercalation hybrid, Molecular environment, Organoclay, Quaternary ammonium cation, Raman, Raman spectroscopy, clay minerals}
+}
+
+@article{Sponer2021InsolubleAl.,
+ title = {{Insoluble organic matter - an “organic” cradle of life: Comment on the paper “Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?” by Marco d'Ischia et al.}},
+ year = {2021},
+ journal = {Physics of Life Reviews},
+ author = {{\v{S}}poner, Judit E. and {\v{S}}poner, Jiří},
+ month = {9},
+ pages = {135--136},
+ volume = {38},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.plrev.2021.05.003},
+ issn = {15710645},
+ pmid = {34049815}
+}
+
+@article{dIschia2021InsolubleLife,
+ title = {{Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?}},
+ year = {2021},
+ journal = {Physics of Life Reviews},
+ author = {d'Ischia, Marco and Manini, Paola and Martins, Zita and Remusat, Laurent and O'D. Alexander, Conel M. and Puzzarini, Cristina and Barone, Vincenzo and Saladino, Raffaele},
+ month = {7},
+ pages = {65--93},
+ volume = {37},
+ publisher = {Elsevier},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S1571064521000130},
+ doi = {10.1016/j.plrev.2021.03.002},
+ issn = {15710645},
+ pmid = {33774429},
+ keywords = {Insoluble organic matter, Melanins, Polycyclic aromatic hydrocarbons (PAHs), Primordial multifunctional organic entity (PRiME)}
+}
+
+@article{Gillies2011InteinsEngineering,
+ title = {{Inteins in Protein Engineering}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Gillies, Alison R. and Wood, David W.},
+ pages = {235--342},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch10},
+ keywords = {Expressed protein ligation (EPL), Inteins, Protein cleaving, Protein cyclization, Protein splicing, Protein trans-splicing (PTS)}
+}
+
+@article{Cassone2021InterstellarBlocks,
+ title = {{Interstellar chemical reactions toward the synthesis of the life's building blocks}},
+ year = {2021},
+ journal = {Physics of Life Reviews},
+ author = {Cassone, Giuseppe and Saija, Franz},
+ month = {9},
+ pages = {140--142},
+ volume = {38},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S1571064521000294},
+ doi = {10.1016/j.plrev.2021.05.001},
+ issn = {15710645},
+ pmid = {34049816}
+}
+
+@article{Lopez-Sepulcre2019InterstellarPrecursor,
+ title = {{Interstellar Formamide (NH2CHO), a Key Prebiotic Precursor}},
+ year = {2019},
+ journal = {ACS Earth and Space Chemistry},
+ author = {L{\'{o}}pez-Sepulcre, Ana and Balucani, Nadia and Ceccarelli, Cecilia and Codella, Claudio and Dulieu, François and Theul{\'{e}}, Patrice},
+ number = {10},
+ month = {10},
+ pages = {2122--2137},
+ volume = {3},
+ publisher = {American Chemical Society},
+ doi = {10.1021/ACSEARTHSPACECHEM.9B00154},
+ issn = {24723452},
+ arxivId = {1909.11770},
+ keywords = {astrochemistry, experiments, interstellar medium, observations, organic molecules, star formation, theoretical chemistry}
+}
+
+@book{Bergaya2013IntroductionMinerals,
+ title = {{Introduction on modified clays and clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {2},
+ pages = {383},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00012-2},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00012-2},
+ issn = {15724352}
+}
+
+@book{Bergaya2013IntroductionCPN,
+ title = {{Introduction to clay-polymer nanocomposites (CPN)}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Detellier, C. and Lambert, J. F. and Lagaly, G.},
+ edition = {2},
+ pages = {655--677},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00020-1},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00020-1},
+ issn = {15724352},
+ keywords = {Clay polymer nanocomposites, Delamination, Exfoliation, Intercalation, Microcomposites, Polymer nomenclature}
+}
+
+@book{Bergaya2013IntroductionMineralsb,
+ title = {{Introduction to Pure Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {1},
+ number = {i},
+ pages = {211},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00007-9},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00007-9},
+ issn = {15724352}
+}
+
+@article{HomasIONMINERALS,
+ title = {{ION ADSORPTION AT CLAY-MINERAL SURFACES: THE HOFMEISTER SERIES FOR HYDRATED SMECTITE MINERALS}},
+ author = {Homas, T and Nderwood, U and Rastova, Valentina E and Greenwell, H Chris},
+ doi = {10.1346/CCMN.2016.0640310},
+ keywords = {BINDING AFFINITY, CATION EXCHANGE, MOLECULAR DYNAMICS, MONTMORILLONITE, WELL-TEMPERED METADYNAMICS}
+}
+
+@article{Qiu2012IonCalculations,
+ title = {{Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations}},
+ year = {2012},
+ journal = {Biochimica et Biophysica Acta - Biomembranes},
+ author = {Qiu, Hu and Shen, Rong and Guo, Wanlin},
+ number = {11},
+ month = {11},
+ pages = {2529--2535},
+ volume = {1818},
+ doi = {10.1016/j.bbamem.2012.06.003},
+ issn = {00052736},
+ keywords = {Ion hydration, Molecular dynamics, Sodium channels, Structural stability}
+}
+
+@article{Madejova2017IRMinerals,
+ title = {{IR Spectra of Clay Minerals}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Madejov{\'{a}}, J. and Gates, W. P. and Petit, S.},
+ pages = {107--149},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00005-9},
+ issn = {15724352},
+ keywords = {Bands assignments, Characteristic vibrations, Clay mineral families, Complementary information, Dioctahedral, MIR and NIR spectral database, Overtone and combination bands, Trioctahedral}
+}
+
+@article{Lin2015IsofunctionalDecarboxylase,
+ title = {{Isofunctional Enzymes PAD1 and UbiX Catalyze Formation of a Novel Cofactor Required by Ferulic Acid Decarboxylase and 4-Hydroxy-3-polyprenylbenzoic Acid Decarboxylase}},
+ year = {2015},
+ journal = {ACS Chemical Biology},
+ author = {Lin, Fengming and Ferguson, Kyle L. and Boyer, David R. and Lin, Xiaoxia Nina and Marsh, E. Neil G.},
+ number = {4},
+ month = {4},
+ pages = {1137--1144},
+ volume = {10},
+ url = {http://pubs.acs.org/doi/abs/10.1021/cb5008103},
+ doi = {10.1021/cb5008103},
+ issn = {1554-8929}
+}
+
+@incollection{2005IsolationMicroorganisms,
+ title = {{Isolation and Preparation of Microorganisms}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {43--60},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch3},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch3}
+}
+
+@article{1998IX-IX.pdf,
+ title = {{IX-IX.pdf}},
+ year = {1998},
+ number = {February},
+ pages = {1998}
+}
+
+@article{2013JOf,
+ title = {{J biosynthesis Synthesis of}},
+ year = {2013},
+ number = {2004},
+ pages = {2013},
+ volume = {410},
+ doi = {10.1038/nri}
+}
+
+@article{2006JacobMonodModel,
+ title = {{Jacob–Monod model}},
+ year = {2006},
+ pages = {129--131}
+}
+
+@article{2006JacobMonodModelb,
+ title = {{Jacob–Monod model}},
+ year = {2006}
+}
+
+@article{Furini2013K+Simulations,
+ title = {{K+ and Na+ Conduction in Selective and Nonselective Ion Channels Via Molecular Dynamics Simulations}},
+ year = {2013},
+ journal = {Biophysical Journal},
+ author = {Furini, Simone and Domene, Carmen},
+ number = {8},
+ month = {10},
+ pages = {1737--1745},
+ volume = {105},
+ publisher = {Biophysical Society},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349513010266},
+ doi = {10.1016/j.bpj.2013.08.049},
+ issn = {00063495}
+}
+
+@book{Detellier2013Kaolinite-polymerNanocomposites,
+ title = {{Kaolinite-polymer nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Detellier, C. and Letaief, S.},
+ edition = {2},
+ pages = {707--719},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00022-5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00022-5},
+ issn = {15724352},
+ keywords = {Delamination, Dickite, Exfoliation, Grafting, Halloysite, Intercalation, Kaolin group, Kaolinite, Kaolinite polymer nanocomposite, Nanohybrid material}
+}
+
+@misc{Codexis2011KETOREDUCTASEESTER,
+ title = {{KETOREDUCTASE POLYPEPTIDES FOR THE STEREOSELECTIVE PRODUCTION OF (S)-2-[3-[3-[2-(7- CHLOR0-2- QUINOLINYL)ETHENYL]PHENYL]-3- HYDROXYPROPYL]-BENZOIC ACID METHYL ESTER}},
+ year = {2011},
+ author = {{Codexis}},
+ number = {October 2010},
+ pages = {1--9},
+ volume = {2010}
+}
+
+@article{Lichtenegger2005Konversatoriumsunterlagen2004/05,
+ title = {{Konversatoriumsunterlagen zur Analysis T1, WS 2004/05}},
+ year = {2005},
+ author = {Lichtenegger, Klaus},
+ url = {https://www.math.tugraz.at/~lichtenegger/unt0405.pdf}
+}
+
+@article{OneLStrand,
+ title = {{L strand}},
+ author = {One, Plos},
+ number = {i},
+ pages = {133--141}
+}
+
+@article{Latex,
+ title = {{Latex}}
+}
+
+@book{Forano2013LayeredLDH,
+ title = {{Layered double hydroxides (LDH)}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Forano, C. and Costantino, U. and Pr{\'{e}}vot, V. and Gueho, C. Taviot},
+ pages = {745--782},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00025-0},
+ issn = {15724352},
+ keywords = {Hydrotalcite, LDH, Layered double hydroxides}
+}
+
+@book{Costantino2013LDHSciences,
+ title = {{LDH in Physical, Chemical, Biochemical, and Life Sciences}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Costantino, U. and Leroux, F. and Nocchetti, M. and Mousty, C.},
+ edition = {2},
+ number = {C},
+ pages = {765--791},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00026-3},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00026-3},
+ issn = {15724352},
+ keywords = {Agriculture, Biotechnology, Catalysts, Environment application, Intercalation of dyes, Layered double hydroxides, Modified LDH, Pharmaceutical technology and cosmetics, Polymers fillers}
+}
+
+@article{Raniolo2020LigandMetadynamics,
+ title = {{Ligand binding free-energy calculations with funnel metadynamics}},
+ year = {2020},
+ journal = {Nature Protocols},
+ author = {Raniolo, Stefano and Limongelli, Vittorio},
+ number = {9},
+ month = {9},
+ pages = {2837--2866},
+ volume = {15},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s41596-020-0342-4},
+ isbn = {4159602003424},
+ doi = {10.1038/s41596-020-0342-4},
+ issn = {1754-2189},
+ pmid = {32814837},
+ keywords = {Computational chemistry, Molecular dynamics, Software}
+}
+
+@article{Nixon2012LimitationsMars,
+ title = {{Limitations to a microbial iron cycle on Mars}},
+ year = {2012},
+ journal = {Planetary and Space Science},
+ author = {Nixon, Sophie L. and Cockell, Charles S. and Tranter, Martyn},
+ number = {1},
+ month = {11},
+ pages = {116--128},
+ volume = {72},
+ publisher = {Pergamon},
+ doi = {10.1016/J.PSS.2012.04.003},
+ issn = {0032-0633},
+ keywords = {Carbonaceous chondrite, Mars, Microbial iron cycle, Organics, Redox couple}
+}
+
+@article{Gagliardi2004LocalApproach,
+ title = {{Local properties of quantum chemical systems: The LoProp approach}},
+ year = {2004},
+ journal = {Journal of Chemical Physics},
+ author = {Gagliardi, Laura and Lindh, Roland and Karlstr{\"{o}}m, Gunnar},
+ number = {10},
+ pages = {4494--4500},
+ volume = {121},
+ doi = {10.1063/1.1778131},
+ issn = {00219606}
+}
+
+@article{Berezovsky2002LoopParadox,
+ title = {{Loop fold structure of proteins: Resolution of Levinthal's paradox}},
+ year = {2002},
+ journal = {Journal of Biomolecular Structure and Dynamics},
+ author = {Berezovsky, Igor N. and Trifonov, Edward N.},
+ number = {1},
+ pages = {5--6},
+ volume = {20},
+ doi = {10.1080/07391102.2002.10506817},
+ issn = {07391102},
+ pmid = {12144347},
+ keywords = {Chain conformation, Closed loops, Levinthal's paradox, Loop fold structure, Protein folding}
+}
+
+@article{Li2016LysineChannels,
+ title = {{Lysine and the Na+/K+ selectivity in mammalian voltage-gated sodium channels}},
+ year = {2016},
+ journal = {PLoS ONE},
+ author = {Li, Yang and Liu, Huihui and Xia, Mengdie and Gong, Haipeng},
+ number = {9},
+ month = {9},
+ volume = {11},
+ publisher = {Public Library of Science},
+ url = {/pmc/articles/PMC5008630/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008630/},
+ doi = {10.1371/journal.pone.0162413},
+ issn = {19326203}
+}
+
+@article{Diag2006MPlasmid,
+ title = {{M plasmid}},
+ year = {2006},
+ author = {Diag, Clin},
+ number = {1},
+ pages = {1878--1885},
+ volume = {187}
+}
+
+@article{Dong2009M-PEIsCells,
+ title = {{M-PEIs nanogels: Potential nonviral vector for systemic plasmid delivery to tumor cells}},
+ year = {2009},
+ journal = {Cancer Gene Therapy},
+ author = {Dong, L. and Xu, H. and Liu, Y. B. and Lu, B. and Xu, D. M. and Li, B. H. and Gao, J. and Wu, M. and Yao, S. D. and Zhao, J. and Guo, Y. J.},
+ number = {7},
+ pages = {561--566},
+ volume = {16},
+ isbn = {9780470747322},
+ doi = {10.1038/cgt.2009.11},
+ issn = {09291903},
+ pmid = {19180143},
+ keywords = {Gene delivery, Nanogels, Nonviral vectors, Polyethylenimine, Systemic delivery}
+}
+
+@article{Bibring2005MarsObservations,
+ title = {{Mars Surface Diversity as Revealed by the OMEGA/Mars Express Observations}},
+ year = {2005},
+ journal = {Science},
+ author = {Bibring, Jean-Pierre and Langevin, Yves and Gendrin, Aline and Gondet, Brigitte and Poulet, François and Berthé, Michel and Soufflot, Alain and Arvidson, Ray and Mangold, Nicolas and Mustard, John and Drossart, P.},
+ number = {5715},
+ month = {3},
+ pages = {1576--1581},
+ volume = {307},
+ url = {https://www.science.org/doi/10.1126/science.1108806},
+ doi = {10.1126/science.1108806},
+ issn = {0036-8075}
+}
+
+@article{Dartnell2007Martian,
+ title = {{Martian sub-surface ionising radiation: biosignatures and geology *}},
+ year = {2007},
+ journal = {Biogeosciences},
+ author = {Dartnell, L R and Desorgher, L and Ward, J M and Coates, A J},
+ pages = {545--558},
+ volume = {4},
+ url = {www.biogeosciences.net/4/545/2007/}
+}
+
+@article{Clayden1906McMurrysMcMurry,
+ title = {{McMurry's Special Method in Elementary Science Special Method in Elementary Science for the Common School. Charles A. McMurry}},
+ year = {1906},
+ journal = {The American Naturalist},
+ author = {Clayden, Jonathan and Greeves, Nick and Warren, Suart Stuart and Wothers, Peter},
+ number = {474},
+ pages = {455--456},
+ volume = {40},
+ url = {http://www.journals.uchicago.edu/doi/10.1086/278635},
+ isbn = {0198503474},
+ doi = {10.1086/278635},
+ issn = {0003-0147},
+ pmid = {640530},
+ arxivId = {arXiv:gr-qc/9809069v1},
+ archivePrefix = {arXiv},
+ eprint = {9809069v1},
+ primaryClass = {gr-qc}
+}
+
+@book{Wagner2013MechanicalMinerals,
+ title = {{Mechanical properties of clays and clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Wagner, J. F.},
+ edition = {1},
+ pages = {347--381},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00011-0},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00011-0},
+ issn = {15724352},
+ keywords = {Black shales, Cohesive soils, Compressibility, Expansive soils, Permeability, Plasticity, Quick clays, Settlement, Shear strength, Shrinkage, Soils}
+}
+
+@article{Dadachova2021MelaninEarth,
+ title = {{Melanin – protecting and enhancing the earliest life on Earth}},
+ year = {2021},
+ journal = {Physics of Life Reviews},
+ author = {Dadachova, Ekaterina},
+ month = {9},
+ pages = {127--128},
+ volume = {38},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S157106452100035X},
+ doi = {10.1016/j.plrev.2021.05.006},
+ issn = {15710645},
+ pmid = {34088610}
+}
+
+@article{Barducci2011Metadynamics,
+ title = {{Metadynamics}},
+ year = {2011},
+ journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
+ author = {Barducci, Alessandro and Bonomi, Massimiliano and Parrinello, Michele},
+ number = {5},
+ month = {9},
+ pages = {826--843},
+ volume = {1},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.31 https://onlinelibrary.wiley.com/doi/abs/10.1002/wcms.31 https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.31},
+ doi = {10.1002/WCMS.31},
+ issn = {1759-0884}
+}
+
+@article{Shell2007MethodsHistograms,
+ title = {{Methods based on probability distributions and histograms}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Shell, M. Scott and Panagiotopoulos, Athanassios and Pohorille, Andrew},
+ pages = {77--118},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}3},
+ issn = {01726218}
+}
+
+@article{Shell2007MethodsEquilibria,
+ title = {{Methods for examining phase equilibria}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Shell, M. Scott and Panagiotopoulos, Athanassios},
+ pages = {353--387},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}10},
+ issn = {01726218}
+}
+
+@incollection{2005MethodsProteins,
+ title = {{Methods for the Investigation of Proteins}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {243--280},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch9},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch9}
+}
+
+@article{Abelson2014MethodsEnzymology,
+ title = {{Methods in enzymology}},
+ year = {2014},
+ author = {Abelson, John N and Simon, Melvin I and Pyle, Anna Marie and Colowick, Sidney P and Kaplan, Nathan O},
+ pages = {96},
+ isbn = {9780124201194}
+}
+
+@article{Petrey2003MethodsEnzymology,
+ title = {{Methods in Enzymology}},
+ year = {2003},
+ journal = {Methods in enzymology},
+ author = {Petrey, Donald and Honig, Barry},
+ pages = {492--509},
+ url = {http://www.sciencedirect.com/science/article/pii/S007668790374021X},
+ isbn = {9780128011850},
+ doi = {10.1016/S0076-6879(03)74021-X},
+ issn = {0076-6879}
+}
+
+@article{1996MethodsAnalysis,
+ title = {{Methods of Soil Analysis}},
+ year = {1996},
+ editor = {Sparks, D.L. and Page, A.L. and Helmke, P.A. and Loeppert, R.H. and Soltanpour, P. N. and Tabatabai, M. A. and Johnston, C. T. and Sumner, M. E.},
+ month = {1},
+ series = {SSSA Book Series},
+ publisher = {Soil Science Society of America, American Society of Agronomy},
+ url = {https://acsess.onlinelibrary.wiley.com/doi/10.2136/sssabookser5.3},
+ address = {Madison, WI, USA},
+ isbn = {9780891188667},
+ doi = {10.2136/SSSABOOKSER5.3}
+}
+
+@article{2008MethodsMethods,
+ title = {{Methods of Soil Analysis Part 5-Mineralogical Methods}},
+ year = {2008},
+ isbn = {9780891188469},
+ doi = {10.2136/SSSABOOKSER}
+}
+
+@misc{MethodsBooks,
+ title = {{Methods of Soil Analysis, Part 3: Chemical Methods - Google Books}},
+ url = {https://books.google.co.uk/books?hl=en&lr=&id=_oDWDwAAQBAJ&oi=fnd&pg=PA161&ots=t73Wy1N76i&sig=3tZr8by_u1dmwrjSV_4MzVcOJjM&redir_esc=y#v=onepage&q&f=false}
+}
+
+@article{Ulery2015MethodsMethods,
+ title = {{Methods of soil analysis, part 5: Mineralogical methods}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Ulery, April and Drees, L. Richard},
+ month = {10},
+ pages = {1--521},
+ volume = {5},
+ publisher = {wiley},
+ url = {https://acsess.onlinelibrary.wiley.com/doi/book/10.2136/sssabookser5.5},
+ isbn = {9780891188575},
+ doi = {10.2136/sssabookser5.5}
+}
+
+@article{Resch2014MichaelDehydrogenase,
+ title = {{Michael hydratase alcohol dehydrogenase or just alcohol dehydrogenase?}},
+ year = {2014},
+ journal = {AMB Express},
+ author = {Resch, Verena and Jin, Jianfeng and Chen, Bi-Shuang and Hanefeld, Ulf},
+ number = {1},
+ month = {12},
+ pages = {30},
+ volume = {4},
+ publisher = {Springer Berlin Heidelberg},
+ url = {http://www.amb-express.com/content/4/1/30},
+ doi = {10.1186/s13568-014-0030-2},
+ issn = {2191-0855},
+ keywords = {Biotechnology, Microbial Genetics and Genomics, Microbiology}
+}
+
+@book{Beloqui2011MicrobesSpace,
+ title = {{Microbes and Enzymes: Recent Trends and New Directions to Expand Protein Space}},
+ year = {2011},
+ booktitle = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Beloqui, Ana and Zum{\`{a}}rraga, Miren and Alcalde, Miguel and Golyshin, Peter N. and Ferrer, Manuel},
+ pages = {233--269},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch9},
+ keywords = {Directed evolution, High throughput screening, Metagenomic, Protein engineering}
+}
+
+@article{Saitta2014MillerSimulations,
+ title = {{Miller experiments in atomistic computer simulations}},
+ year = {2014},
+ journal = {Proceedings of the National Academy of Sciences},
+ author = {Saitta, Antonino Marco and Saija, Franz},
+ number = {38},
+ month = {9},
+ pages = {13768--13773},
+ volume = {111},
+ publisher = {PNAS},
+ url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1402894111},
+ doi = {10.1073/pnas.1402894111},
+ issn = {0027-8424}
+}
+
+@article{Hazen2010MineralLife,
+ title = {{Mineral Surfaces, Geochemical Complexities, and the Origins of Life}},
+ year = {2010},
+ journal = {Cold Spring Harbor Perspectives in Biology},
+ author = {Hazen, R. M. and Sverjensky, D. A.},
+ number = {5},
+ month = {5},
+ pages = {a002162-a002162},
+ volume = {2},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/0169534788900316 http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a002162},
+ doi = {10.1101/cshperspect.a002162},
+ issn = {1943-0264}
+}
+
+@article{BlattmannMineralogicalOcean,
+ title = {{Mineralogical control on the fate of continentally derived organic matter in the ocean}},
+ author = {Blattmann, T M and Liu, Z and Zhang, Y and Zhao, Y and Haghipour, N and Montlu{\c{c}}on, D B and Pl{\"{o}}tze, M and Eglinton, T I},
+ url = {https://www.science.org}
+}
+
+@book{2021MineralsHealth,
+ title = {{Minerals latu sensu and Human Health}},
+ year = {2021},
+ editor = {Gomes, Celso and Rautureau, Michel},
+ publisher = {Springer International Publishing},
+ url = {https://doi.org/10.1007/978-3-030-65706-2 https://link.springer.com/10.1007/978-3-030-65706-2},
+ address = {Cham},
+ isbn = {978-3-030-65705-5},
+ doi = {10.1007/978-3-030-65706-2}
+}
+
+@misc{Maffeo2012ModelingChannels,
+ title = {{Modeling and simulation of ion channels}},
+ year = {2012},
+ booktitle = {Chemical Reviews},
+ author = {Maffeo, Christopher and Bhattacharya, Swati and Yoo, Jejoong and Wells, David and Aksimentiev, Aleksei},
+ number = {12},
+ month = {12},
+ pages = {6250--6284},
+ volume = {112},
+ doi = {10.1021/cr3002609},
+ issn = {00092665},
+ pmid = {23035940}
+}
+
+@article{Bourg2007ModelingMontmorillonite,
+ title = {{Modeling the acid-base surface chemistry of montmorillonite}},
+ year = {2007},
+ journal = {Journal of Colloid and Interface Science},
+ author = {Bourg, Ian C. and Sposito, Garrison and Bourg, Alain C.M.},
+ number = {2},
+ month = {8},
+ pages = {297--310},
+ volume = {312},
+ doi = {10.1016/J.JCIS.2007.03.062},
+ issn = {00219797},
+ keywords = {Acid-base properties, Montmorillonite, Potentiometric titration, Smectite, Surface complexation model}
+}
+
+@article{Hadi2013ModellingRefinements,
+ title = {{Modelling CEC variations versus structural iron reduction levels in dioctahedral smectites. Existing approaches, new data and model refinements}},
+ year = {2013},
+ journal = {Journal of Colloid and Interface Science},
+ author = {Hadi, Jebril and Tournassat, Christophe and Ignatiadis, Ioannis and Greneche, Jean Marc and Charlet, Laurent},
+ month = {10},
+ pages = {397--409},
+ volume = {407},
+ publisher = {Academic Press},
+ doi = {10.1016/J.JCIS.2013.05.014},
+ issn = {0021-9797},
+ keywords = {Clay, Iron, Layer charge, Nontronite, Reduction, Structural}
+}
+
+@article{Zamaraev1997ModellingStage,
+ title = {{Modelling of the prebiotic synthesis of oligopeptides: silicate catalysts help to overcome the critical stage}},
+ year = {1997},
+ journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
+ author = {Zamaraev, Kirill I. and Romannikov, Vyacheslav N. and Salganik, Rudolph I. and Wlassoff, Wjatschesslaw A. and Khramtsov, Valeriy V.},
+ number = {4},
+ pages = {325--337},
+ volume = {27},
+ publisher = {Orig Life Evol Biosph},
+ url = {https://pubmed.ncbi.nlm.nih.gov/11536826/},
+ doi = {10.1023/A:1006571800690},
+ issn = {0169-6149},
+ pmid = {11536826},
+ keywords = {Aluminum Silicates / chemistry, Catalysis, Chemical, Clay, Evolution, Glycine / chemistry*, Glycylglycine / chemistry*, Hydrogen-Ion Concentration, K I Zamaraev, MEDLINE, Molecular*, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Non-U.S. Gov't, Oligopeptides / chemical synthesis*, Origin of Life, Piperazines / chemical synthesis*, PubMed Abstract, Research Support, Silicates / chemistry*, V N Romannikov, V V Khramtsov, Zeolites / chemical synthesis, Zeolites / chemistry, doi:10.1023/a:1006571800690, pmid:11536826}
+}
+
+@article{Chryssikos2017ModernMethods,
+ title = {{Modern Infrared and Raman Instrumentation and Sampling Methods}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Chryssikos, G. D.},
+ pages = {34--63},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00003-5},
+ issn = {15724352},
+ keywords = {ATR (attenuated total reflectance), Clay mineral, Diffuse reflectance, External-internal reflection, High-throughput, IR, IR spectroscopy, Instrumentation, Noninvasive spectral acquisition, Raman, Raman Spectroscopy, Real-time monitoring, Sampling configurations, Transmission}
+}
+
+@article{Kaneko2004ModuleShuffling,
+ title = {{Module shuffling}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Kaneko, Satoshi},
+ number = {2000},
+ pages = {22--34},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88003-0},
+ issn = {00766879},
+ pmid = {15289058}
+}
+
+@incollection{2005MolecularBiocatalysis,
+ title = {{Molecular Biology Tools for Biocatalysis}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {61--90},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch4},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch4}
+}
+
+@article{Li2017MolecularChannel,
+ title = {{Molecular dynamics study of ion transport through an open model of voltage-gated sodium channel}},
+ year = {2017},
+ journal = {Biochimica et Biophysica Acta - Biomembranes},
+ author = {Li, Yang and Sun, Ruining and Liu, Huihui and Gong, Haipeng},
+ number = {5},
+ month = {5},
+ pages = {879--887},
+ volume = {1859},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.bbamem.2017.02.003},
+ issn = {18792642},
+ keywords = {Channel conductance, Ion permeation, Ion translocation, Molecular dynamics simulations, NaV channels}
+}
+
+@article{Allen1999MolecularChannel,
+ title = {{Molecular dynamics study of the KcsA potassium channel}},
+ year = {1999},
+ journal = {Biophysical Journal},
+ author = {Allen, Toby W. and Kuyucak, Serdar and Chung, Shin Ho},
+ number = {5},
+ pages = {2502--2516},
+ volume = {77},
+ publisher = {Biophysical Society},
+ doi = {10.1016/S0006-3495(99)77086-4},
+ issn = {00063495}
+}
+
+@article{Cygan2009MolecularMaterials,
+ title = {{Molecular models and simulations of layered materials}},
+ year = {2009},
+ journal = {Journal of Materials Chemistry},
+ author = {Cygan, Randall T. and Greathouse, Jeffery A. and Heinz, Hendrik and Kalinichev, Andrey G.},
+ number = {17},
+ pages = {2470--2481},
+ volume = {19},
+ doi = {10.1039/B819076C},
+ issn = {09599428}
+}
+
+@article{Cygan2004MolecularField,
+ title = {{Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry B},
+ author = {Cygan, Randall T. and Liang, Jian Jie and Kalinichev, Andrey G.},
+ number = {4},
+ month = {1},
+ pages = {1255--1266},
+ volume = {108},
+ publisher = {American Chemical Society},
+ doi = {10.1021/JP0363287},
+ issn = {15206106}
+}
+
+@article{Catterall1986MolecularChannels,
+ title = {{Molecular Properties of Voltage-Sensitive Sodium Channels}},
+ year = {1986},
+ journal = {Annual Review of Biochemistry},
+ author = {Catterall, W A},
+ number = {1},
+ month = {6},
+ pages = {953--985},
+ volume = {55},
+ url = {http://www.annualreviews.org/doi/10.1146/annurev.bi.55.070186.004513},
+ doi = {10.1146/annurev.bi.55.070186.004513},
+ issn = {0066-4154}
+}
+
+@article{Sampath2020MolecularSimulations,
+ title = {{Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations}},
+ year = {2020},
+ journal = {npj Computational Materials 2020 6:1},
+ author = {Sampath, Janani and Kullman, Andrew and Gebhart, Rachel and Drobny, Gary and Pfaendtner, Jim},
+ number = {1},
+ month = {4},
+ pages = {1--8},
+ volume = {6},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s41524-020-0288-7},
+ doi = {10.1038/s41524-020-0288-7},
+ issn = {2057-3960},
+ keywords = {Biomedical materials, Biophysics}
+}
+
+@book{Greathouse2013MolecularMinerals,
+ title = {{Molecular Simulation of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Greathouse, J. A. and Cygan, R. T.},
+ edition = {2},
+ number = {C},
+ pages = {405--423},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00016-0},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00016-0},
+ issn = {15724352},
+ keywords = {Clay mineral, Layered mineral, Monte Carlo, Simulation molecular dynamics}
+}
+
+@article{Murad2013MossbauerSpectroscopy,
+ title = {{M{\"{o}}ssbauer Spectroscopy}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {Murad, E.},
+ number = {C},
+ pages = {11--24},
+ volume = {5},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00003-2},
+ issn = {15724352},
+ keywords = {Clay firing, Fe (hydr)oxides, Magnetism, Mars, M{\"{o}}ssbauer spectroscopy, gamma rays}
+}
+
+@article{Payer2018MultienzymePhenols,
+ title = {{Multienzyme One-Pot Cascade for the Stereoselective Hydroxyethyl Functionalization of Substituted Phenols}},
+ year = {2018},
+ journal = {Organic Letters},
+ author = {Payer, Stefan E. and Pollak, Hannah and Schmidbauer, Benjamin and Hamm, Florian and Juri{\v{c}}i{\'{c}}, Filip and Faber, Kurt and Glueck, Silvia M.},
+ number = {17},
+ month = {9},
+ pages = {5139--5143},
+ volume = {20},
+ url = {https://pubs.acs.org/doi/10.1021/acs.orglett.8b02058},
+ doi = {10.1021/acs.orglett.8b02058},
+ issn = {1523-7060}
+}
+
+@book{2009Natural,
+ title = {{Natural Polyester - Related Proteins : Structure , Function ,}},
+ year = {2009},
+ isbn = {9783527318506}
+}
+
+@article{Nelson1996,
+ title = {{nelson1996}}
+}
+
+@article{Besenmatter2004NewModules,
+ title = {{New enzymes from combinatorial library modules}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Besenmatter, Werner and Kast, Peter and Hilvert, Donald},
+ number = {1996},
+ pages = {91--102},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88009-1},
+ issn = {00766879},
+ pmid = {15289064}
+}
+
+@article{Madejova2017NIRMinerals,
+ title = {{NIR Contribution to The Study of Modified Clay Minerals}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Madejov{\'{a}}, J. and P{\'{a}}lkov{\'{a}}, H.},
+ pages = {447--481},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00013-8},
+ issn = {15724352},
+ keywords = {Acid treatment, Clay based hybrid materials, Clay mineral, Dry grinding, Layer charge reduction, NIR spectra interpretation, Organoclays, Structural changes}
+}
+
+@article{2004NoTitle,
+ title = {{No Title}},
+ year = {2004}
+}
+
+@article{Roux1993Non-additivityChannel,
+ title = {{Non-additivity in cation-peptide interactions. A molecular dynamics and ab initio study of Na+ in the gramicidin channel}},
+ year = {1993},
+ journal = {Chemical Physics Letters},
+ author = {Roux, Benoît},
+ number = {3-4},
+ month = {9},
+ pages = {231--240},
+ volume = {212},
+ doi = {10.1016/0009-2614(93)89319-D},
+ issn = {00092614}
+}
+
+@article{Hummer2007NonequilibriumCalculations,
+ title = {{Nonequilibrium methods for equilibrium free energy calculations}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Hummer, Gerhard},
+ pages = {171--198},
+ volume = {86},
+ publisher = {Springer New York},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}5},
+ issn = {01726218}
+}
+
+@article{Furini2012NonselectiveSites,
+ title = {{Nonselective conduction in a mutated NaK channel with three cation-binding sites}},
+ year = {2012},
+ journal = {Biophysical Journal},
+ author = {Furini, Simone and Domene, Carmen},
+ number = {10},
+ month = {11},
+ pages = {2106--2114},
+ volume = {103},
+ doi = {10.1016/j.bpj.2012.10.004},
+ issn = {00063495}
+}
+
+@book{Sanz2013NuclearSpectroscopy,
+ title = {{Nuclear Magnetic Resonance Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Sanz, J. and Massiot, D.},
+ edition = {1},
+ number = {C},
+ pages = {233--274},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00010-X},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00010-X},
+ issn = {15724352},
+ keywords = {Acid and alkaline activation, Adsorption, Catalysis, Magic-angle spinning technique, Nuclear magnetic resonance, Thermal reactions}
+}
+
+@article{Resch2013OnAcids,
+ title = {{On the Michael Addition of Water to {$\alpha$},{$\beta$}-Unsaturated Ketones Using Amino Acids}},
+ year = {2013},
+ journal = {European Journal of Organic Chemistry},
+ author = {Resch, Verena and Seidler, Christiane and Chen, Bi-Shuang and Degeling, Ian and Hanefeld, Ulf},
+ number = {34},
+ month = {12},
+ pages = {7697--7704},
+ volume = {2013},
+ url = {http://doi.wiley.com/10.1002/ejoc.201301230},
+ doi = {10.1002/ejoc.201301230},
+ issn = {1434193X}
+}
+
+@misc{Roux2002On2,
+ title = {{On the potential functions used in molecular dynamics simulations of ion channels [2]}},
+ year = {2002},
+ booktitle = {Biophysical Journal},
+ author = {Roux, Benoît and Bern{\`{e}}che, Simon},
+ number = {3},
+ month = {3},
+ pages = {1681--1684},
+ volume = {82},
+ publisher = {Biophysical Society},
+ doi = {10.1016/S0006-3495(02)75520-3},
+ issn = {00063495}
+}
+
+@article{Favre1996OnChannel,
+ title = {{On the structural basis for ionic selectivity among Na+, K+, and Ca2+ in the voltage-gated sodium channel}},
+ year = {1996},
+ journal = {Biophysical Journal},
+ author = {Favre, Isabelle and Moczydlowski, Edward and Schild, Laurent},
+ number = {6},
+ pages = {3110--3125},
+ volume = {71},
+ publisher = {Biophysical Society},
+ doi = {10.1016/S0006-3495(96)79505-X},
+ issn = {00063495}
+}
+
+@article{Vakalova2018OptimisingSoils,
+ title = {{Optimising rational chemical analysis for quantitative determination of the composition of clay in soils}},
+ year = {2018},
+ journal = {Applied Clay Science},
+ author = {Vakalova, Tatyana and Pogrebenkov, Valeriy and Vereshagin, Vladimir and Khabas, Tamara and Revva, Inna},
+ month = {10},
+ pages = {153--163},
+ volume = {163},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.clay.2018.07.014},
+ issn = {01691317},
+ keywords = {Clay, Clay minerals, Colloids, Kaolinite, Montmorillonite, Rational chemical analysis}
+}
+
+@article{Broz2020OrganicMars,
+ title = {{Organic Matter Preservation in Ancient Soils of Earth and Mars}},
+ year = {2020},
+ journal = {Life},
+ author = {Broz, Adrian P.},
+ number = {7},
+ month = {7},
+ pages = {113},
+ volume = {10},
+ publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
+ url = {/pmc/articles/PMC7400377/ /pmc/articles/PMC7400377/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400377/ https://www.mdpi.com/2075-1729/10/7/113},
+ doi = {10.3390/life10070113},
+ issn = {2075-1729},
+ pmid = {32708606},
+ keywords = {Aqueous alteration, Astrobiology, Astropedology, Biosignature detection, Martian paleosols, Precambrian paleosols}
+}
+
+@article{Hartman2019OriginPolynucleotides,
+ title = {{Origin of the Genetic Code Is Found at the Transition between a Thioester World of Peptides and the Phosphoester World of Polynucleotides}},
+ year = {2019},
+ journal = {Life 2019, Vol. 9, Page 69},
+ author = {Hartman, Hyman and Smith, Temple F.},
+ number = {3},
+ month = {8},
+ pages = {69},
+ volume = {9},
+ publisher = {Multidisciplinary Digital Publishing Institute},
+ url = {https://www.mdpi.com/2075-1729/9/3/69/htm https://www.mdpi.com/2075-1729/9/3/69},
+ doi = {10.3390/LIFE9030069},
+ issn = {20751729},
+ keywords = {early peptides, genetic code origin, metabolism, nucleotidyltransferases, ribosome, synthetase, tRNA, tRNA accretion model, thioester}
+}
+
+@article{NarayananNair2021OverviewClays,
+ title = {{Overview of the Adsorption and Transport Properties of Water, Ions, Carbon Dioxide, and Methane in Swelling Clays}},
+ year = {2021},
+ journal = {ACS Earth and Space Chemistry},
+ author = {Narayanan Nair, Arun Kumar and Cui, Ronghao and Sun, Shuyu},
+ number = {10},
+ month = {10},
+ pages = {2599--2611},
+ volume = {5},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/acsearthspacechem.1c00160},
+ doi = {10.1021/ACSEARTHSPACECHEM.1C00160},
+ issn = {24723452},
+ keywords = {adsorption, diffusion, grand canonical Monte Carlo simulations, molecular dynamics simulations, montmorillonite−carbon dioxide−methane system, shale}
+}
+
+@article{Saleh2016OxidationSamples,
+ title = {{Oxidation and Complexation-Based Spectrophotometric Methods for Sensitive Determination of Tartrazine E102 in Some Commercial Food Samples}},
+ year = {2016},
+ journal = {Computational Chemistry},
+ author = {Saleh, Magda M. S. and Hashem, Elham Y. and Salahi, Najat O. A. Al-},
+ number = {02},
+ pages = {51--64},
+ volume = {04},
+ url = {http://www.scirp.org/journal/doi.aspx?DOI=10.4236/cc.2016.42005},
+ doi = {10.4236/cc.2016.42005},
+ issn = {2332-5968}
+}
+
+@book{LossPElement,
+ title = {{P element}},
+ author = {Loss, A and Ca, San Diego and Hybridization, A},
+ number = {1},
+ pages = {173--206},
+ isbn = {0792363078}
+}
+
+@article{Reback2020Pandas-dev/pandas:1.0.3,
+ title = {{pandas-dev/pandas: Pandas 1.0.3}},
+ year = {2020},
+ author = {Reback, Jeff and McKinney, Wes and {jbrockmendel} and Bossche, Joris Van den and Augspurger, Tom and Cloud, Phillip and {gfyoung} and {Sinhrks} and Klein, Adam and Roeschke, Matthew and Hawkins, Simon and Tratner, Jeff and She, Chang and Ayd, William and Petersen, Terji and Garcia, Marc and Schendel, Jeremy and Hayden, Andy and {MomIsBestFriend} and Jancauskas, Vytautas and Battiston, Pietro and Seabold, Skipper and {chris-b1} and {h-vetinari} and Hoyer, Stephan and Overmeire, Wouter and {alimcmaster1} and Dong, Kaiqi and Whelan, Christopher and Mehyar, Mortada},
+ month = {3},
+ url = {https://zenodo.org/record/3715232},
+ doi = {10.5281/ZENODO.3715232}
+}
+
+@incollection{Bish2013ParallelsZeolites,
+ title = {{Parallels and Distinctions Between Clay Minerals and Zeolites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bish, D.L.},
+ edition = {2},
+ pages = {783--800},
+ volume = {5},
+ publisher = {Copyright {\&}copy; 2013, 2006 Elsevier Ltd. All rights reserved.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00026-2 https://linkinghub.elsevier.com/retrieve/pii/B9780080982588000262},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00026-2},
+ issn = {15724352},
+ keywords = {Adsorption, Chabazite, Clinoptilolite, Dehydration, Enthalpy, Hydration, Laumontite, Nontronite, Phase transition, Smectite, Zeolite}
+}
+
+@article{Li2015ParameterizationWater,
+ title = {{Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water}},
+ year = {2015},
+ journal = {Journal of Physical Chemistry B},
+ author = {Li, Pengfei and Song, Lin Frank and Merz, Kenneth M.},
+ number = {3},
+ month = {1},
+ pages = {883--895},
+ volume = {119},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/jp505875v},
+ doi = {10.1021/JP505875V/SUPPL{\_}FILE/JP505875V{\_}SI{\_}003.PDF},
+ issn = {15205207},
+ pmid = {25145273}
+}
+
+@article{Li2021ParametrizationModels,
+ title = {{Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models}},
+ year = {2021},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Li, Zhen and Song, Lin Frank and Li, Pengfei and Merz, Kenneth M.},
+ number = {4},
+ month = {4},
+ pages = {2342--2354},
+ volume = {17},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c01320},
+ doi = {10.1021/ACS.JCTC.0C01320/SUPPL{\_}FILE/CT0C01320{\_}SI{\_}001.PDF},
+ issn = {15499626},
+ pmid = {33793233}
+}
+
+@article{Danger2012PathwaysEnvironments,
+ title = {{Pathways for the formation and evolution of peptides in prebiotic environments}},
+ year = {2012},
+ journal = {Chemical Society reviews},
+ author = {Danger, Grégoire and Plasson, Raphaël and Pascal, Robert},
+ number = {16},
+ month = {7},
+ pages = {5416--5429},
+ volume = {41},
+ publisher = {Chem Soc Rev},
+ url = {https://pubmed.ncbi.nlm.nih.gov/22688720/},
+ doi = {10.1039/C2CS35064E},
+ issn = {1460-4744},
+ pmid = {22688720},
+ keywords = {Amino Acids / chemistry*, Amino Acids / metabolism, Catalysis, Chemical*, Evolution, Gr{\'{e}}goire Danger, MEDLINE, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Non-U.S. Gov't, Origin of Life*, Peptides / chemistry*, Peptides / metabolism, Polymerization, PubMed Abstract, Rapha{\"{e}}l Plasson, Research Support, Review, Robert Pascal, Thermodynamics, doi:10.1039/c2cs35064e, pmid:22688720}
+}
+
+@article{Ojha2017Pd-Boron-CatalyzedTemperature,
+ title = {{Pd-Boron-Catalyzed One Carbon Isomerization of Olefins: Water Assisted Process at Room Temperature}},
+ year = {2017},
+ journal = {Journal of Organic Chemistry},
+ author = {Ojha, Devi Prasan and Gadde, Karthik and Prabhu, Kandikere Ramaiah},
+ doi = {10.1021/acs.joc.7b00580},
+ issn = {15206904}
+}
+
+@article{Lahav1978PeptideEnvironments,
+ title = {{Peptide Formation in the Prebiotic Era: Thermal Condensation of Glycine in Fluctuating Clay Environments}},
+ year = {1978},
+ journal = {Science},
+ author = {Lahav, N. and White, D. and Chang, S.},
+ number = {4350},
+ pages = {67--69},
+ volume = {201},
+ publisher = {{\\\} American Association for the Advancement of Science{\\\} },
+ url = {https://www.science.org/doi/abs/10.1126/science.663639},
+ doi = {10.1126/SCIENCE.663639},
+ issn = {00368075},
+ pmid = {663639}
+}
+
+@article{Fuchida2014PeptideConditions,
+ title = {{Peptide formation mechanism on montmorillonite under thermal conditions}},
+ year = {2014},
+ journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
+ author = {Fuchida, Shigeshi and Masuda, Harue and Shinoda, Keiji},
+ number = {1},
+ pages = {13--28},
+ volume = {44},
+ publisher = {Orig Life Evol Biosph},
+ url = {https://pubmed.ncbi.nlm.nih.gov/24917118/},
+ doi = {10.1007/S11084-014-9359-4},
+ issn = {1573-0875},
+ pmid = {24917118},
+ keywords = {Aluminum Silicates / chemistry, Bentonite / chemistry*, Chemical*, Clay, Evolution, Glycine / chemistry*, Harue Masuda, Hot Temperature, Keiji Shinoda, MEDLINE, Minerals / chemistry, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, Non-U.S. Gov't, Origin of Life, Peptides / chemistry*, PubMed Abstract, Research Support, Shigeshi Fuchida, Water / chemistry, doi:10.1007/s11084-014-9359-4, pmid:24917118}
+}
+
+@article{Sroga2004PeriplasmicReactivities,
+ title = {{Periplasmic expression as a basis for whole cell kinetic screening of unnatural enzyme reactivities}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Sroga, Grazyna E. and Dordick, Jonathan S.},
+ number = {1999},
+ pages = {145--156},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88013-3},
+ issn = {00766879},
+ pmid = {15289068}
+}
+
+@article{Lynn2015PetrographicMounts,
+ title = {{Petrographic microscope techniques for identifying soil minerals in grain mounts}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Lynn, Warren and Thomas, J. E. and Moody, L. E.},
+ month = {10},
+ pages = {161--190},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C6},
+ keywords = {Grain mounts, Optical properties, Particle-size separation, Pedon descriptions, Petrographic microscope techniques, Sample collection, Sample preparation, Site selection, Soil mineral identification}
+}
+
+@incollection{2005PharmaceuticalBiocatalysis,
+ title = {{Pharmaceutical Applications of Biocatalysis}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {373--411},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch13},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch13}
+}
+
+@article{Poulet2005PhyllosilicatesClimate,
+ title = {{Phyllosilicates on Mars and implications for early martian climate}},
+ year = {2005},
+ journal = {Nature},
+ author = {Poulet, F. and Bibring, J. P. and Mustard, J. F. and Gendrin, A. and Mangold, N. and Langevin, Y. and Arvidson, R. E. and Gondet, B. and Gomez, C. and Berthe, M. and Erard, S. and Forni, O. and Manaud, N. and Poulleau, G. and Soufflot, A. and Combes, M. and Drossart, P. and Encrenaz, T. and Fouchet, T. and Melchiorri, R. and Bellucci, G. and Altieri, F. and Formisano, V. and Fonti, S. and Capaccioni, F. and Cerroni, P. and Coradini, A. and Korablev, O. and Kottsov, V. and Ignatiev, N. and Titov, D. and Zasova, L. and Pinet, P. and Schmitt, B. and Sotin, C. and Hauber, E. and Hoffmann, H. and Jaumann, R. and Keller, U. and Forget, F.},
+ number = {7068},
+ month = {12},
+ pages = {623--627},
+ volume = {438},
+ publisher = {Nature Publishing Group},
+ doi = {10.1038/nature04274},
+ issn = {14764687},
+ pmid = {16319882}
+}
+
+@book{Vicente2013PillaredMinerals,
+ title = {{Pillared clays and clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Vicente, M. A. and Gil, A. and Bergaya, F.},
+ edition = {2},
+ pages = {523--557},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00017-1},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00017-1},
+ issn = {15724352},
+ keywords = {PILC properties, Pillared clays, Pillaring methods, Pillaring species}
+}
+
+@misc{Inakollu2020PolarisableSimulations,
+ title = {{Polarisable force fields: what do they add in biomolecular simulations?}},
+ year = {2020},
+ booktitle = {Current Opinion in Structural Biology},
+ author = {Inakollu, VS Sandeep and Geerke, Daan P. and Rowley, Christopher N. and Yu, Haibo},
+ month = {4},
+ pages = {182--190},
+ volume = {61},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.sbi.2019.12.012},
+ issn = {1879033X},
+ pmid = {32044671},
+ arxivId = {1910.14237}
+}
+
+@misc{Halgren2001PolarizableFields,
+ title = {{Polarizable force fields}},
+ year = {2001},
+ booktitle = {Current Opinion in Structural Biology},
+ author = {Halgren, Thomas A. and Damm, Wolfgang},
+ number = {2},
+ month = {4},
+ pages = {236--242},
+ volume = {11},
+ doi = {10.1016/S0959-440X(00)00196-2},
+ issn = {0959440X},
+ pmid = {11297934}
+}
+
+@article{Yu2012PossibleBiofilm,
+ title = {{Possible inhibitory molecular mechanism of farnesol on the development of fluconazole resistance in Candida albicans biofilm}},
+ year = {2012},
+ journal = {Antimicrobial Agents and Chemotherapy},
+ author = {Yu, Li Hua and Wei, Xin and Ma, Ming and Chen, Xiao Jun and Xu, Shuang Bo},
+ number = {2},
+ pages = {770--775},
+ volume = {56},
+ isbn = {1098-6596 (Electronic){\textbackslash}n0066-4804 (Linking)},
+ doi = {10.1128/AAC.05290-11},
+ issn = {00664804},
+ pmid = {22106223}
+}
+
+@article{Biggin2001PotassiumSimulations,
+ title = {{Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations}},
+ year = {2001},
+ journal = {Biochimica et Biophysica Acta - Biomembranes},
+ author = {Biggin, P. C. and Smith, G. R. and Shrivastava, I. and Choe, S. and Sansom, M. S.P.},
+ number = {1-2},
+ month = {2},
+ pages = {1--9},
+ volume = {1510},
+ doi = {10.1016/S0005-2736(00)00345-X},
+ issn = {00052736},
+ keywords = {Ion channel, KcsA, Molecular dynamics, Potassium, Selectivity}
+}
+
+@article{Pratt2007PotentialSolutions,
+ title = {{Potential distribution methods and free energy models of molecular solutions}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Pratt, Lawrence R. and Asthagiri, Dilip},
+ pages = {323--351},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}9},
+ issn = {01726218}
+}
+
+@article{Roux1995PotentialStudy,
+ title = {{Potential energy function for cation–peptide interactions: An ab initio study}},
+ year = {1995},
+ journal = {Journal of Computational Chemistry},
+ author = {Roux, Benoît and Karplus, Martin},
+ number = {6},
+ pages = {690--704},
+ volume = {16},
+ doi = {10.1002/jcc.540160605},
+ issn = {1096987X}
+}
+
+@article{Liu2020PotentialMedicines,
+ title = {{Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines}},
+ year = {2020},
+ journal = {Journal of Genetics and Genomics},
+ author = {Liu, Xin and Wang, Xiu-Jie},
+ number = {2},
+ month = {2},
+ pages = {119--121},
+ volume = {47},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S1673852720300278},
+ doi = {10.1016/j.jgg.2020.02.001},
+ issn = {16738527},
+ pmid = {32173287}
+}
+
+@article{Perez-Villa2020PrebioticSimulations,
+ title = {{Prebiotic chemistry and origins of life research with atomistic computer simulations}},
+ year = {2020},
+ journal = {Physics of Life Reviews},
+ author = {P{\'{e}}rez-Villa, Andrea and Pietrucci, Fabio and Saitta, A Marco},
+ month = {12},
+ pages = {105--135},
+ volume = {34-35},
+ url = {www.sciencedirect.comwww.elsevier.com/locate/plrev https://linkinghub.elsevier.com/retrieve/pii/S157106451830109X},
+ doi = {10.1016/j.plrev.2018.09.004},
+ issn = {15710645},
+ keywords = {Atomistic computer simulations, Origins of life, Prebiotic chemistry}
+}
+
+@article{2006Preface,
+ title = {{Preface}},
+ year = {2006},
+ journal = {Developments in Clay Science},
+ number = {C},
+ volume = {2},
+ doi = {10.1016/S1572-4352(06)02013-7},
+ issn = {15724352}
+}
+
+@article{Kuhnel2013PrefaceEdition,
+ title = {{Preface to the First Edition}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {K{\"{u}}hnel, Radko A.},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.09986-7},
+ issn = {15724352}
+}
+
+@article{Bergaya2013PrefaceEdition,
+ title = {{Preface to the Second Edition}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {Bergaya, Faïza and Lagaly, Gerhard},
+ number = {December 2012},
+ pages = {2012},
+ volume = {5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.09985-5},
+ issn = {15724352}
+}
+
+@article{Soukup2015PreparingAnalyses,
+ title = {{Preparing soils for mineralogical analyses}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Soukup, D. A. and Buck, B. J. and Harris, W.},
+ month = {10},
+ pages = {13--31},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C2},
+ keywords = {Carbonate removal, Freeze-drying, Organic matter removal, Particle-size fractionation, Pretreatments, Soil mineralogical analysis, Soil preparation, Soluble salt removal}
+}
+
+@article{BlancoPreservationExobiology,
+ title = {{Preservation of biosignatures in clay-rich systems: implications for Martian exobiology}},
+ journal = {Mem. S.A.It. Suppl},
+ author = {Blanco, A and Licchelli, D and Orofino, V and Fonti, S and Marzo, Ga},
+ pages = {101},
+ volume = {16},
+ keywords = {Exobiology-, Mars-spectroscopy}
+}
+
+@article{Thakur2016ProgrammableLogic,
+ title = {{Programmable Potentials: Approximate N-body potentials from coarse-level logic}},
+ year = {2016},
+ journal = {Scientific Reports},
+ author = {Thakur, Gunjan S. and Mohr, Ryan and Mezi{\'{c}}, Igor},
+ number = {1},
+ month = {9},
+ pages = {1--15},
+ volume = {6},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/srep33415},
+ doi = {10.1038/srep33415},
+ issn = {20452322},
+ keywords = {Applied mathematics, Atomic and molecular physics, Chemical physics}
+}
+
+@book{Stucki2013PropertiesMinerals,
+ title = {{Properties and behaviour of iron in clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Stucki, J. W.},
+ edition = {2},
+ number = {1988},
+ pages = {559--611},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00018-3},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00018-3},
+ issn = {15724352},
+ keywords = {Alkylammonium ions, Bacteria, Chlorinated aliphatics, Colour, Dithionite, EXAFS, Electron microscopy, Ferric ions, Ferrous ions, Infrared, Intervalence transfer, Iron, Microorganisms, M{\"{o}}ssbauer, Nitroaromatics, Organo-clay interactions, Oxidation, Pesticides, Redox, Redox-active metals, Reduction, Synchrotron methods, UV-visible spectroscopy}
+}
+
+@article{Russell2019ProspectingLife,
+ title = {{Prospecting for life}},
+ year = {2019},
+ journal = {Interface Focus},
+ author = {Russell, Michael J},
+ number = {6},
+ month = {12},
+ pages = {20190050},
+ volume = {9},
+ publisher = {Royal Society Publishing},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/31641430 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC6802130 https://royalsocietypublishing.org/doi/10.1098/rsfs.2019.0050},
+ doi = {10.1098/rsfs.2019.0050},
+ issn = {2042-8898},
+ pmid = {31641430},
+ keywords = {alkaline vent, emergence of life, fougerite, green rust}
+}
+
+@article{Jaber2018ProteinMinerals,
+ title = {{Protein adsorption on clay minerals}},
+ year = {2018},
+ journal = {Developments in Clay Science},
+ author = {Jaber, Maguy and Lambert, Jean François and Balme, Sébastien},
+ month = {1},
+ pages = {255--288},
+ volume = {9},
+ publisher = {Elsevier},
+ doi = {10.1016/B978-0-08-102432-4.00008-1},
+ issn = {1572-4352},
+ keywords = {Adsorption isotherms, Adsorption kinetic, Binding sites, Interlayer cation, NMR, Soft and hard proteins, Time-resolved fluorescence, pH}
+}
+
+@book{Zimmermann2011ProteinFunction,
+ title = {{Protein dynamics and the evolution of novel protein function}},
+ year = {2011},
+ booktitle = {Protein Engineering {\ldots}},
+ author = {Zimmermann, J and Thielges, MC},
+ pages = {147--185},
+ url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527634026.ch6/summary},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch6}
+}
+
+@book{Urvoas2009ProteinDisplay,
+ title = {{Protein Engineering by Phage Display}},
+ year = {2009},
+ author = {Urvoas, Agathe and Minard, Philippe and Soumillion, Patrice},
+ isbn = {9783527318506}
+}
+
+@article{Saab-Rincon2008ProteinRecombination,
+ title = {{Protein engineering by structure guided SCHEMA recombination}},
+ year = {2008},
+ journal = {Protein Engineering Handbook},
+ author = {Saab-Rincon, G and Michelle, Meyer and Carbone, Martina and Landwher, M and {Arnold FH}},
+ pages = {481--492},
+ isbn = {9783527318506}
+}
+
+@book{Lutz2008ProteinHandbook,
+ title = {{Protein Engineering Handbook}},
+ year = {2008},
+ author = {Lutz, Stefan and Bornscheuer, Uwe T.},
+ volume = {1},
+ url = {http://doi.wiley.com/10.1002/9783527634026},
+ isbn = {9783527634026},
+ doi = {10.1002/9783527634026}
+}
+
+@book{Chen2011ProteinSynthases,
+ title = {{Protein Engineering of Modular Polyketide Synthases}},
+ year = {2011},
+ booktitle = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Chen, Alice Y. and Khosla, Chaitan},
+ pages = {797--827},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch32},
+ keywords = {6-deoxyerythronolide B synthase (DEBS), Acyl-carrier protein, Acyltransferase, Ketosynthase, Polyketide combinatorial biosynthesis, Polyketide synthase, Protein engineering}
+}
+
+@article{Urlacher2004ProteinMegaterium,
+ title = {{Protein engineering of the cytochrome P450 monooxygenase from Bacillus megaterium}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Urlacher, Vlada B. and Schmid, Rolf D.},
+ number = {2002},
+ pages = {208--224},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88019-4},
+ issn = {00766879},
+ pmid = {15289074}
+}
+
+@article{Fisher2009ProteinAssays,
+ title = {{Protein Folding and Solubility : Pathways and High - Throughput Assays}},
+ year = {2009},
+ author = {Fisher, Adam C and Mansell, Thomas J and Delisa, Matthew P},
+ isbn = {9783527318506}
+}
+
+@article{Ying2011ProteinSystem,
+ title = {{Protein Generation Using a Reconstituted System}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Ying, Bei Wen and Ueda, Takuya},
+ pages = {515--535},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch22},
+ keywords = {Cell-free translation, Chaperone, In vitro selection, Membrane protein, Protein folding, Pure ribosome display (PRD), Ribosome, Translation process}
+}
+
+@article{Stakkestad2011ProteinIsoform,
+ title = {{Protein kinase A type i activates a CRE-element more efficiently than protein kinase A type II regardless of C subunit isoform}},
+ year = {2011},
+ journal = {BMC Biochemistry},
+ author = {Stakkestad, Oystein and Larsen, Anja Cv and Kvissel, Anne Katrine and Eikvar, Sissel and {\O}rstavik, Sigurd and Sk{\aa}lhegg, Bjørn S.},
+ number = {1},
+ volume = {12},
+ isbn = {1471-2091 (Electronic){\textbackslash}r1471-2091 (Linking)},
+ doi = {10.1186/1471-2091-12-7},
+ issn = {14712091},
+ pmid = {21303506}
+}
+
+@article{Berezovsky2003ProteinCode,
+ title = {{Protein sequences yield a proteomic code}},
+ year = {2003},
+ journal = {Journal of Biomolecular Structure and Dynamics},
+ author = {Berezovsky, Igor N. and Kirzhner, Alla and Kirzhner, Valery M. and Rosenfeld, Vladimir R. and Trifonov, Edward N.},
+ number = {3},
+ pages = {317--325},
+ volume = {21},
+ doi = {10.1080/07391102.2003.10506928},
+ issn = {15380254}
+}
+
+@article{Berezovsky2001ProteinStart,
+ title = {{Protein structure and folding: A new start}},
+ year = {2001},
+ journal = {Journal of Biomolecular Structure and Dynamics},
+ author = {Berezovsky, Igor N. and Trifonov, Edward N.},
+ number = {3},
+ pages = {397--403},
+ volume = {19},
+ doi = {10.1080/07391102.2001.10506749},
+ issn = {15380254},
+ pmid = {11790139}
+}
+
+@book{Bergaya2013PurificationClays,
+ title = {{Purification of natural clays}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {1},
+ pages = {213--221},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00008-0},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00008-0},
+ issn = {15724352},
+ keywords = {Decomposition of carbonates, Dialysis, Dissolution of (hydr)oxides, Dissolution of silica, Fractionation, Oxidation of organic material, Particle size, Purification, Washing}
+}
+
+@article{Pna2007QBases,
+ title = {{Q bases}},
+ year = {2007},
+ author = {Pna, Quencher-labeled and Jolla, La and Qext, Multiplex and Gmbh, Qiagen and Struct, Nature and Biol, Mol and Res, Nucleic Acids and Res, Nucleic Acids and Dna, Quadruplex and Res, Nucleic Acids},
+ number = {34},
+ pages = {207--209}
+}
+
+@article{Zhao2020QuantifyingEnzymes.,
+ title = {{Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes.}},
+ year = {2020},
+ journal = {Life (Basel, Switzerland)},
+ author = {Zhao, Daniel and Bartlett, Stuart and Yung, Yuk L},
+ number = {12},
+ month = {12},
+ pages = {1--9},
+ volume = {10},
+ publisher = {MDPI AG},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/33321803 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC7764262},
+ doi = {10.3390/life10120338},
+ issn = {2075-1729},
+ pmid = {33321803},
+ keywords = {astrobiology, enzymes, ligand, minerals, origin of life}
+}
+
+@article{Barone2015QuantumMolecules,
+ title = {{Quantum chemistry meets spectroscopy for astrochemistry: Increasing complexity toward prebiotic molecules}},
+ year = {2015},
+ journal = {Accounts of Chemical Research},
+ author = {Barone, Vincenzo and Biczysko, Malgorzata and Puzzarini, Cristina},
+ number = {5},
+ month = {5},
+ pages = {1413--1422},
+ volume = {48},
+ publisher = {American Chemical Society},
+ doi = {10.1021/AR5003285},
+ issn = {15204898},
+ pmid = {25894724}
+}
+
+@article{Beck2007QuantumFluids,
+ title = {{Quantum contributions to free energy changes in fluids}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Beck, Thomas L.},
+ pages = {389--422},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}11},
+ issn = {01726218}
+}
+
+@article{Proteins2006RLoop,
+ title = {{R loop}},
+ year = {2006},
+ author = {Proteins, P and Natl, Proc and Sci, Acad and Pcr, Nested},
+ number = {1},
+ pages = {387--392},
+ volume = {38}
+}
+
+@book{Allard2013RadiationMinerals,
+ title = {{Radiation Effects on Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Allard, T. and Balan, E. and Calas, G.},
+ edition = {1},
+ number = {i},
+ pages = {127--138},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00004-3},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00004-3},
+ issn = {15724352},
+ keywords = {Amorphization, Dating, Dosimetry, EPR, Irradiation, Point defect, Uranium transfer}
+}
+
+@article{Kloprogge2017RamanMinerals,
+ title = {{Raman and Infrared Spectroscopies of Intercalated Kaolinite Groups Minerals}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Kloprogge, J. T.},
+ pages = {343--410},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00011-4},
+ issn = {15724352},
+ keywords = {Aprotic solvent, Clay mineral, Dipole interaction, H bond acceptors, H bond donors, Hydrogen bonding, IR, IR spectroscopy, Raman, Raman spectroscopy}
+}
+
+@article{Kloprogge2017RamanMineralsb,
+ title = {{Raman Spectroscopy of Clay Minerals}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Kloprogge, J. T.},
+ pages = {150--199},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00006-0},
+ issn = {15724352},
+ keywords = {Clay mineral, Clay mineral representatives, IR, IR spectroscopy, Low wavenumber region, OH stretching region, Raman, Raman Spectroscopy, Structural units, Theoretical calculations, Vibrational modes assignment}
+}
+
+@article{Tsuji2004RandomReaction,
+ title = {{Random multirecombinant polymerase chain reaction}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Tsuji, Toru and Onimaru, Michiko and Kitagawa, Masanobu and Kojoh, Kanehisa and Tabata, Noriko and Yanagawa, Hiroshi},
+ number = {2001},
+ pages = {61--75},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88007-8},
+ issn = {00766879},
+ pmid = {15289062}
+}
+
+@article{Feutrill1972ReactionsAryloxyacetates,
+ title = {{Reactions with thioethoxide ion in dimethylformamide: II. O-alkyl cleavage of methylene ethers, methyl esters, and aryloxyacetates}},
+ year = {1972},
+ journal = {Australian Journal of Chemistry},
+ author = {Feutrill, G. I. and Mirrington, R. N.},
+ doi = {10.1071/CH9721731},
+ issn = {14450038}
+}
+
+@article{Boulet2006RecentCalculations,
+ title = {{Recent advances in understanding the structure and reactivity of clays using electronic structure calculations}},
+ year = {2006},
+ journal = {Journal of Molecular Structure: THEOCHEM},
+ author = {Boulet, P. and Greenwell, H. C. and Stackhouse, S. and Coveney, P. V.},
+ number = {1-3},
+ month = {4},
+ pages = {33--48},
+ volume = {762},
+ publisher = {Elsevier},
+ doi = {10.1016/J.THEOCHEM.2005.10.028},
+ issn = {0166-1280},
+ keywords = {Ab initio calculations, Clays, Structure-property relationships}
+}
+
+@article{Wuensch2012RegioselectiveDerivatives,
+ title = {{Regioselective Enzymatic Carboxylation of Phenols and Hydroxystyrene Derivatives}},
+ year = {2012},
+ journal = {Organic Letters},
+ author = {Wuensch, Christiane and Glueck, Silvia M. and Gross, Johannes and Koszelewski, Dominik and Schober, Markus and Faber, Kurt},
+ number = {8},
+ month = {4},
+ pages = {1974--1977},
+ volume = {14},
+ url = {https://pubs.acs.org/doi/10.1021/ol300385k},
+ isbn = {1523-7060},
+ doi = {10.1021/ol300385k},
+ issn = {1523-7060},
+ pmid = {22471935},
+ arxivId = {arXiv:1011.1669v3}
+}
+
+@article{Wuensch2012RegioselectiveDerivativesb,
+ title = {{Regioselective enzymatic carboxylation of phenols and hydroxystyrene derivatives}},
+ year = {2012},
+ journal = {Organic Letters},
+ author = {Wuensch, Christiane and Glueck, Silvia M. and Gross, Johannes and Koszelewski, Dominik and Schober, Markus and Faber, Kurt},
+ number = {8},
+ pages = {1974--1977},
+ volume = {14},
+ isbn = {1523-7060},
+ doi = {10.1021/ol300385k},
+ issn = {15237060},
+ pmid = {22471935},
+ arxivId = {arXiv:1011.1669v3}
+}
+
+@article{Wuensch2015RegioselectiveDecarboxylases,
+ title = {{Regioselective enzymatic {$\beta$}-carboxylation of para-hydroxy-styrene derivatives catalyzed by phenolic acid decarboxylases}},
+ year = {2015},
+ journal = {Advanced Synthesis and Catalysis},
+ author = {Wuensch, Christiane and Pavkov-Keller, Tea and Steinkellner, Georg and Gross, Johannes and Fuchs, Michael and Hromic, Altijana and Lyskowski, Andrzej and Fauland, Kerstin and Gruber, Karl and Glueck, Silvia M. and Faber, Kurt},
+ doi = {10.1002/adsc.201401028},
+ issn = {16154169},
+ pmid = {26190963},
+ keywords = {biotransformations, enzyme catalysis, para-hydroxystyrenes, phenolic acid decarboxylases, reaction mechanism, regioselective carboxylation}
+}
+
+@techreport{Moraitakis2001ReportsAl,
+ title = {{Reports on Progress in Physics To cite this article: Serdar Kuyucak et al}},
+ year = {2001},
+ booktitle = {Rep. Prog. Phys},
+ author = {Moraitakis, George and Purkiss, Andrew G and Goodfellow, Julia M},
+ pages = {1427},
+ volume = {64}
+}
+
+@article{Lee2015RETRACTEDMutagenesis,
+ title = {{RETRACTED ARTICLE: Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis}},
+ year = {2015},
+ journal = {Applied Microbiology and Biotechnology},
+ author = {Lee, Hyunji and Park, Jiyoung and Jung, Chaewon and Han, Dongfei and Seo, Jiyoung and Ahn, Joong-Hoon and Chong, Youhoon and Hur, Hor-Gil},
+ number = {22},
+ month = {11},
+ pages = {9473--9481},
+ volume = {99},
+ url = {http://link.springer.com/10.1007/s00253-015-6717-8},
+ doi = {10.1007/s00253-015-6717-8},
+ issn = {0175-7598}
+}
+
+@article{Rosazza1995Review:Product.,
+ title = {{Review: biocatalytic transformations of ferulic acid: an abundant aromatic natural product.}},
+ year = {1995},
+ journal = {Journal of industrial microbiology},
+ author = {Rosazza, J P and Huang, Z and Dostal, L and Volm, T and Rousseau, B},
+ number = {6},
+ month = {12},
+ pages = {457--71},
+ volume = {15},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/8821508},
+ issn = {0169-4146},
+ pmid = {8821508}
+}
+
+@article{RichtlinienChemie,
+ title = {{Richtlinien zur Erstellung einer Bachelorarbeit im Bachelorstudium Chemie}}
+}
+
+@article{Rimola2019RoleStudies,
+ title = {{Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies}},
+ year = {2019},
+ journal = {Life 2019, Vol. 9, Page 10},
+ author = {Rimola, Albert and Sodupe, Mariona and Ugliengo, Piero},
+ number = {1},
+ month = {1},
+ pages = {10},
+ volume = {9},
+ publisher = {Multidisciplinary Digital Publishing Institute},
+ url = {https://www.mdpi.com/2075-1729/9/1/10/htm https://www.mdpi.com/2075-1729/9/1/10},
+ doi = {10.3390/LIFE9010010},
+ issn = {2075-1729},
+ keywords = {density functional theory, early earth, mineral surfaces, origin of life, prebiotic chemistry, surface modelling, theoretical chemistry}
+}
+
+@article{Rimola2019RoleStudiesb,
+ title = {{Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies}},
+ year = {2019},
+ journal = {Life (Basel, Switzerland)},
+ author = {Rimola, Albert and Sodupe, Mariona and Ugliengo, Piero},
+ number = {1},
+ month = {3},
+ volume = {9},
+ publisher = {Life (Basel)},
+ url = {https://pubmed.ncbi.nlm.nih.gov/30658501/},
+ doi = {10.3390/LIFE9010010},
+ issn = {2075-1729},
+ pmid = {30658501},
+ keywords = {Albert Rimola, MEDLINE, Mariona Sodupe, NCBI, NIH, NLM, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, PMC6463156, Piero Ugliengo, PubMed Abstract, Review, doi:10.3390/life9010010, pmid:30658501}
+}
+
+@article{Brucato2019RoleConditions,
+ title = {{Role of Mineral Surfaces in Prebiotic Processes and Space-Like Conditions}},
+ year = {2019},
+ journal = {Advances in Astrobiology and Biogeophysics},
+ author = {Brucato, John Robert and Fornaro, Teresa},
+ pages = {183--204},
+ publisher = {Springer, Cham},
+ url = {https://link.springer.com/chapter/10.1007/978-3-319-96175-0_9},
+ doi = {10.1007/978-3-319-96175-0{\_}9},
+ issn = {16131851}
+}
+
+@incollection{Brucato2019RoleConditionsb,
+ title = {{Role of Mineral Surfaces in Prebiotic Processes and Space-Like Conditions}},
+ year = {2019},
+ author = {Brucato, John Robert and Fornaro, Teresa},
+ editor = {Cavalazzi, Barbara and Westall, Frances},
+ pages = {183--204},
+ publisher = {Springer International Publishing},
+ url = {http://link.springer.com/10.1007/978-3-319-96175-0_9},
+ doi = {10.1007/978-3-319-96175-0{\_}9}
+}
+
+@article{Kashyap2004S.,
+ title = {{S ( 1 ) .}},
+ year = {2004},
+ journal = {Matrix},
+ author = {Kashyap, Navin and Siegel, Paul H},
+ number = {6},
+ pages = {1327--1331},
+ volume = {50},
+ doi = {10.1215/00127094-2009-003}
+}
+
+@article{Soukup2015SamplingAnalyses,
+ title = {{Sampling soils for mineralogical analyses}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Soukup, D. A. and Drees, L. R. and Lynn, W. C.},
+ month = {10},
+ pages = {1--11},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C1},
+ keywords = {Sample preservation, Sampling plan, Sampling strategy, Site selection, Soil mineralogical studies, Soil variability, Specific-site characteristics}
+}
+
+@article{White2015ScanningMicroscopy,
+ title = {{Scanning electron microscopy}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {White, G. Norman},
+ month = {10},
+ pages = {269--297},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C10},
+ keywords = {Compositional characteristics, Energy dispersive x-ray spectrometry, Polished block, Sample preparation, Scanning electron microscopy, Single mineral grains, Soil mineral identification, Thin sections, Visual characteristics}
+}
+
+@article{Silberg2004SCHEMA-guidedRecombination,
+ title = {{SCHEMA-guided protein recombination}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Silberg, Jonathan J. and Endelman, Jeffrey B. and Arnold, Frances H.},
+ number = {2003},
+ pages = {35--42},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88004-2},
+ issn = {00766879},
+ pmid = {15289059}
+}
+
+@article{Cherry2004ScreeningResistance,
+ title = {{Screening for oxidative resistance}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Cherry, Joel R. and Lamsa, Michael H.},
+ number = {M},
+ pages = {167--175},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88015-7},
+ issn = {00766879},
+ pmid = {15289070}
+}
+
+@article{Aharoni2011ScreeningFormation,
+ title = {{Screening Methodologies for Glycosidic Bond Formation}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Aharoni, Amir and Withers, Stephen G.},
+ pages = {605--620},
+ volume = {2},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch25},
+ keywords = {Directed evolution, Flow cytometry, Glycosyltransferases, Glycosynthases, High-throughput screening}
+}
+
+@article{Shang2015SelectiveSediments,
+ title = {{Selective dissolution techniques for mineral analysis of soils and sediments}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Shang, Chao and Zelazny, Lucian W.},
+ month = {10},
+ pages = {33--80},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C3},
+ keywords = {Carbonate removal, Mineral analysis, Phosphorus fractionation schemes, Sediment samples, Selective dissolution techniques, Selective sequential extraction, Sequential fractionation, Soil samples, Trace metal distributions}
+}
+
+@article{MattiaBizzarri2018SilicaChemistry,
+ title = {{Silica Metal Oxide Vesicles Catalyze Comprehensive Prebiotic Chemistry}},
+ year = {2018},
+ journal = {Chemistry – A European Journal},
+ author = {Mattia Bizzarri, Bruno and Botta, Lorenzo and P{\'{e}}rez-Valverde, Maritza Iveth and Saladino, Raffaele and Di Mauro, Ernesto and Garc{\'{i}}a-Ruiz, Juan Manuel},
+ number = {32},
+ month = {6},
+ pages = {8126--8132},
+ volume = {24},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/chem.201706162 https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201706162 https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/chem.201706162},
+ doi = {10.1002/CHEM.201706162},
+ issn = {1521-3765},
+ pmid = {29603465},
+ keywords = {biomolecules and condensing agents, catalysis, formamide, prebiotic chemistry, silica microdrops}
+}
+
+@article{Wang2011SilkBioengineering,
+ title = {{Silk Proteins - Biomaterials and Bioengineering}},
+ year = {2011},
+ journal = {Protein Engineering Handbook},
+ author = {Wang, Xiaoqin and Cebe, Peggy and Kaplan, David. L.},
+ pages = {939--959},
+ url = {http://doi.wiley.com/10.1002/9783527634026.ch37},
+ isbn = {9783527634026},
+ doi = {10.1002/9783527634026.ch37}
+}
+
+@article{Shrivastava2000SimulationsBilayer,
+ title = {{Simulations of ion permeation through a potassium channel: Molecular dynamics of KcsA in a phospholipid bilayer}},
+ year = {2000},
+ journal = {Biophysical Journal},
+ author = {Shrivastava, Indira H. and Sansom, Mark S.P.},
+ number = {2},
+ pages = {557--570},
+ volume = {78},
+ publisher = {Biophysical Society},
+ doi = {10.1016/S0006-3495(00)76616-1},
+ issn = {00063495}
+}
+
+@article{Mamajanov2021Single-moleculeFeasibility,
+ title = {{Single-molecule origin of life scenario: Necessity and feasibility}},
+ year = {2021},
+ journal = {Physics of Life Reviews},
+ author = {Mamajanov, Irena},
+ month = {9},
+ pages = {143--144},
+ volume = {38},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S157106452100021X},
+ doi = {10.1016/j.plrev.2021.04.007},
+ issn = {15710645},
+ pmid = {34274248}
+}
+
+@article{Kagami2004Single-strandedShuffling,
+ title = {{Single-stranded DNA family shuffling}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Kagami, Osamu and Kikuchi, Miho and Harayama, Shigeaki},
+ pages = {11--21},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88002-9},
+ issn = {00766879},
+ pmid = {15289057}
+}
+
+@article{Winz2012Site-specificChemistry,
+ title = {{Site-specific terminal and internal labeling of RNA by poly(A) polymerase tailing and copper-catalyzed or copper-free strain-promoted click chemistry}},
+ year = {2012},
+ journal = {Nucleic Acids Research},
+ author = {Winz, Marie Luise and Samanta, Ayan and Benzinger, Dirk and J{\"{a}}schke, Andres},
+ number = {10},
+ volume = {40},
+ isbn = {1362-4962 (Electronic){\textbackslash}r0305-1048 (Linking)},
+ doi = {10.1093/nar/gks062},
+ issn = {03051048},
+ pmid = {22344697}
+}
+
+@article{Milner-White2005Sitesnests,
+ title = {{Sites for phosphates and iron-sulfur thiolates in the first membranes: 3 to 6 residue anion-binding motifs (nests)}},
+ year = {2005},
+ journal = {Origins of Life and Evolution of the Biosphere},
+ author = {Milner-White, E. James and Russell, Michael J.},
+ number = {1},
+ month = {2},
+ pages = {19--27},
+ volume = {35},
+ doi = {10.1007/S11084-005-4582-7},
+ issn = {01696149},
+ pmid = {15889648},
+ keywords = {Anion, Hydrothermal, Inorganic membrane, Iron-sulfur proteins, Origin of life, Phosphate, Pre-biotic, Protonmotive force, RNA world, Thiolates}
+}
+
+@article{Russell2020SixMackinawite,
+ title = {{Six ‘Must-Have’ Minerals for Life’s Emergence: Olivine, Pyrrhotite, Bridgmanite, Serpentine, Fougerite and Mackinawite}},
+ year = {2020},
+ journal = {Life},
+ author = {Russell, Michael and Ponce, Adrian},
+ number = {11},
+ month = {11},
+ pages = {291},
+ volume = {10},
+ publisher = {MDPI AG},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/33228029 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC7699418 https://www.mdpi.com/2075-1729/10/11/291},
+ doi = {10.3390/life10110291},
+ issn = {2075-1729},
+ pmid = {33228029},
+ keywords = {Hadean, astrobiology, carbonic ocean, emergence of life, exoplanets, proton gradient, redox gradient, solar system, submarine alkaline vents}
+}
+
+@article{Raanan2020SmallNetwork,
+ title = {{Small protein folds at the root of an ancient metabolic network}},
+ year = {2020},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Raanan, Hagai and Poudel, Saroj and Pike, Douglas H. and Nanda, Vikas and Falkowski, Paul G.},
+ number = {13},
+ pages = {7193--7199},
+ volume = {117},
+ doi = {10.1073/pnas.1914982117},
+ issn = {10916490},
+ pmid = {32188785},
+ keywords = {Biological networks, Electron transfer, Ferredoxin, Flavodoxin, Rossmann fold}
+}
+
+@book{Cohaut2013Small-AngleTechniques,
+ title = {{Small-Angle Scattering Techniques}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Cohaut, N. and Tchoubar, D.},
+ edition = {2},
+ number = {C},
+ pages = {177--211},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00008-1},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00008-1},
+ issn = {15724352},
+ keywords = {Clay–polymer nanocomposite, Light, Neutron, Small-angle scattering, Swelling clay mineral, X-ray}
+}
+
+@book{Lambert2013Smectite-polymerNanocomposites,
+ title = {{Smectite-polymer nanocomposites}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Lambert, J. F. and Bergaya, F.},
+ edition = {2},
+ pages = {679--706},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00021-3},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00021-3},
+ issn = {15724352},
+ keywords = {Biopolymers, Clay-polymer nanocomposites, Preparation methods, Smectites}
+}
+
+@article{Vepraskas2015SoilApplications,
+ title = {{Soil micromorphology: Concepts, techniques, and applications}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Vepraskas, M. J. and Wilson, M. A.},
+ month = {10},
+ pages = {191--225},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C7},
+ keywords = {Dyes, Quantitative analysis, Sampling, Sampling method, Site selection, Soil micromorphology, Stains, Thin section examination}
+}
+
+@book{Bergaya2013SomeMinerals,
+ title = {{Some other materials related to clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Bergaya, F. and Lagaly, G.},
+ edition = {2},
+ pages = {743},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00024-9},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00024-9},
+ issn = {15724352}
+}
+
+@article{Jorgensen2007SpecialPolarization,
+ title = {{Special Issue on Polarization}},
+ year = {2007},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Jorgensen, William L.},
+ number = {6},
+ month = {11},
+ pages = {1877--1877},
+ volume = {3},
+ url = {https://pubs.acs.org/doi/10.1021/ct700252g},
+ doi = {10.1021/ct700252g},
+ issn = {1549-9618}
+}
+
+@article{Andricioaei2007SpecializedSimulations,
+ title = {{Specialized methods for improving ergodic sampling using molecular dynamics and Monte Carlo simulations}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Andricioaei, Ioan},
+ pages = {277--322},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}8},
+ issn = {01726218}
+}
+
+@techreport{2004SPECIFICAREA,
+ title = {{SPECIFIC SURFACE AREA}},
+ year = {2004},
+ booktitle = {Pharmacopeial Forum},
+ number = {4},
+ pages = {1465},
+ volume = {30},
+ publisher = {The United States Pharmacopeial Convention, Inc.},
+ keywords = {SSA2004}
+}
+
+@article{Chryssikos2017SpectralAnalysis,
+ title = {{Spectral Manipulation and Introduction to Multivariate Analysis}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Chryssikos, G. D. and Gates, W. P.},
+ pages = {64--106},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00004-7},
+ issn = {15724352},
+ keywords = {Band decomposition, Beer–Lambert law, Calibration, Chemometrics, Clay mineral, Derivative analysis, IR, IR spectroscopy, Principal Component Analysis (PCA), Principal Component Regression (PCR), Process monitoring, Projection to Latent Structures (PLS), Raman, Raman spectroscopy, Smoothing, Validation}
+}
+
+@article{Berezovsky2003SpellingStructure,
+ title = {{Spelling protein structure}},
+ year = {2003},
+ journal = {Journal of Biomolecular Structure and Dynamics},
+ author = {Berezovsky, Igor N. and Kirzhner, Alla and Kirzhner, Valery M. and Trifonov, Edward N.},
+ number = {3},
+ pages = {327--339},
+ volume = {21},
+ doi = {10.1080/07391102.2003.10506929},
+ issn = {15380254},
+ keywords = {Loop-n-lock elements, Protein structure, Proteomic code, Prototype units, Sequence/structure prototype, Spelling protein structure}
+}
+
+@misc{2021Sphinx,
+ title = {{Sphinx}},
+ year = {2021},
+ publisher = {Georg Brandl and the Sphinx team},
+ url = {https://www.sphinx-doc.org/en/master/index.html}
+}
+
+@article{Chipot2007SpringerIntroduction,
+ title = {{Springer Series in Chemical Physics: Introduction}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Chipot, Christophe and Shell, M. Scott and Pohorille, Andrew},
+ pages = {1--31},
+ volume = {86},
+ publisher = {Springer New York},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}1},
+ issn = {01726218}
+}
+
+@article{Lavikainen2015StabilityModels,
+ title = {{Stability of dioctahedral 2:1 phyllosilicate edge structures based on pyrophyllite models}},
+ year = {2015},
+ journal = {Theoretical Chemistry Accounts},
+ author = {Lavikainen, Lasse P. and Hirvi, Janne T. and Kasa, Seppo and Schatz, Timothy and Pakkanen, Tapani A.},
+ number = {9},
+ month = {9},
+ pages = {1--8},
+ volume = {134},
+ publisher = {Springer New York LLC},
+ url = {https://link.springer.com/article/10.1007/s00214-015-1715-6},
+ doi = {10.1007/S00214-015-1715-6/TABLES/1},
+ issn = {1432881X},
+ keywords = {Clay, Cleavage, Edge, Phyllosilicate, Pyrophyllite, Surface}
+}
+
+@incollection{2005StabilityProteins,
+ title = {{Stability of Proteins}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {487--510},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch17},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch17}
+}
+
+@article{Zhao2004StaggeredRecombination,
+ title = {{Staggered extension process in vitro DNA recombination}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Zhao, Huimin},
+ number = {1994},
+ pages = {42--49},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88005-4},
+ issn = {00766879},
+ pmid = {15289060}
+}
+
+@article{Miao2016StereochemicalEngineering,
+ title = {{Stereochemical Control of Enzymatic Carbon–Carbon Bond-Forming Michael-Type Additions by “Substrate Engineering”}},
+ year = {2016},
+ journal = {European Journal of Organic Chemistry},
+ author = {Miao, Yufeng and Tepper, Pieter G. and Geertsema, Edzard M. and Poelarends, Gerrit J.},
+ doi = {10.1002/ejoc.201601126},
+ issn = {10990690},
+ pmid = {27917069},
+ keywords = {Catalytic promiscuity, Enzyme catalysis, Michael addition, Substituent effects, Substrate engineering}
+}
+
+@article{Chen2015StereochemistryBonds,
+ title = {{Stereochemistry of enzymatic water addition to C = C bonds}},
+ year = {2015},
+ journal = {Biotechnology Advances},
+ author = {Chen, Bi-Shuang and Otten, Linda G. and Hanefeld, Ulf},
+ number = {5},
+ month = {9},
+ pages = {526--546},
+ volume = {33},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/S0734975015000208},
+ doi = {10.1016/j.biotechadv.2015.01.007},
+ issn = {07349750}
+}
+@article{Carnell1999,
+ title = {{Stereoinversions using microbial redox-reactions.}},
+ year = {1999},
+ journal = {Advances in biochemical engineering/biotechnology},
+ author = {Carnell, a J},
+ pages = {57--72},
+ volume = {63},
+ issn = {0724-6145},
+ pmid = {9933981},
+ keywords = {deracemization, epimerase, microbial, redox, stereoinversion}
+}
+
+@article{Bourg2017,
+ title = {{Stern Layer Structure and Energetics at Mica-Water Interfaces}},
+ year = {2017},
+ journal = {Journal of Physical Chemistry C},
+ author = {Bourg, Ian C. and Lee, Sang Soo and Fenter, Paul and Tournassat, Christophe},
+ number = {17},
+ month = {5},
+ pages = {9402--9412},
+ volume = {121},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.7b01828},
+ issn = {19327455}
+}
+
+@article{Porion2007,
+ title = {{Structural and dynamical properties of the water molecules confined in dense clay sediments: A study combining2H NMR spectroscopy and multiscale numerical modeling}},
+ year = {2007},
+ journal = {Journal of Physical Chemistry C},
+ author = {Porion, Patrice and Michot, Laurent J. and Faug{\`{e}}re, Anne Marie and Delville, Alfred},
+ number = {14},
+ month = {4},
+ pages = {5441--5453},
+ volume = {111},
+ doi = {10.1021/jp067907p},
+ issn = {19327447}
+}
+
+@article{Friedlander2015,
+ title = {{Structural and spectroscopic changes to natural nontronite induced by experimental impacts between 10 and 40 GPa}},
+ year = {2015},
+ journal = {Journal of Geophysical Research E: Planets},
+ author = {Friedlander, Lonia R. and Glotch, Timothy D. and Bish, David L. and Dyar, M. Darby and Sharp, Thomas G. and Sklute, Elizabeth C. and Michalski, Joseph R.},
+ number = {5},
+ month = {5},
+ pages = {888--912},
+ volume = {120},
+ publisher = {Blackwell Publishing Ltd},
+ url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014JE004638 https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2014JE004638 https://agupubs.onlinelibrary.wiley.com/doi/10.1002/2014JE004638},
+ doi = {10.1002/2014JE004638},
+ issn = {21699100},
+ keywords = {Mars, geochemistry, phyllosilicates, shock metamorphism, spectroscopy}
+}
+
+@misc{Catterall2015,
+ title = {{Structural basis for pharmacology of voltage-gated sodium and calcium channels}},
+ year = {2015},
+ booktitle = {Molecular Pharmacology},
+ author = {Catterall, William A. and Swanson, Teresa M.},
+ number = {1},
+ month = {7},
+ pages = {141--150},
+ volume = {88},
+ publisher = {American Society for Pharmacology and Experimental Therapy},
+ doi = {10.1124/mol.114.097659},
+ issn = {15210111},
+ pmid = {25848093}
+}
+
+@article{Lee2009,
+ title = {{Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds}},
+ year = {2009},
+ journal = {Journal of Biological Chemistry},
+ author = {Lee, Cheng-Chung and Kuo, Chih-Jung and Ko, Tzu-Ping and Hsu, Min-Feng and Tsui, Yao-Chen and Chang, Shih-Cheng and Yang, Syaulan and Chen, Shu-Jen and Chen, Hua-Chien and Hsu, Ming-Chu and Shih, Shin-Ru and Liang, Po-Huang and Wang, Andrew H.J.},
+ number = {12},
+ month = {3},
+ pages = {7646--7655},
+ volume = {284},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/19144641 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2658058 http://www.jbc.org/lookup/doi/10.1074/jbc.M807947200},
+ doi = {10.1074/jbc.M807947200},
+ issn = {0021-9258}
+}
+
+@article{Zhou2014,
+ title = {{Structure and dynamic properties of water saturated CTMA-montmorillonite: molecular dynamics simulations}},
+ year = {2014},
+ journal = {Applied Clay Science},
+ author = {Zhou, Qing and Shen, Wei and Zhu, Jianxi and Zhu, Runliang and He, Hongping and Zhou, Jinhong and Yuan, Peng},
+ month = {8},
+ pages = {62--71},
+ volume = {97-98},
+ publisher = {Elsevier Ltd},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0169131714001938},
+ doi = {10.1016/j.clay.2014.05.029},
+ issn = {01691317},
+ keywords = {Confining effect, Interlayer structures, Mobility, Molecular dynamic, Organo-montmorillonite, Water saturated condition}
+}
+
+@article{Tommaso2010,
+ title = {{Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations}},
+ year = {2010},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Tommaso, Devis Di and Leeuw, Nora H. de},
+ number = {4},
+ month = {1},
+ pages = {894--901},
+ volume = {12},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2010/cp/b915329b https://pubs.rsc.org/en/content/articlelanding/2010/cp/b915329b},
+ doi = {10.1039/B915329B},
+ issn = {1463-9084}
+}
+
+@article{Arab2003,
+ title = {{Structure and dynamics of the interlayer water in an uncharged 2 : 1 clay}},
+ year = {2003},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Arab, Mehdi and Bougeard, Daniel and Smirnov, Konstantin S.},
+ number = {20},
+ month = {10},
+ pages = {4699--4707},
+ volume = {5},
+ doi = {10.1039/b307486b},
+ issn = {14639076}
+}
+
+@article{Marry2008,
+ title = {{Structure and dynamics of water at a clay surface from molecular dynamics simulation}},
+ year = {2008},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {Marry, Virginie and Rotenberg, Benjamin and Turq, Pierre},
+ number = {32},
+ month = {8},
+ pages = {4802--4813},
+ volume = {10},
+ publisher = {The Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2008/cp/b807288d https://pubs.rsc.org/en/content/articlelanding/2008/cp/b807288d},
+ doi = {10.1039/b807288d},
+ issn = {14639076}
+}
+
+@article{Szczerba2016,
+ title = {{Structure and dynamics of Water-Smectite interfaces: Hydrogen bonding and the origin of the sharp O-Dw/O-Hw infrared band from molecular simulations}},
+ year = {2016},
+ journal = {Clays and Clay Minerals},
+ author = {Szczerba, Marek and Kuligiewicz, Artur and Derkowski, Arkadiusz and Gionis, Vassilis and Chryssikos, Georgios D. and Kalinichev, Andrey G.},
+ number = {4},
+ month = {8},
+ pages = {452--471},
+ volume = {64},
+ publisher = {Clay Minerals Society},
+ url = {www.clays.org/JOURNAL/JournalDeposits.html},
+ doi = {10.1346/CCMN.2016.0640409},
+ issn = {15528367},
+ keywords = {Adsorbed water, Clay-water interface, Infrared spectroscopy, Molecular dynamics, Smectite}
+}
+
+@article{Catterall2014,
+ title = {{Structure and function of voltage-gated sodium channels at atomic resolution}},
+ year = {2014},
+ journal = {Experimental Physiology},
+ author = {Catterall, William A},
+ number = {1},
+ month = {1},
+ pages = {35--51},
+ volume = {99},
+ url = {http://doi.wiley.com/10.1113/expphysiol.2013.071969},
+ doi = {10.1113/expphysiol.2013.071969},
+ issn = {09580670}
+}
+
+@incollection{Brigatti2013,
+ title = {{Structure and Mineralogy of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Brigatti, M.F. and Gal{\'{a}}n, E. and Theng, B.K.G.},
+ pages = {21--81},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B978008098258800002X},
+ doi = {10.1016/B978-0-08-098258-8.00002-X},
+ keywords = {Allophane, Clay minerals, Imogolite, Mixed-layer clays, Modulated layer silicates, Phyllosilicates 1:1, Phyllosilicates 2:1}
+}
+
+@article{Pouvreau2017,
+ title = {{Structure of Hydrated Gibbsite and Brucite Edge Surfaces: DFT Results and Further Development of the ClayFF Classical Force Field with Metal–O–H Angle Bending Terms}},
+ year = {2017},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Pouvreau, Maxime and Greathouse, Jeffery A. and Cygan, Randall T. and Kalinichev, Andrey G.},
+ number = {27},
+ month = {7},
+ pages = {14757--14771},
+ volume = {121},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acs.jpcc.7b05362},
+ doi = {10.1021/acs.jpcc.7b05362},
+ issn = {1932-7447}
+}
+
+@article{Pouvreau2019,
+ title = {{Structure of Hydrated Kaolinite Edge Surfaces: DFT Results and Further Development of the ClayFF Classical Force Field with Metal–O–H Angle Bending Terms}},
+ year = {2019},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Pouvreau, Maxime and Greathouse, Jeffery A. and Cygan, Randall T. and Kalinichev, Andrey G.},
+ number = {18},
+ month = {5},
+ pages = {11628--11638},
+ volume = {123},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.9b00514 https://pubs.acs.org/doi/10.1021/acs.jpcc.9b00514},
+ doi = {10.1021/acs.jpcc.9b00514},
+ issn = {1932-7447}
+}
+
+@article{Pan2018,
+ title = {{Structure of the human voltage-gated sodium channel Na v 1.4 in complex with {$\beta$}1}},
+ year = {2018},
+ journal = {Science},
+ author = {Pan, Xiaojing and Li, Zhangqiang and Zhou, Qiang and Shen, Huaizong and Wu, Kun and Huang, Xiaoshuang and Chen, Jiaofeng and Zhang, Juanrong and Zhu, Xuechen and Lei, Jianlin and Xiong, Wei and Gong, Haipeng and Xiao, Bailong and Yan, Nieng},
+ number = {6412},
+ month = {10},
+ pages = {eaau2486},
+ volume = {362},
+ publisher = {American Association for the Advancement of Science},
+ url = {http://www.sciencemag.org/lookup/doi/10.1126/science.aau2486},
+ doi = {10.1126/science.aau2486},
+ issn = {10959203}
+}
+
+@article{Johnson2005,
+ title = {{STRUCTURE, FUNCTION, AND FORMATION OF BIOLOGICAL IRON-SULFUR CLUSTERS}},
+ year = {2005},
+ journal = {http://dx.doi.org/10.1146/annurev.biochem.74.082803.133518},
+ author = {Johnson, Deborah C. and Dean, Dennis R. and Smith, Archer D. and Johnson, Michael K.},
+ month = {6},
+ pages = {247--281},
+ volume = {74},
+ publisher = { Annual Reviews },
+ url = {https://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.74.082803.133518},
+ doi = {10.1146/ANNUREV.BIOCHEM.74.082803.133518},
+ issn = {00664154},
+ pmid = {15952888},
+ keywords = {chaperones, cysteine desulfurase, iron-sulfur clusters, scaffolds}
+}
+
+@article{Matthews1999,
+ title = {{Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes}},
+ year = {1999},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Matthews, D. A. and Dragovich, P. S. and Webber, S. E. and Fuhrman, S. A. and Patick, A. K. and Zalman, L. S. and Hendrickson, T. F. and Love, R. A. and Prins, T. J. and Marakovits, J. T. and Zhou, R. and Tikhe, J. and Ford, C. E. and Meador, J. W. and Ferre, R. A. and Brown, E. L. and Binford, S. L. and Brothers, M. A. and DeLisle, D. M. and Worland, S. T.},
+ number = {20},
+ month = {9},
+ pages = {11000--11007},
+ volume = {96},
+ publisher = {National Academy of Sciences},
+ doi = {10.1073/pnas.96.20.11000},
+ issn = {00278424}
+}
+
+@article{Alder1959,
+ title = {{Studies in Molecular Dynamics. I. General Method}},
+ year = {1959},
+ journal = {The Journal of Chemical Physics},
+ author = {Alder, B. J. and Wainwright, T. E.},
+ number = {2},
+ month = {8},
+ pages = {459--466},
+ volume = {31},
+ url = {http://aip.scitation.org/doi/10.1063/1.1730376},
+ doi = {10.1063/1.1730376},
+ issn = {0021-9606}
+}
+
+@article{Ehlmann2011,
+ title = {{Subsurface water and clay mineral formation during the early history of Mars}},
+ year = {2011},
+ author = {Ehlmann, Bethany L and Mustard, John F and Murchie, Scott L and Bibring, Jean-Pierre and Meunier, Alain and Fraeman, Abigail A and Langevin, Yves},
+ doi = {10.1038/nature10582}
+}
+
+@incollection{LokaBharathi2008,
+ title = {{Sulfur Cycle}},
+ year = {2008},
+ booktitle = {Encyclopedia of Ecology, Five-Volume Set},
+ author = {Loka Bharathi, P. A.},
+ month = {1},
+ pages = {3424--3431},
+ publisher = {Elsevier Inc.},
+ isbn = {9780080914565},
+ doi = {10.1016/B978-008045405-4.00761-8},
+ keywords = {Ecology, Geochemical implications, Oxidative cycle, Reductive cycle, Sulfur, Sulfur flux}
+}
+
+@article{Arute2019a,
+ title = {{Supplementary information for "Quantum supremacy using a programmable superconducting processor"}},
+ year = {2019},
+ journal = {Nature},
+ author = {Arute, Frank and Arya, Kunal and Babbush, Ryan and Bacon, Dave and Bardin, Joseph C. and Barends, Rami and Biswas, Rupak and Boixo, Sergio and Brandao, Fernando G. S. L. and Buell, David A. and Burkett, Brian and Chen, Yu and Chen, Zijun and Chiaro, Ben and Collins, Roberto and Courtney, William and Dunsworth, Andrew and Farhi, Edward and Foxen, Brooks and Fowler, Austin and Gidney, Craig and Giustina, Marissa and Graff, Rob and Guerin, Keith and Habegger, Steve and Harrigan, Matthew P. and Hartmann, Michael J. and Ho, Alan and Hoffmann, Markus R. and Huang, Trent and Humble, Travis S. and Isakov, Sergei V. and Jeffrey, Evan and Jiang, Zhang and Kafri, Dvir and Kechedzhi, Kostyantyn and Kelly, Julian and Klimov, Paul V. and Knysh, Sergey and Korotkov, Alexander N. and Kostritsa, Fedor and Landhuis, David and Lindmark, Mike and Lucero, Erik and Lyakh, Dmitry and Mandra, Salvatore and McClean, Jarrod R. and McEwen, Matt and Megrant, Anthony and Mi, Xiao and Michielsen, Kristel and Mohseni, Masoud and Mutus, Josh and Naaman, Ofer and Neeley, Matthew and Neill, Charles and Niu, Murphy Yuezhen and Ostby, Eric and Petukhov, Andre and Platt, John C. and Quintana, Chris and Rieffel, Eleanor G. and Roushan, Pedram and Rubin, Nicholas C. and Sank, Daniel and Satzinger, Kevin J. and Smelyanskiy, Vadim and Sung, Kevin J. and Trevithick, Matthew D. and Vainsencher, Amit and Villalonga, Benjamin and White, Theodore and Yao, Z. Jamie and Yeh, Ping and Zalcman, Adam and Neven, Hartmut and Martinis, John M.},
+ number = {July},
+ volume = {574},
+ publisher = {Springer US},
+ url = {http://arxiv.org/abs/1910.11333%0Ahttp://dx.doi.org/10.1038/s41586-019-1666-5},
+ isbn = {4158601916},
+ doi = {10.1038/s41586-019-1666-5},
+ issn = {14764687},
+ arxivId = {1910.11333}
+}
+
+@incollection{Schoonheydt2013,
+ title = {{Surface and Interface Chemistry of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Schoonheydt, R.A. and Johnston, C.T.},
+ pages = {139--172},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982588000055},
+ doi = {10.1016/B978-0-08-098258-8.00005-5},
+ keywords = {Dyes, Films, Hydroxyls, Kaolinite, Proteins, Smectites, Transition metal ions, Water}
+}
+
+@incollection{Michot2013,
+ title = {{Surface Area and Porosity}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Michot, L. J. and Villi{\'{e}}ras, F.},
+ number = {C},
+ month = {1},
+ pages = {319--332},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00012-3},
+ issn = {15724352},
+ keywords = {Gas adsorption, Porosity, Specific surface area, Surface heterogeneity, Swelling, Water adsorption}
+}
+
+@article{Liu2020,
+ title = {{Surface Chemisty, Microstructure, and Rheology of Thixotropic 1-D Sepiolite Gels}},
+ year = {2020},
+ journal = {Clays and Clay Minerals},
+ author = {Liu, Pengfei and Du, Mingyong and Clode, Peta and Li, Hualong and Liu, Jishan and Leong, Yee Kwong},
+ number = {1},
+ month = {2},
+ pages = {9--22},
+ volume = {68},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1007/s42860-019-00050-z},
+ doi = {10.1007/s42860-019-00050-z},
+ issn = {15528367},
+ keywords = {1-D material, Ageing, Dispersion, Drilling fluids, Microstructure, Temperature}
+}
+
+@article{Sposito1999,
+ title = {{Surface geochemistry of the clay minerals}},
+ year = {1999},
+ journal = {Proceedings of the National Academy of Sciences},
+ author = {Sposito, Garrison and Skipper, Neal T. and Sutton, Rebecca and Park, S.-h. and Soper, Alan K. and Greathouse, Jeffery A.},
+ number = {7},
+ month = {3},
+ pages = {3358--3364},
+ volume = {96},
+ publisher = {National Academy of Sciences},
+ url = {www.pnas.org. http://www.pnas.org/cgi/doi/10.1073/pnas.96.7.3358},
+ doi = {10.1073/pnas.96.7.3358},
+ issn = {0027-8424},
+ pmid = {10097044}
+}
+
+@article{Sposito1999b,
+ title = {{Surface geochemistry of the clay minerals}},
+ year = {1999},
+ journal = {Proceedings of the National Academy of Sciences},
+ author = {Sposito, Garrison and Skipper, Neal T. and Sutton, Rebecca and Park, Sung Ho and Soper, Alan K. and Greathouse, Jeffery A.},
+ number = {7},
+ month = {3},
+ pages = {3358--3364},
+ volume = {96},
+ publisher = {National Academy of Sciences},
+ url = {https://www.pnas.org/content/96/7/3358 https://www.pnas.org/content/96/7/3358.abstract},
+ doi = {10.1073/PNAS.96.7.3358},
+ issn = {0027-8424},
+ pmid = {10097044}
+}
+
+@article{Teich-McGoldrick2015,
+ title = {{Swelling Properties of Montmorillonite and Beidellite Clay Minerals from Molecular Simulation: Comparison of Temperature, Interlayer Cation, and Charge Location Effects}},
+ year = {2015},
+ journal = {The Journal of Physical Chemistry C},
+ author = {Teich-McGoldrick, Stephanie L. and Greathouse, Jeffery A. and Jov{\'{e}}-Col{\'{o}}n, Carlos F. and Cygan, Randall T.},
+ number = {36},
+ month = {9},
+ pages = {20880--20891},
+ volume = {119},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acs.jpcc.5b03253},
+ doi = {10.1021/acs.jpcc.5b03253},
+ issn = {1932-7447}
+}
+
+@article{Muchowska2019,
+ title = {{Synthesis and breakdown of universal metabolic precursors promoted by iron}},
+ year = {2019},
+ journal = {Nature 2019 569:7754},
+ author = {Muchowska, Kamila B. and Varma, Sreejith J. and Moran, Joseph},
+ number = {7754},
+ month = {5},
+ pages = {104--107},
+ volume = {569},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s41586-019-1151-1},
+ isbn = {1278512799},
+ doi = {10.1038/s41586-019-1151-1},
+ issn = {1476-4687},
+ pmid = {31043728},
+ keywords = {Chemical origin of life, Iron}
+}
+
+@article{Ilgen2017,
+ title = {{Synthesis and characterization of redox-active ferric nontronite}},
+ year = {2017},
+ journal = {Chemical Geology},
+ author = {Ilgen, A. G. and Kukkadapu, R. K. and Dunphy, D. R. and Artyushkova, K. and Cerrato, J. M. and Kruichak, J. N. and Janish, M. T. and Sun, C. J. and Argo, J. M. and Washington, R. E.},
+ month = {10},
+ pages = {1--12},
+ volume = {470},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/j.chemgeo.2017.07.010},
+ issn = {00092541},
+ keywords = {Arsenic oxidation, Iron speciation, Phyllosilicate, Smectite, Synthetic nontronite}
+}
+
+@article{Chemtob2015,
+ title = {{Synthesis and structural characterization of ferrous trioctahedral smectites: Implications for clay mineral genesis and detectability on Mars}},
+ year = {2015},
+ journal = {Journal of Geophysical Research: Planets},
+ author = {Chemtob, Steven M. and Nickerson, Ryan D. and Morris, Richard V. and Agresti, David G. and Catalano, Jeffrey G.},
+ number = {6},
+ month = {6},
+ pages = {1119--1140},
+ volume = {120},
+ publisher = {Blackwell Publishing Ltd},
+ url = {http://doi.wiley.com/10.1002/2014JE004763},
+ doi = {10.1002/2014JE004763},
+ issn = {21699097},
+ keywords = {Mars, VNIR, X-ray diffraction, X-ray spectroscopy, clay mineralogy, smectite}
+}
+
+@incollection{Jaber2013,
+ title = {{Synthesis of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Jaber, M. and Komarneni, S. and Zhou, C. H.},
+ pages = {223--241},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00009-2},
+ issn = {15724352},
+ keywords = {Beidellite, Chlorite, Fluorohectorite, Functionalization, Grafting, Hectorite, Industrial synthesis, Inorganic-organic hybride materials, Kaolinite, Laponite, Layered materials, Montmorillonite, Organoclay synthesis, Organohectorite, Saponite, Smectite}
+}
+
+@article{Karypidou2018,
+ title = {{Synthesis, biological evaluation and molecular modeling of a novel series of fused 1,2,3-triazoles as potential anti-coronavirus agents}},
+ year = {2018},
+ journal = {Bioorganic and Medicinal Chemistry Letters},
+ author = {Karypidou, Konstantina and Ribone, Sergio R. and Quevedo, Mario A. and Persoons, Leentje and Pannecouque, Christophe and Helsen, Christine and Claessens, Frank and Dehaen, Wim},
+ number = {21},
+ month = {11},
+ pages = {3472--3476},
+ volume = {28},
+ publisher = {Elsevier Ltd},
+ doi = {10.1016/j.bmcl.2018.09.019},
+ issn = {14643405},
+ keywords = {1,2,3-triazole, 3CL protease, Biological evaluation, Coronavirus, Respiratory syndrome}
+}
+
+@article{HPII65,
+ title = {{Synthetic route to an aromatic analog of strigol}},
+ year = {1979},
+ journal = {The Journal of Organic Chemistry},
+ author = {Kendall, Peter M. and Johnson, Julius V. and Cook, C. E.},
+ number = {9},
+ month = {4},
+ pages = {1421--1424},
+ volume = {44},
+ url = {http://pubs.acs.org/doi/abs/10.1021/jo01323a013},
+ doi = {10.1021/jo01323a013},
+ issn = {0022-3263}
+}
+
+@incollection{Pacioni2015,
+ title = {{Synthetic Routes for the Preparation of Silver Nanoparticles}},
+ year = {2015},
+ booktitle = {Silver Nanoparticle Applications: In the Fabrication and Design of Medical and Biosensing Devices},
+ author = {Pacioni, Natalia L and Borsarelli, Claudio D and Rey, Valentina and Veglia, Alicia V},
+ editor = {Alarcon, Emilio I and Griffith, May and Udekwu, Klas I},
+ pages = {13--46},
+ publisher = {Springer International Publishing},
+ url = {https://doi.org/10.1007/978-3-319-11262-6_2 http://link.springer.com/10.1007/978-3-319-11262-6_2},
+ address = {Cham},
+ isbn = {978-3-319-11262-6},
+ doi = {10.1007/978-3-319-11262-6{\_}2}
+}
+
+@article{Yeh2004,
+ title = {{System-size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry B},
+ author = {Yeh, In Chul and Hummer, Gerhard},
+ number = {40},
+ month = {10},
+ pages = {15873--15879},
+ volume = {108},
+ publisher = { American Chemical Society },
+ url = {https://pubs.acs.org/sharingguidelines},
+ doi = {10.1021/jp0477147},
+ issn = {15206106}
+}
+
+@article{Thiebault2020,
+ title = {{Technology Raw and modified clays and clay minerals for the removal of pharmaceutical products from aqueous solutions : State of the art and future perspectives solutions : State of the art and future perspectives}},
+ year = {2020},
+ journal = {Critical Reviews in Environmental Science and Technology},
+ author = {Thiebault, Thomas and Thiebault, Thomas},
+ number = {14},
+ month = {7},
+ pages = {1451--1514},
+ volume = {50},
+ publisher = {Taylor {\&} Francis},
+ url = {https://www.tandfonline.com/doi/abs/10.1080/10643389.2019.1663065 https://www.tandfonline.com/action/journalInformation?journalCode=best20 https://doi.org/10.1080/10643389.2019.1663065},
+ doi = {10.1080/10643389.2019.1663065},
+ issn = {1064-3389},
+ keywords = {Pharmaceutical products, adsorption, and water treatment operators, clay minerals, ion exchange, onmental compartments challenges the, pps, practicable, products, scientific community, the occurrence of pharmaceutical, thermal treatment, to find suitable and, water treatment, within envir-}
+}
+
+@article{Schlick2013,
+ title = {{The 2013 Nobel Prize in Chemistry Celebrates Computations in Chemistry and Biology}},
+ year = {2013},
+ journal = {SIAM News},
+ author = {Schlick, T},
+ number = {10},
+ pages = {1--4},
+ volume = {46},
+ url = {http://siam.org/pdf/news/2122.pdf}
+}
+
+@article{Bean2007,
+ title = {{The action potential in mammalian central neurons}},
+ year = {2007},
+ journal = {Nature Reviews Neuroscience},
+ author = {Bean, Bruce P.},
+ number = {6},
+ month = {6},
+ pages = {451--465},
+ volume = {8},
+ publisher = {Nature Publishing Group},
+ url = {http://www.nature.com/articles/nrn2148},
+ doi = {10.1038/nrn2148},
+ issn = {1471-003X},
+ keywords = {Animal Genetics and Genomics, Behavioral Sciences, Biological Techniques, Biomedicine, Neurobiology, Neurosciences, general}
+}
+
+@article{Case2005,
+ title = {{The Amber biomolecular simulation programs}},
+ year = {2005},
+ journal = {Journal of Computational Chemistry},
+ author = {Case, David A. and Cheatham, Thomas E. and Darden, Tom and Gohlke, Holger and Luo, Ray and Merz, Kenneth M. and Onufriev, Alexey and Simmerling, Carlos and Wang, Bing and Woods, Robert J.},
+ number = {16},
+ month = {12},
+ pages = {1668--1688},
+ volume = {26},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.20290 https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20290 https://onlinelibrary.wiley.com/doi/10.1002/jcc.20290},
+ doi = {10.1002/jcc.20290},
+ issn = {0192-8651},
+ pmid = {16200636},
+ keywords = {Amber, biomolecular simulation programs}
+}
+
+@book{Rapaport2004a,
+ title = {{The Art of Molecular Dynamics Simulation}},
+ year = {2004},
+ author = {Rapaport, D. C.},
+ month = {4},
+ publisher = {Cambridge University Press},
+ url = {https://www.cambridge.org/core/product/identifier/9780511816581/type/book},
+ isbn = {9780521825689},
+ doi = {10.1017/CBO9780511816581}
+}
+
+@book{Rapaport2004,
+ title = {{The Art of Molecular Dynamics Simulation}},
+ year = {2004},
+ booktitle = {The Art of Molecular Dynamics Simulation},
+ author = {Rapaport, D. C.},
+ month = {4},
+ publisher = {Cambridge University Press},
+ doi = {10.1017/cbo9780511816581}
+}
+
+@incollection{Rich1960,
+ title = {{The Clay Fraction Of Soils}},
+ year = {1960},
+ author = {Rich, C.I. and Thomas, G.W.},
+ pages = {1--39},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S0065211308600802},
+ doi = {10.1016/S0065-2113(08)60080-2}
+}
+
+@incollection{Levy1985,
+ title = {{The Constrained Search Formulation of Density Functional Theory}},
+ year = {1985},
+ booktitle = {Density Functional Methods In Physics},
+ author = {Levy, Mel and Perdew, John P},
+ editor = {Dreizler, Reiner M and da Provid{\^{e}}ncia, João},
+ pages = {11--30},
+ publisher = {Springer US},
+ url = {https://doi.org/10.1007/978-1-4757-0818-9_2},
+ address = {Boston, MA},
+ isbn = {978-1-4757-0818-9},
+ doi = {10.1007/978-1-4757-0818-9{\_}2}
+}
+
+@article{Lowenstein1954,
+ title = {{THE DISTRIBUTION OF ALUMINUM IN THE TETRA-HEDRA OF SILICATES AND ALUMINATES}},
+ year = {1954},
+ journal = {The American mineralogist.},
+ author = {Lowenstein, Walter},
+ number = {1},
+ pages = {92--96},
+ volume = {39},
+ issn = {0003-004X}
+}
+
+@misc{dlpoly,
+ title = {{THE DL{\_}POLY{\_}2 USER MANUAL}},
+ year = {2006},
+ author = {Smith, W. and Forester, T. R. and Todorov, I. T. and Leslie, M.},
+ publisher = {CCLRC Daresbury Laboratory},
+ address = {Daresbury}
+}
+
+@article{Merlet2014,
+ title = {{The electric double layer has a life of its own}},
+ year = {2014},
+ journal = {Journal of Physical Chemistry C},
+ author = {Merlet, Céline and Limmer, David T. and Salanne, Mathieu and Van Roij, René and Madden, Paul A. and Chandler, David and Rotenberg, Benjamin},
+ number = {32},
+ month = {8},
+ pages = {18291--18298},
+ volume = {118},
+ publisher = {American Chemical Society},
+ doi = {10.1021/jp503224w},
+ issn = {19327455},
+ arxivId = {1404.0343}
+}
+
+@article{Martra2014,
+ title = {{The formation and self-assembly of long prebiotic oligomers produced by the condensation of unactivated amino acids on oxide surfaces}},
+ year = {2014},
+ journal = {Angewandte Chemie - International Edition},
+ author = {Martra, Gianmario and Deiana, Chiara and Sakhno, Yuriy and Barberis, Ilvis and Fabbiani, Marco and Pazzi, Marco and Vincenti, Marco},
+ number = {18},
+ month = {4},
+ pages = {4671--4674},
+ volume = {53},
+ publisher = {Wiley-VCH Verlag},
+ doi = {10.1002/anie.201311089},
+ issn = {15213773},
+ pmid = {24616011},
+ keywords = {amino acids, catalytic polymerization, self-assembly, silica, titanium dioxide}
+}
+
+@article{Meleshyn2005,
+ title = {{The gap between crystalline and osmotic swelling of Na-montmorillonite: A Monte Carlo study}},
+ year = {2005},
+ journal = {The Journal of Chemical Physics},
+ author = {Meleshyn, Artur and Bunnenberg, Claus},
+ number = {3},
+ month = {1},
+ pages = {034705},
+ volume = {122},
+ publisher = {American Institute of Physics Inc.},
+ url = {http://aip.scitation.org/doi/10.1063/1.1834499},
+ doi = {10.1063/1.1834499},
+ issn = {0021-9606}
+}
+
+@article{Frost2002,
+ title = {{The Garfield and Uley nontronites - An infrared spectroscopic comparison}},
+ year = {2002},
+ journal = {Spectrochimica Acta - Part A Molecular and Biomolecular Spectroscopy},
+ author = {Frost, Ray L. and Kloprogge, J. Theo and Ding, Zhe},
+ number = {9},
+ month = {7},
+ pages = {1881--1894},
+ volume = {58},
+ publisher = {Spectrochim Acta A Mol Biomol Spectrosc},
+ url = {https://pubmed.ncbi.nlm.nih.gov/12164487/},
+ doi = {10.1016/S1386-1425(01)00638-2},
+ issn = {13861425},
+ pmid = {12164487},
+ keywords = {Dehydroxylation, FT-IR, Infrared emission spectroscopy, Montmorillonite, Nontronite, Smectite}
+}
+
+@article{Marra2003,
+ title = {{The Genome Sequence of the SARS-Associated Coronavirus}},
+ year = {2003},
+ journal = {Science},
+ author = {Marra, Marco A.},
+ number = {5624},
+ month = {5},
+ pages = {1399--1404},
+ volume = {300},
+ publisher = {Science},
+ url = {https://www.sciencemag.org/lookup/doi/10.1126/science.1085953},
+ doi = {10.1126/science.1085953},
+ issn = {00368075},
+ pmid = {12730501}
+}
+
+@article{Michels2020,
+ title = {{The Impact of Thermal History on Water Adsorption in a Synthetic Nanolayered Silicate with Intercalated Li+or Na+}},
+ year = {2020},
+ journal = {Journal of Physical Chemistry C},
+ author = {Michels, L. and Da Fonseca, C. L.S. and M{\'{e}}heust, Y. and Alto{\'{e}}, M. A.S. and Dos Santos, E. C. and Grassi, G. and Droppa, R. and Knudsen, K. D. and Cavalcanti, L. P. and Hunvik, K. W.B. and Fossum, J. O. and Da Silva, G. J. and Bordallo, H. N.},
+ number = {45},
+ month = {11},
+ pages = {24690--24703},
+ volume = {124},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.0c05847},
+ issn = {19327455}
+}
+
+@article{Dalai2017,
+ title = {{The Influence of Mineral Matrices on the Thermal Behavior of Glycine}},
+ year = {2017},
+ journal = {Origins of Life and Evolution of Biospheres},
+ author = {Dalai, Punam and Pleyer, Hannes Lukas and Strasdeit, Henry and Fox, Stefan},
+ number = {4},
+ month = {12},
+ pages = {427--452},
+ volume = {47},
+ publisher = {Springer Netherlands},
+ doi = {10.1007/s11084-016-9523-0},
+ issn = {15730875},
+ pmid = {27757771},
+ keywords = {Clay minerals, Dry heating, Early Earth and Mars, Evaporites, Glycine homopeptides, Martian regolith simulants}
+}
+
+@article{Falconer1933,
+ title = {{The laws of soil colloidal behavior: XIII. Osmotic imbibition}},
+ year = {1933},
+ journal = {Soil Science},
+ author = {Falconer, Joseph G. and Mattson, Sante},
+ number = {4},
+ pages = {317--327},
+ volume = {36},
+ doi = {10.1097/00010694-193310000-00007}
+}
+
+@article{MULJADI1966,
+ title = {{THE MECHANISM OF PHOSPHATE ADSORPTION BY KAOLINITE, GIBBSITE, AND PSEUDOBOEHMITE: PART I. THE ISOTHERMS AND THE EFFECT OF pH ON ADSORPTION}},
+ year = {1966},
+ journal = {Journal of Soil Science},
+ author = {MULJADI, D. and POSNER, A. M. and QUIRK, J. P.},
+ number = {2},
+ pages = {212--228},
+ volume = {17},
+ doi = {10.1111/j.1365-2389.1966.tb01467.x},
+ issn = {13652389}
+}
+
+@article{Benner2000,
+ title = {{The missing organic molecules on Mars}},
+ year = {2000},
+ journal = {Proceedings of the National Academy of Sciences of the United States of America},
+ author = {Benner, Steven A. and Devine, Kevin G. and Matveeva, Lidia N. and Powell, David H.},
+ number = {6},
+ month = {3},
+ pages = {2425--2430},
+ volume = {97},
+ doi = {10.1073/pnas.040539497},
+ issn = {00278424},
+ pmid = {10706606},
+ keywords = {Astrobiology, Exobiology, Organic compounds, Viking}
+}
+
+@article{Berendsen1987,
+ title = {{The missing term in effective pair potentials}},
+ year = {1987},
+ journal = {Journal of Physical Chemistry},
+ author = {Berendsen, H. J.C. and Grigera, J. R. and Straatsma, T. P.},
+ number = {24},
+ pages = {6269--6271},
+ volume = {91},
+ doi = {10.1021/j100308a038},
+ issn = {00223654}
+}
+
+@article{Grauby1994,
+ title = {{The nontronite-saponite series: An experimental approach}},
+ year = {1994},
+ journal = {European Journal of Mineralogy},
+ author = {Grauby, Olivier and Petit, Sabine and Decarreau, Alain and Baronnet, Alain},
+ number = {1},
+ month = {2},
+ pages = {99--112},
+ volume = {6},
+ publisher = {Schweizerbart},
+ doi = {10.1127/ejm/6/1/0099},
+ issn = {0935-1221},
+ keywords = {ditrioctahedral lattice, nontronite, saponite, solid solution, spectroscopic methods, synthesis}
+}
+
+@article{Evans1985,
+ title = {{The Nose–Hoover thermostat}},
+ year = {1985},
+ journal = {The Journal of Chemical Physics},
+ author = {Evans, Denis J. and Holian, Brad Lee},
+ number = {8},
+ month = {10},
+ pages = {4069--4074},
+ volume = {83},
+ publisher = {American Institute of PhysicsAIP},
+ url = {http://aip.scitation.org/doi/10.1063/1.449071},
+ doi = {10.1063/1.449071},
+ issn = {0021-9606},
+ keywords = {COMPUTERIZED SIMULATION, LIQUID STRUCTURE, MOLECULAR DYNAMICS CALCULATION, NONEQUILIBRIUM, SHEAR FLOW, VISCOSITY}
+}
+
+@misc{Neese2012,
+ title = {{The ORCA program system}},
+ year = {2012},
+ booktitle = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
+ author = {Neese, Frank},
+ number = {1},
+ pages = {73--78},
+ volume = {2},
+ publisher = {Wiley Interdiscip. Rev.: Comput. Mol. Sci.},
+ doi = {10.1002/wcms.81},
+ issn = {17590876}
+}
+
+@article{VanderWerf1994,
+ title = {{The potential of lyases for the industrial production of optically active compounds}},
+ year = {1994},
+ journal = {Trends in Biotechnology},
+ author = {van der Werf, Mariët J. and van den Tweel, Will J.J. and Kamphuis, Johan and Hartmans, Sybe and de Bont, Jan A.M.},
+ number = {3},
+ month = {3},
+ pages = {95--103},
+ volume = {12},
+ url = {http://linkinghub.elsevier.com/retrieve/pii/0167779994901120},
+ isbn = {0167-7799},
+ doi = {10.1016/0167-7799(94)90112-0},
+ issn = {01677799},
+ pmid = {7764830}
+}
+
+@inproceedings{Kunz2004,
+ title = {{The present state of affairs with Hofmeister effects}},
+ year = {2004},
+ booktitle = {Current Opinion in Colloid and Interface Science},
+ author = {Kunz, W. and Lo Nostro, P. and Ninham, B. W.},
+ number = {1-2},
+ month = {8},
+ pages = {1--18},
+ volume = {9},
+ publisher = {Elsevier},
+ doi = {10.1016/j.cocis.2004.05.004},
+ issn = {13590294},
+ keywords = {Dispersion forces, Electrolytes, Hofmeister effects, Hydrophobic interactions, Molecular interactions}
+}
+
+@incollection{Dohrmann2013,
+ title = {{The Role of Clays for Safe Storage of Nuclear Waste}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Dohrmann, R. and Kaufhold, S. and Lundqvist, B.},
+ number = {C},
+ month = {1},
+ pages = {677--710},
+ volume = {5},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B978008098259500024X},
+ doi = {10.1016/B978-0-08-098259-5.00024-X},
+ keywords = {Argillaceous host rock, Bentonite buffer, Long-term safety, Multi-barrier system}
+}
+
+@inproceedings{PerezSanchez2014,
+ title = {{The role of high performance computing in Bioinformatics}},
+ year = {2014},
+ booktitle = {Proceedings IWBBIO 2014},
+ author = {Per´ez-S´anchez, Horacio and Cecilia, Jos´e M. and Merelli, Ivan},
+ pages = {494--506},
+ keywords = {bioin-, computational biology, formatics, heterogeneous computing, hpc, parallel computing}
+}
+
+@article{Resch2015,
+ title = {{The selective addition of water}},
+ year = {2015},
+ journal = {Catalysis Science {\&} Technology},
+ author = {Resch, Verena and Hanefeld, Ulf},
+ number = {3},
+ pages = {1385--1399},
+ volume = {5},
+ url = {http://xlink.rsc.org/?DOI=C4CY00692E},
+ isbn = {10.1039/C4CY00692E},
+ doi = {10.1039/C4CY00692E},
+ issn = {2044-4753}
+}
+
+@article{Resch2015b,
+ title = {{The selective addition of water}},
+ year = {2015},
+ journal = {Catalysis Science {\&} Technology},
+ author = {Resch, Verena and Hanefeld, Ulf},
+ number = {3},
+ pages = {1385--1399},
+ volume = {5},
+ url = {http://xlink.rsc.org/?DOI=C4CY00692E},
+ isbn = {10.1039/C4CY00692E},
+ doi = {10.1039/C4CY00692E},
+ issn = {2044-4753}
+}
+
+@article{Newman1984,
+ title = {{The Significance of Clays in Agriculture and Soils}},
+ year = {1984},
+ journal = {Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences},
+ author = {Newman, A C D},
+ pages = {375--389},
+ volume = {311},
+ url = {https://about.jstor.org/terms}
+}
+
+@article{Yang2015,
+ title = {{The size and structure of selected hydrated ions and implications for ion channel selectivity}},
+ year = {2015},
+ journal = {RSC Advances},
+ author = {Yang, Zhong Hua},
+ number = {2},
+ pages = {1213--1219},
+ volume = {5},
+ url = {www.rsc.org/advances http://xlink.rsc.org/?DOI=C4RA10987B},
+ doi = {10.1039/c4ra10987b},
+ issn = {20462069}
+}
+
+@article{KosterVanGroos2009,
+ title = {{The stability of methane hydrate intercalates of montmorillonite and nontronite: Implications for carbon storage in ocean-floor environments}},
+ year = {2009},
+ journal = {American Mineralogist},
+ author = {Koster Van Groos, A F and Guggenheim, Stephen},
+ pages = {372--379},
+ volume = {94},
+ url = {http://pubs.geoscienceworld.org/msa/ammin/article-pdf/94/2-3/372/3622971/20_3018Koster.pdf},
+ doi = {10.2138/am.2009.3018},
+ keywords = {Methane hydrate, carbon cycle, carbon storage, smectite}
+}
+
+@article{Skipper1991a,
+ title = {{The structure of interlayer water in vermiculite}},
+ year = {1991},
+ journal = {The Journal of Chemical Physics},
+ author = {Skipper, N. T. and Soper, A. K. and McConnell, J. D.C.},
+ number = {8},
+ pages = {5751--5760},
+ volume = {94},
+ doi = {10.1063/1.460457},
+ issn = {00219606}
+}
+
+@article{Norrish1954,
+ title = {{THE SWELLING OF MONTMORILLONITE}},
+ year = {1954},
+ author = {Norrish, K}
+}
+
+@article{Cockell2000,
+ title = {{The Ultraviolet Environment of Mars: Biological Implications Past, Present, and Future}},
+ year = {2000},
+ journal = {Icarus},
+ author = {Cockell, Charles S. and Catling, David C. and Davis, Wanda L. and Snook, Kelly and Kepner, Ray L. and Lee, Pascal and McKay, Christopher P.},
+ number = {2},
+ month = {8},
+ pages = {343--359},
+ volume = {146},
+ doi = {10.1006/icar.2000.6393},
+ issn = {00191035},
+ pmid = {11543504},
+ keywords = {Atmospheres, Evolution, Exobiology, Mars, Photochemistry, Radiative transfer}
+}
+
+@article{Gerlach2014,
+ title = {{The X-Ray Standing Wave Technique}},
+ year = {2014},
+ journal = {Handbook of Spectroscopy: Second, Enlarged Edition},
+ author = {Gerlach, Alexander and Schreiber, Frank},
+ month = {6},
+ pages = {1507--1522},
+ volume = {4-4},
+ publisher = {Wiley Blackwell},
+ isbn = {9783527654703},
+ doi = {10.1002/9783527654703.CH44},
+ keywords = {Organic adsorbates, PTCDA, Photo yield, Standing wave, Wave fields, X-ray standing wave}
+}
+
+@techreport{Hirshfeld1977,
+ title = {{THEORETICA CHIMICA ACTA Bonded-Atom Fragments for Describing Molecular Charge Densities}},
+ year = {1977},
+ booktitle = {Theoret. Claim. Acta (Berl.)},
+ author = {Hirshfeld, F L},
+ pages = {129--138},
+ volume = {44},
+ keywords = {Bonded atoms-, Dipole moments, Electron density-, Populations-}
+}
+
+@article{Sheng2017,
+ title = {{Theoretical Study of Enzyme Promiscuity: Mechanisms of Hydration and Carboxylation Activities of Phenolic Acid Decarboxylase}},
+ year = {2017},
+ journal = {ACS Catalysis},
+ author = {Sheng, Xiang and Himo, Fahmi},
+ number = {3},
+ month = {3},
+ pages = {1733--1741},
+ volume = {7},
+ url = {http://pubs.acs.org/doi/10.1021/acscatal.6b03249},
+ doi = {10.1021/acscatal.6b03249},
+ issn = {2155-5435},
+ keywords = {cluster approach, density functional theory, enantioselectivity, enzyme promiscuity, quantum chemistry, reaction mechanism}
+}
+
+@article{Hernandez-Haro2014,
+ title = {{Theoretical study on the influence of the Mg2+ and Al3+ octahedral cations on the vibrational spectra of the hydroxy groups of dioctahedral 2:1 phyllosilicate models}},
+ year = {2014},
+ journal = {Journal of Molecular Modeling 2014 20:9},
+ author = {Hern{\'{a}}ndez-Haro, N. and Ortega-Castro, J. and Pruneda, M. and Sainz-D{\'{i}}az, C. I. and Hern{\'{a}}ndez-Laguna, A.},
+ number = {9},
+ month = {9},
+ pages = {1--10},
+ volume = {20},
+ publisher = {Springer},
+ url = {https://link.springer.com/article/10.1007/s00894-014-2402-6},
+ doi = {10.1007/S00894-014-2402-6},
+ issn = {0948-5023},
+ keywords = {Characterization and Evaluation of Materials, Computer Appl. in Life Sciences, Computer Applications in Chemistry, Molecular Medicine, Theoretical and Computational Chemistry}
+}
+
+@article{Tantillo1998,
+ title = {{Theozymes and compuzymes: theoretical models for biological catalysis}},
+ year = {1998},
+ journal = {Current Opinion in Chemical Biology},
+ author = {Tantillo, Dean J. and Jiangang, Chen and Houk, Kendall N.},
+ number = {6},
+ month = {1},
+ pages = {743--750},
+ volume = {2},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/S1367593198801129},
+ doi = {10.1016/S1367-5931(98)80112-9},
+ issn = {13675931}
+}
+
+@article{Li2020,
+ title = {{Therapeutic options for the 2019 novel coronavirus (2019-nCoV)}},
+ year = {2020},
+ journal = {Nature Reviews Drug Discovery},
+ author = {Li, Guangdi and De Clercq, Erik},
+ number = {3},
+ month = {3},
+ pages = {149--150},
+ volume = {19},
+ publisher = {NLM (Medline)},
+ url = {http://www.nature.com/articles/d41573-020-00016-0},
+ doi = {10.1038/d41573-020-00016-0},
+ issn = {1474-1776}
+}
+
+@article{Li2020b,
+ title = {{Therapeutic options for the 2019 novel coronavirus (2019-nCoV)}},
+ year = {2020},
+ journal = {Nature Reviews Drug Discovery},
+ author = {Li, Guangdi and De Clercq, Erik},
+ number = {3},
+ month = {3},
+ pages = {149--150},
+ volume = {19},
+ publisher = {NLM (Medline)},
+ url = {http://www.nature.com/articles/d41573-020-00016-0 http://dx.doi.org/10.1038/d41573-020-00016-0},
+ doi = {10.1038/d41573-020-00016-0},
+ issn = {1474-1776},
+ pmid = {32127666}
+}
+
+@incollection{Rouquerol2013,
+ title = {{Thermal Analysis}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Rouquerol, F. and Rouquerol, J. and Llewellyn, P.},
+ month = {1},
+ pages = {361--379},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-098259-5.00014-7},
+ issn = {15724352},
+ keywords = {Conventional thermal analysis, Differential thermal analysis, Evolved gas detection, Sample-controlled thermal analysis, Thermodilatometry, Thermogravimetry}
+}
+
+@incollection{Heller-Kallai2013,
+ title = {{Thermally modified clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Heller-Kallai, L.},
+ pages = {411--433},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00014-6},
+ issn = {15724352},
+ keywords = {Freezing, acidity, de- and rehydration, dehydroxylation, porosity, structural changes, texture}
+}
+
+@article{Heinz2013,
+ title = {{Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: The INTERFACE force field}},
+ year = {2013},
+ journal = {Langmuir},
+ author = {Heinz, Hendrik and Lin, Tzu Jen and Kishore Mishra, Ratan and Emami, Fateme S.},
+ number = {6},
+ month = {2},
+ pages = {1754--1765},
+ volume = {29},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/la3038846},
+ doi = {10.1021/LA3038846/SUPPL{\_}FILE/LA3038846{\_}SI{\_}002.ZIP},
+ issn = {07437463},
+ pmid = {23276161}
+}
+
+@incollection{Blanc2013,
+ title = {{Thermodynamics of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Blanc, P. and Vieillard, P. and Gailhanou, H. and Gaboreau, S.},
+ pages = {173--210},
+ volume = {5},
+ publisher = {Elsevier B.V.},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00006-7},
+ issn = {15724352},
+ keywords = {Calorimetry, Clay minerals, Equilibrium, Models, Thermodynamic}
+}
+
+@article{Kuligiewicz2017,
+ title = {{Tightly bound water in smectites}},
+ year = {2017},
+ journal = {American Mineralogist},
+ author = {Kuligiewicz, Artur and Derkowski, Arkadiusz},
+ number = {5},
+ month = {5},
+ pages = {1073--1090},
+ volume = {102},
+ publisher = {Walter de Gruyter GmbH},
+ url = {https://www.degruyter.com/document/doi/10.2138/am-2017-5918/html},
+ doi = {10.2138/am-2017-5918},
+ issn = {19453027},
+ keywords = {Smectite, activation energy, clay-bound water, dehydration, thermogravimetry}
+}
+
+@article{Lagardere2018,
+ title = {{Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields}},
+ year = {2018},
+ journal = {Chemical Science},
+ author = {Lagard{\`{e}}re, Louis and Jolly, Luc-Henri and Lipparini, Filippo and Aviat, Félix and Stamm, Benjamin and Jing, Zhifeng F. and Harger, Matthew and Torabifard, Hedieh and Cisneros, G. Andrés and Schnieders, Michael J. and Gresh, Nohad and Maday, Yvon and Ren, Pengyu Y. and Ponder, Jay W. and Piquemal, Jean-Philip},
+ number = {4},
+ pages = {956--972},
+ volume = {9},
+ url = {http://xlink.rsc.org/?DOI=C7SC04531J},
+ doi = {10.1039/C7SC04531J},
+ issn = {2041-6520}
+}
+
+@article{deprot,
+ title = {{Total Synthesis of (±)-Paeonilide}},
+ year = {2006},
+ journal = {Organic Letters},
+ author = {Wang, Chenying and Liu, Jikai and Ji, Yanhua and Zhao, Jingfeng and Li, Liang and Zhang, Hongbin},
+ number = {12},
+ month = {6},
+ pages = {2479--2481},
+ volume = {8},
+ url = {http://pubs.acs.org/doi/abs/10.1021/ol060382z},
+ doi = {10.1021/ol060382z},
+ issn = {1523-7060}
+}
+
+@misc{Price2000,
+ title = {{Toward More Accurate Model Intermolecular Potentials for Organic Molecules}},
+ year = {2000},
+ booktitle = {Reviews in Computational Chemistry},
+ author = {Price, Sarah L},
+ month = {1},
+ pages = {225--289},
+ series = {Reviews in Computational Chemistry},
+ url = {https://doi.org/10.1002/9780470125915.ch4},
+ isbn = {9780470125915},
+ doi = {doi:10.1002/9780470125915.ch4}
+}
+
+@article{Murray2000,
+ title = {{Traditional and new applications for kaolin, smectite, and palygorskite: A general overview}},
+ year = {2000},
+ journal = {Applied Clay Science},
+ author = {Murray, HH},
+ pages = {207--221},
+ volume = {17}
+}
+
+@incollection{bonds,
+ title = {{Typical interatomic distances: organic compounds}},
+ year = {2006},
+ booktitle = {International Tables for Crystallography},
+ author = {Allen, F. H. and Watson, D. G. and Brammer, L. and Orpen, A. G. and Taylor, R.},
+ editor = {Prince, E},
+ month = {10},
+ pages = {790--811},
+ publisher = {Springer Netherlands},
+ url = {https://doi.org/10.1107/97809553602060000621 http://xrpp.iucr.org/cgi-bin/itr?url_ver=Z39.88-2003&rft_dat=what%3Dchapter%26volid%3DCb%26chnumo%3D9o5%26chvers%3Dv0001},
+ address = {Dordrecht},
+ isbn = {978-1-4020-5408-2},
+ doi = {10.1107/97809553602060000621}
+}
+
+@article{Wan2021,
+ title = {{Uncertainty quantification in classical molecular dynamics}},
+ year = {2021},
+ journal = {Philosophical Transactions of the Royal Society A},
+ author = {Wan, Shunzhou and Sinclair, Robert C. and Coveney, Peter V.},
+ number = {2197},
+ month = {5},
+ volume = {379},
+ publisher = {{\\\}The Royal Society Publishing{\\\}},
+ url = {https://royalsocietypublishing.org/doi/abs/10.1098/rsta.2020.0082},
+ doi = {10.1098/RSTA.2020.0082},
+ keywords = {free energy calculation, molecular dynamics simulation, uncertainty quantification}
+}
+
+@book{Frenkel2002,
+ title = {{Understanding Molecular Simulation}},
+ year = {2002},
+ booktitle = {Understanding Molecular Simulation},
+ author = {Frenkel, Daan and Smit, Berend},
+ publisher = {Elsevier},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780122673511X50007},
+ isbn = {9780122673511},
+ doi = {10.1016/b978-0-12-267351-1.x5000-7}
+}
+
+@article{Badyal2004,
+ title = {{Understanding the effects of concentration on the solvation structure of Ca 2+ in aqueous solution. II: Insights into longer range order from neutron diffraction isotope substitution}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry A},
+ author = {Badyal, Yaspal S. and Barnes, Adrian C. and Cuello, Gabriel J. and Simonson, John M.},
+ number = {52},
+ month = {12},
+ pages = {11819--11827},
+ volume = {108},
+ doi = {10.1021/jp046476c},
+ issn = {10895639}
+}
+
+@book{Naumer1996,
+ title = {{Untersuchungsmethoden in der Chemie}},
+ year = {1996},
+ booktitle = {Untersuchungsmethoden in der Chemie},
+ editor = {Naumer, Hans and Heller, Wolfgang},
+ month = {12},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/9783527630929},
+ address = {Weinheim, Germany},
+ isbn = {9783527630929},
+ doi = {10.1002/9783527630929}
+}
+
+@article{Klauda2010,
+ title = {{Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types}},
+ year = {2010},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Klauda, Jeffery B. and Venable, Richard M. and Freites, J. Alfredo and O’Connor, Joseph W. and Tobias, Douglas J. and Mondragon-Ramirez, Carlos and Vorobyov, Igor and MacKerell, Alexander D. and Pastor, Richard W.},
+ number = {23},
+ month = {6},
+ pages = {7830--7843},
+ volume = {114},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/10.1021/jp101759q},
+ doi = {10.1021/jp101759q},
+ issn = {1520-6106}
+}
+
+@incollection{Marry2015,
+ title = {{Upscaling Strategies for Modeling Clay-Rock Properties}},
+ year = {2015},
+ booktitle = {Developments in Clay Science},
+ author = {Marry, Virginie and Rotenberg, Benjamin},
+ month = {1},
+ pages = {399--417},
+ volume = {6},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100027-4.00011-5},
+ issn = {15724352},
+ keywords = {Coarse-graining, Molecular simulation, Multiscale simulation, Representative elementary volume, Upscaling}
+}
+
+@article{Aguzzi2007,
+ title = {{Use of clays as drug delivery systems: Possibilities and limitations}},
+ year = {2007},
+ journal = {Applied Clay Science},
+ author = {Aguzzi, C. and Cerezo, P. and Viseras, C. and Caramella, C.},
+ number = {1-3},
+ month = {4},
+ pages = {22--36},
+ volume = {36},
+ publisher = {Elsevier},
+ doi = {10.1016/j.clay.2006.06.015},
+ issn = {01691317},
+ keywords = {Bioavailability, Cation-exchange, Clays, Modified drug release, Special excipients}
+}
+
+@article{Besson1983,
+ title = {{Use of diffraction and M{\"{o}}ssbauer methods for the structural and crystallochemical characterization of nontronites}},
+ year = {1983},
+ journal = {Journal of Applied Crystallography},
+ author = {Besson, G. and Bookin, A. S. and Dainyak, L. G. and Rautureau, M. and Tsipursky, S. I. and Tchoubar, C. and Drits, V. A.},
+ number = {4},
+ month = {8},
+ pages = {374--383},
+ volume = {16},
+ url = {http://scripts.iucr.org/cgi-bin/paper?S0021889883010651},
+ doi = {10.1107/S0021889883010651},
+ issn = {00218898}
+}
+
+@article{Bussi2020,
+ title = {{Using metadynamics to explore complex free-energy landscapes}},
+ year = {2020},
+ journal = {Nature Reviews Physics},
+ author = {Bussi, Giovanni and Laio, Alessandro},
+ number = {4},
+ month = {4},
+ pages = {200--212},
+ volume = {2},
+ publisher = {Springer Nature},
+ url = {www.nature.com/natrevphys},
+ doi = {10.1038/s42254-020-0153-0},
+ issn = {25225820},
+ keywords = {Computational science, Molecular dynamics}
+}
+
+@article{DeJong2010,
+ title = {{Utilizing high performance computing for chemistry: parallel computational chemistry}},
+ year = {2010},
+ journal = {Physical Chemistry Chemical Physics},
+ author = {de Jong, Wibe A. and Bylaska, Eric and Govind, Niranjan and Janssen, Curtis L. and Kowalski, Karol and M{\"{u}}ller, Thomas and Nielsen, Ida M. B. and van Dam, Hubertus J. J. and Veryazov, Valera and Lindh, Roland},
+ number = {26},
+ pages = {6896},
+ volume = {12},
+ url = {http://xlink.rsc.org/?DOI=c002859b},
+ doi = {10.1039/c002859b},
+ issn = {1463-9076}
+}
+
+@article{Vasu2016,
+ title = {{Van der Waals pressure and its effect on trapped interlayer molecules}},
+ year = {2016},
+ journal = {Nature Communications},
+ author = {Vasu, K. S. and Prestat, E. and Abraham, J. and Dix, J. and Kashtiban, R. J. and Beheshtian, J. and Sloan, J. and Carbone, P. and Neek-Amal, M. and Haigh, S. J. and Geim, A. K. and Nair, R. R.},
+ number = {1},
+ month = {11},
+ pages = {12168},
+ volume = {7},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/ncomms12168 https://www.nature.com/articles/ncomms12168/fig_tab http://www.nature.com/articles/ncomms12168},
+ doi = {10.1038/ncomms12168},
+ issn = {2041-1723},
+ keywords = {Nanoscience and technology, Surfaces, Thermodynamics, interfaces and thin films}
+}
+
+@article{DelRio2011,
+ title = {{Variability in sepiolite: Diffraction studies}},
+ year = {2011},
+ journal = {American Mineralogist},
+ author = {Del R{\'{i}}o, Manuel Sánchez and Garc{\'{i}}a-Romero, Emilia and Su{\'{a}}rez, Mercedes and Da Silva, Iván and Fuentes-Montero, Luis and Mart{\'{i}}nez-Criado, Gema},
+ number = {10},
+ month = {10},
+ pages = {1443--1454},
+ volume = {96},
+ publisher = {De Gruyter},
+ url = {https://www.degruyter.com/document/doi/10.2138/am.2011.3761/html},
+ doi = {10.2138/am.2011.3761},
+ issn = {0003004X},
+ keywords = {2D diffraction pattern, Ab initio simulations, Rietveld, SAED, SEM, Sepiolite, TEM, X-ray diffraction}
+}
+
+@techreport{Suarez,
+ title = {{Variability of the surface properties of sepiolite}},
+ author = {Suarez, M and Garcia-Romero, E},
+ keywords = {Electron microscopy, Microporosity, Sepiolite, Specific surface area BET, Texture}
+}
+
+@article{Boulard1992,
+ title = {{Vibrational spectra in fluoride crystals and glasses at normal and high pressures by computer simulation}},
+ year = {1992},
+ journal = {Journal of Non-Crystalline Solids},
+ author = {Boulard, B. and Kieffer, J. and Phifer, C. C. and Angell, C. A.},
+ number = {C},
+ month = {1},
+ pages = {350--358},
+ volume = {140},
+ publisher = {North-Holland},
+ doi = {10.1016/S0022-3093(05)80795-1},
+ issn = {00223093}
+}
+
+@misc{Wang2020,
+ title = {{Virtual Screening of Approved Clinic Drugs with Main Protease (3CLpro) Reveals Potential Inhibitory Effects on SARS-CoV-2}},
+ year = {2020},
+ author = {Wang, Qiang and Zhao, Ying and Chen, Xiaojia and Hong, An},
+ month = {3},
+ publisher = {Preprints},
+ url = {https://www.preprints.org/manuscript/202003.0144/v1},
+ keywords = {3CLpro, SARS-CoV-2, approved drugs, virtual screening}
+}
+
+@article{UIUC2016,
+ title = {{VMD User ’ s Guide Verstion 1.9.3}},
+ year = {2016},
+ author = {{UIUC}}
+}
+
+@article{Humphrey1996,
+ title = {{VMD: Visual molecular dynamics}},
+ year = {1996},
+ journal = {Journal of Molecular Graphics},
+ author = {Humphrey, William and Dalke, Andrew and Schulten, Klaus},
+ number = {1},
+ month = {2},
+ pages = {33--38},
+ volume = {14},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/0263785596000185},
+ doi = {10.1016/0263-7855(96)00018-5},
+ issn = {02637855}
+}
+
+@article{Catterall2012,
+ title = {{Voltage-gated sodium channels at 60: structure, function and pathophysiology}},
+ year = {2012},
+ journal = {The Journal of Physiology},
+ author = {Catterall, William A.},
+ number = {11},
+ month = {6},
+ pages = {2577--2589},
+ volume = {590},
+ url = {http://doi.wiley.com/10.1113/jphysiol.2011.224204},
+ doi = {10.1113/jphysiol.2011.224204},
+ issn = {00223751}
+}
+
+@article{Oakes2016,
+ title = {{Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations}},
+ year = {2016},
+ journal = {Current Topics in Membranes},
+ author = {Oakes, V. and Furini, S. and Domene, C.},
+ pages = {183--214},
+ volume = {78},
+ publisher = {Academic Press Inc.},
+ isbn = {9780128053867},
+ doi = {10.1016/bs.ctm.2015.12.002},
+ issn = {10635823},
+ keywords = {Conduction, Free energy methods, Ion channels, Permeation, Selectivity}
+}
+
+@article{Agnew1984,
+ title = {{Voltage-Regulated Sodium Channel Molecules}},
+ year = {1984},
+ journal = {Annual Review of Physiology},
+ author = {Agnew, W S},
+ number = {1},
+ month = {10},
+ pages = {517--530},
+ volume = {46},
+ publisher = {Annual Reviews},
+ url = {http://www.annualreviews.org/doi/10.1146/annurev.ph.46.030184.002505},
+ doi = {10.1146/annurev.ph.46.030184.002505},
+ issn = {0066-4278}
+}
+
+@article{Rotenberg2007,
+ title = {{Water and ions in clays: Unraveling the interlayer/micropore exchange using molecular dynamics}},
+ year = {2007},
+ journal = {Geochimica et Cosmochimica Acta},
+ author = {Rotenberg, Benjamin and Marry, Virginie and Vuilleumier, Rodolphe and Malikova, Natalie and Simon, Christian and Turq, Pierre},
+ number = {21},
+ month = {11},
+ pages = {5089--5101},
+ volume = {71},
+ doi = {10.1016/j.gca.2007.08.018},
+ issn = {00167037}
+}
+
+@article{Marry2011,
+ title = {{Water dynamics in hectorite clays: Infuence of temperature studied by coupling neutron spin echo and molecular dynamics}},
+ year = {2011},
+ journal = {Environmental Science and Technology},
+ author = {Marry, Virginie and Dubois, Emmanuelle and Malikova, Natalie and Durand-Vidal, Serge and Longeville, Stéphane and Breu, Josef},
+ number = {7},
+ month = {4},
+ pages = {2850--2855},
+ volume = {45},
+ doi = {10.1021/es1031932},
+ issn = {0013936X},
+ pmid = {21381672}
+}
+
+@article{Rotenberg2014,
+ title = {{Water in clay nanopores}},
+ year = {2014},
+ journal = {MRS Bulletin},
+ author = {Rotenberg, Benjamin},
+ number = {12},
+ month = {12},
+ pages = {1074--1081},
+ volume = {39},
+ publisher = {Materials Research Society},
+ doi = {10.1557/mrs.2014.251},
+ issn = {08837694},
+ keywords = {Water, ion exchange material, nanoscale, porosity, simulation}
+}
+
+@article{Kelch2019,
+ title = {{Water Trapping Dynamics in Carbohydrate-Populated Smectite Interlayer Nanopores}},
+ year = {2019},
+ journal = {Journal of Physical Chemistry C},
+ author = {Kelch, Sabrina E. and Ferrage, Eric and Lanson, Bruno and Charlet, Laurent and Aristilde, Ludmilla},
+ number = {47},
+ month = {11},
+ pages = {28816--28827},
+ volume = {123},
+ publisher = {American Chemical Society},
+ doi = {10.1021/acs.jpcc.9b09246},
+ issn = {19327455}
+}
+
+@article{Pozzuoli1992,
+ title = {{Weathering of biotite to vermiculite in Quaternary lahars from Monti Ernici, Central Italy}},
+ year = {1992},
+ journal = {Clay Minerals},
+ author = {Pozzuoli, A. and Vila, E. and Franco, E. and Ruiz-Amil, A. and De La Calle, C.},
+ number = {2},
+ month = {6},
+ pages = {175--184},
+ volume = {27},
+ publisher = {Mineralogical Society},
+ url = {https://www.cambridge.org/core/journals/clay-minerals/article/abs/weathering-of-biotite-to-vermiculite-in-quaternary-lahars-from-monti-ernici-central-italy/1F8CB47F988F7EF99326A87C04E17F44},
+ doi = {10.1180/claymin.1992.027.2.03},
+ issn = {0009-8558}
+}
+
+@book{Borisenko2004,
+ title = {{Wht is What in the Nanoworld A Handbook in Nanoscience and Nanotechnology}},
+ year = {2004},
+ author = {Borisenko, Victor E and Ossicini, Stefano},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ isbn = {3527404937}
+}
+
+@article{Hensen2002,
+ title = {{Why Clays Swell}},
+ year = {2002},
+ journal = {The Journal of Physical Chemistry B},
+ author = {Hensen, Emiel J. M. and Smit, Berend},
+ number = {49},
+ month = {12},
+ pages = {12664--12667},
+ volume = {106},
+ url = {https://pubs.acs.org/doi/10.1021/jp0264883},
+ doi = {10.1021/jp0264883},
+ issn = {1520-6106}
+}
+
+@incollection{Gates2013,
+ title = {{X-ray Absorption Spectroscopy}},
+ year = {2013},
+ booktitle = {Handbook of Clay Science},
+ author = {Gates, W.P.},
+ edition = {2},
+ month = {1},
+ pages = {137--160},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982595000068 http://dx.doi.org/10.1016/B978-0-08-098259-5.00006-8},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00006-8},
+ issn = {1572-4352},
+ keywords = {Ferrihydrite, K-edge, L-edge, Synthetic nontronite, Tetrahedral iron}
+}
+
+@article{Janssens2014,
+ title = {{X-Ray Fluorescence Analysis}},
+ year = {2014},
+ journal = {Handbook of Spectroscopy: Second, Enlarged Edition},
+ author = {Janssens, Koen},
+ month = {6},
+ pages = {449--506},
+ volume = {2-4},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/9783527654703.ch14 https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527654703.ch14 https://onlinelibrary.wiley.com/doi/10.1002/9783527654703.ch14},
+ isbn = {9783527654703},
+ doi = {10.1002/9783527654703.CH14},
+ keywords = {harmonics, instrumentation, matrix effects, photoelectric effect, scattering, spectrochemical determination}
+}
+
+@incollection{Sakharov2013,
+ title = {{X-ray Identification of Mixed-Layer Structures: Modelling of Diffraction Effects}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Sakharov, B. A. and Lanson, B.},
+ number = {C},
+ month = {1},
+ pages = {51--135},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00005-6},
+ issn = {15724352},
+ keywords = {Defective lamellar structures, Interstratification, Mixed layer structures, X-ray diffraction}
+}
+
+@incollection{Seyama2013,
+ title = {{X-Ray Photoelectron Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Seyama, H. and Soma, M. and Theng, B. K.G.},
+ number = {C},
+ month = {1},
+ pages = {161--176},
+ volume = {5},
+ doi = {10.1016/B978-0-08-098259-5.00007-X},
+ issn = {15724352},
+ keywords = {Auger parameter, Chemical bonding state, Chemical-state plot, Photoelectron microscopy, X-ray photoelectron diffraction, X-ray photoelectron spectroscopy (XPS)}
+}
+
+@article{Fink1964,
+ title = {{X-Ray Studies of Crystalline Swelling in Montmorillonites}},
+ year = {1964},
+ journal = {Soil Science Society of America Journal},
+ author = {Fink, D. H. and Thomas, G. W.},
+ number = {6},
+ month = {11},
+ pages = {747--750},
+ volume = {28},
+ publisher = {Wiley},
+ doi = {10.2136/SSSAJ1964.03615995002800060021X}
+}
+
+@article{Ilgen2019,
+ title = {{“Switching on” iron in clay minerals}},
+ year = {2019},
+ journal = {Environmental Science: Nano},
+ author = {Ilgen, A. G. and Kukkadapu, R. K. and Leung, K. and Washington, R. E.},
+ number = {6},
+ pages = {1704--1715},
+ volume = {6},
+ publisher = {Royal Society of Chemistry},
+ url = {http://xlink.rsc.org/?DOI=C9EN00228F},
+ doi = {10.1039/C9EN00228F},
+ issn = {2051-8153}
+}
+
+@book{AdamMoserKevinRange2008a,
+ title = {{基因的改变NIH Public Access}},
+ year = {2008},
+ booktitle = {Bone},
+ author = {Adam Moser, Kevin Range, and Darrin M. York},
+ number = {1},
+ pages = {1--7},
+ volume = {23},
+ isbn = {6176321972},
+ doi = {10.1038/jid.2014.371},
+ issn = {15378276},
+ pmid = {1000000221},
+ arxivId = {NIHMS150003},
+ keywords = {epiblast, gfp fusion, histone h2b-, icm, lineage specification, live imaging, mouse blastocyst, pdgfr {$\alpha$}, primitive endoderm}
+}
+
+@article{Boda2007StericChains,
+ title = {{Steric selectivity in Na channels arising from protein polarization and mobile side chains}},
+ year = {2007},
+ journal = {Biophysical Journal},
+ author = {Boda, Dezso and Nonner, Wolfgang and Valisk{\'{o}}, Mónika and Henderson, Douglas and Eisenberg, Bob and Gillespie, Dirk and Eisenberg, R. S.},
+ number = {6},
+ month = {9},
+ pages = {1960--1980},
+ volume = {93},
+ publisher = {Biophysical Society},
+ doi = {10.1529/biophysj.107.105478},
+ issn = {00063495}
+}
+
+@article{Dass2016StochasticSystems,
+ title = {{Stochastic Prebiotic Chemistry within Realistic Geological Systems}},
+ year = {2016},
+ journal = {ChemistrySelect},
+ author = {Dass, Avinash Vicholous and Hickman-Lewis, Keyron and Brack, André and Kee, Terence P. and Westall, Frances},
+ number = {15},
+ month = {9},
+ pages = {4906--4926},
+ volume = {1},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ url = {https://onlinelibrary.wiley.com/doi/full/10.1002/slct.201600829 https://onlinelibrary.wiley.com/doi/abs/10.1002/slct.201600829 https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/slct.201600829},
+ doi = {10.1002/SLCT.201600829},
+ issn = {2365-6549},
+ keywords = {Hadean, Origins of life, mineral surfaces, prebiotic chemistry, stochastic chemistry, systems chemistry}
+}
+
+@article{Karathanasis2015StructuralComponents,
+ title = {{Structural allocation of clay mineral elemental components}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Karathanasis, A. D.},
+ month = {10},
+ pages = {465--483},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C15},
+ keywords = {Bulk chemical analysis, Charge distribution, Chemical composition, Clay mineral elemental components, Layer silicate mineral groups, Soil clays, Structural allocation, Weathering trends}
+}
+
+@misc{Catterall2015StructuralChannels,
+ title = {{Structural basis for pharmacology of voltage-gated sodium and calcium channels}},
+ year = {2015},
+ booktitle = {Molecular Pharmacology},
+ author = {Catterall, William A. and Swanson, Teresa M.},
+ number = {1},
+ month = {7},
+ pages = {141--150},
+ volume = {88},
+ publisher = {American Society for Pharmacology and Experimental Therapy},
+ doi = {10.1124/mol.114.097659},
+ issn = {15210111},
+ pmid = {25848093}
+}
+
+@article{Wander2007StructureRust,
+ title = {{Structure and charge hopping dynamics in green rust}},
+ year = {2007},
+ journal = {Journal of Physical Chemistry C},
+ author = {Wander, Matthew C.F. and Rosso, Kevin M. and Schoonen, Martin A.A.},
+ number = {30},
+ month = {8},
+ pages = {11414--11423},
+ volume = {111},
+ doi = {10.1021/JP072762N},
+ issn = {19327447}
+}
+
+@article{Bhuiya2015StructureCerevisiae,
+ title = {{Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae}},
+ year = {2015},
+ journal = {Applied and Environmental Microbiology},
+ author = {Bhuiya, Mohammad Wadud and Lee, Soon Goo and Jez, Joseph M. and Yu, Oliver},
+ editor = {Brakhage, A. A.},
+ number = {12},
+ month = {6},
+ pages = {4216--4223},
+ volume = {81},
+ url = {http://aem.asm.org/lookup/doi/10.1128/AEM.00762-15},
+ doi = {10.1128/AEM.00762-15},
+ issn = {0099-2240}
+}
+
+@incollection{Brigatti2013StructureMinerals,
+ title = {{Structure and Mineralogy of Clay Minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Brigatti, M.F. and Gal{\'{a}}n, E. and Theng, B.K.G.},
+ pages = {21--81},
+ volume = {5},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B978008098258800002X},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00002-X},
+ issn = {15724352},
+ keywords = {Allophane, Clay minerals, Imogolite, Mixed-layer clays, Modulated layer silicates, Phyllosilicates 1:1, Phyllosilicates 2:1}
+}
+
+@article{Pouvreau2017StructureTerms,
+ title = {{Structure of Hydrated Gibbsite and Brucite Edge Surfaces: DFT Results and Further Development of the ClayFF Classical Force Field with Metal-O-H Angle Bending Terms}},
+ year = {2017},
+ journal = {Journal of Physical Chemistry C},
+ author = {Pouvreau, Maxime and Greathouse, Jeffery A. and Cygan, Randall T. and Kalinichev, Andrey G.},
+ number = {27},
+ month = {7},
+ pages = {14757--14771},
+ volume = {121},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/full/10.1021/acs.jpcc.7b05362},
+ doi = {10.1021/ACS.JPCC.7B05362/ASSET/IMAGES/LARGE/JP-2017-05362R{\_}0008.JPEG},
+ issn = {19327455}
+}
+
+@article{2006SubjectIndex,
+ title = {{Subject Index}},
+ year = {2006},
+ pages = {179--180},
+ doi = {10.1016/S1572-4352(06)02014-9}
+}
+
+@article{2015SubjectIndex,
+ title = {{Subject Index}},
+ year = {2015},
+ month = {10},
+ pages = {509--521},
+ doi = {10.2136/SSSABOOKSER5.5.INDEX},
+ keywords = {10 Albite, 10 Aluminosilicate materials, 140-141 Ammonium dihydrogen phosphate, 175, 179 AFM see Atomic force microscopy Agarose coating procedure, 183-185 Acetone replacement, 200-201, 22 Aluminosilicates, 248 Accessory minerals, 248 Acid dissolution technique, 25 Air drying samples, 251 Aggregating agents, 261, 271 hydroxylamine hydrochloride treatment, 291, 316 AEC see Anion exchange capacity Aegirine-augite, 336 Absorption bands, 345 Ammonium oxalate dissolution see AOD treatment Amorphous AL, 349 Accelerator, 350-351 Absorption edges, 378-380 Absorption correction, 387 Accelerating voltage, 389-393 Abundant soil minerals, 392-394 Absorption, 42 Acidity, 42 Adhesive force, 422-423 Absorbed electrons, 424-425 Alkaline extractants, 47, 475 Aligning spectra, 477-479 Acid-base accounting, 48-50 treatment reagents, 487-489 Allophanes, 488 Alkylammonium method, 490-495 Alkylammonium cations, 50-54 EDS patterns and, 56-57 pyrophosphate extraction, 57-59 Alkylamine hydrochlorides, 63-65, 63-65 Alteration, 63-65 Aluminum AOD treatment, 63-65 Alunite, 63-65 Amorphous materials, 98, AFM, Ab initio simulations, Al, EXAF, Fe, Mn, Si dissolution, TEM, WDS diffrac-tion, X-rays, XANES, air drying soil samples, alteration and, clay mineral allocation, clay minerals layer charge, confi gurations, diffuse refl ectance spectroscopy analysis, electron microprobe, layer charge, optical properties of, removing, short-range-order, sulfi de oxidation, synthesis, thin section preparation, treatment reagents}
+}
+
+@article{Ehlmann2011SubsurfaceMars,
+ title = {{Subsurface water and clay mineral formation during the early history of Mars}},
+ year = {2011},
+ journal = {Nature},
+ author = {Ehlmann, Bethany L. and Mustard, John F. and Murchie, Scott L. and Bibring, Jean Pierre and Meunier, Alain and Fraeman, Abigail A. and Langevin, Yves},
+ number = {7371},
+ month = {11},
+ pages = {53--60},
+ volume = {479},
+ doi = {10.1038/nature10582},
+ issn = {00280836},
+ pmid = {22051674}
+}
+
+@article{Pohorille2007SummaryOutlook,
+ title = {{Summary and outlook}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Pohorille, Andrew and Chipot, Christophe},
+ pages = {503--513},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}14},
+ issn = {01726218}
+}
+
+@article{NandinsurenSUPPLEMENTARYDerivatives,
+ title = {{SUPPLEMENTARY MATERIAL Natural Products as Sources of New Fungicides (Ⅱ): Antiphytopathogenic activity of 2,4-dihydroxyphenyl ethanone derivatives}},
+ author = {Nandinsuren, Tseden and Shi, Wei and Zhang, An-Ling and Bai, Yu-Bin and Gao, Jin-Ming},
+ url = {http://www.tandfonline.com/doi/suppl/10.1080/14786419.2015.1041140/suppl_file/gnpl_a_1041140_sm1668.pdf}
+}
+
+@article{1800SupplementaryW,
+ title = {{Supplementary Table 1 : Summary of the systems modelled , their composition and simulation times * Realistic mix : relative amino acid concentration matching naturally occurring one 1 . MIX3 : 10 dimeric and 15 hexameric different random chains produced w}},
+ year = {1800}
+}
+
+@book{Schoonheydt2013SurfaceMinerals,
+ title = {{Surface and interface chemistry of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Schoonheydt, R. A. and Johnston, C. T.},
+ edition = {1},
+ pages = {139--172},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00005-5},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00005-5},
+ issn = {15724352},
+ keywords = {Dyes, Films, Hydroxyls, Kaolinite, Proteins, Smectites, Transition metal ions, Water}
+}
+
+@incollection{Michot2013SurfacePorosity,
+ title = {{Surface Area and Porosity}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Michot, L.J. and Villi{\'{e}}ras, F.},
+ number = {C},
+ pages = {319--332},
+ volume = {5},
+ url = {https://linkinghub.elsevier.com/retrieve/pii/B9780080982595000123},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00012-3},
+ issn = {15724352},
+ keywords = {Gas adsorption, Porosity, Specific surface area, Surface heterogeneity, Swelling, Water adsorption}
+}
+
+@article{Michot2013SurfacePorosityb,
+ title = {{Surface Area and Porosity}},
+ year = {2013},
+ journal = {Developments in Clay Science},
+ author = {Michot, L. J. and Villi{\'{e}}ras, F.},
+ number = {C},
+ month = {1},
+ pages = {319--332},
+ volume = {5},
+ publisher = {Elsevier},
+ doi = {10.1016/B978-0-08-098259-5.00012-3},
+ issn = {1572-4352},
+ keywords = {Gas adsorption, Porosity, Specific surface area, Surface heterogeneity, Swelling, Water adsorption}
+}
+
+@book{Jaber2013SynthesisMinerals,
+ title = {{Synthesis of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Jaber, M. and Komarneni, S. and Zhou, C. H.},
+ edition = {1},
+ number = {ii},
+ pages = {223--241},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00009-2},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00009-2},
+ issn = {15724352},
+ keywords = {Beidellite, Chlorite, Fluorohectorite, Functionalization, Grafting, Hectorite, Industrial synthesis, Inorganic-organic hybride materials, Kaolinite, Laponite, Layered materials, Montmorillonite, Organoclay synthesis, Organohectorite, Saponite, Smectite}
+}
+
+@article{Li2020SystematicModels,
+ title = {{Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models}},
+ year = {2020},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Li, Zhen and Song, Lin Frank and Li, Pengfei and Merz, Kenneth M.},
+ number = {7},
+ month = {7},
+ pages = {4429--4442},
+ volume = {16},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c00194},
+ doi = {10.1021/ACS.JCTC.0C00194/SUPPL{\_}FILE/CT0C00194{\_}SI{\_}001.PDF},
+ issn = {15499626},
+ pmid = {32510956}
+}
+
+@incollection{2005SystemsBiocatalysis,
+ title = {{Systems Biology for Biocatalysis}},
+ year = {2005},
+ booktitle = {Biocatalysis},
+ month = {1},
+ pages = {433--455},
+ publisher = {Wiley-VCH Verlag GmbH {\&} Co. KGaA},
+ url = {http://doi.wiley.com/10.1002/3527602364.ch15},
+ address = {Weinheim, FRG},
+ doi = {10.1002/3527602364.ch15}
+}
+
+@article{CloningT-cell-tropicStrains,
+ title = {{T-cell-tropic strains}},
+ author = {Cloning, T A}
+}
+
+@article{Li2014TakingIons,
+ title = {{Taking into account the ion-induced dipole interaction in the nonbonded model of ions}},
+ year = {2014},
+ journal = {Journal of Chemical Theory and Computation},
+ author = {Li, Pengfei and Merz, Kenneth M.},
+ number = {1},
+ month = {1},
+ pages = {289--297},
+ volume = {10},
+ publisher = {American Chemical Society},
+ url = {https://pubs.acs.org/doi/abs/10.1021/ct400751u},
+ doi = {10.1021/CT400751U/SUPPL{\_}FILE/CT400751U{\_}SI{\_}003.PDF},
+ issn = {15499618}
+}
+
+@article{Russell2021TheReview.,
+ title = {{The "Water Problem"(sic), the Illusory Pond and Life's Submarine Emergence-A Review.}},
+ year = {2021},
+ journal = {Life (Basel, Switzerland)},
+ author = {Russell, Michael J},
+ number = {5},
+ month = {5},
+ volume = {11},
+ publisher = {MDPI AG},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/34068713 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC8151828},
+ doi = {10.3390/life11050429},
+ issn = {2075-1729},
+ pmid = {34068713},
+ keywords = {Hadean Ocean, emergence of life, fougerite/green rust, hydrazine, mushy mantle, peptide membrane, submarine alkaline vents}
+}
+
+@article{Aharoni2005TheFunctions,
+ title = {{The 'evolvability' of promiscuous protein functions}},
+ year = {2005},
+ journal = {Nature Genetics},
+ author = {Aharoni, Amir and Gaidukov, Leonid and Khersonsky, Olga and Gould, Stephen Mc Q. and Roodveldt, Cintia and Tawfik, Dan S.},
+ number = {1},
+ month = {1},
+ pages = {73--76},
+ volume = {37},
+ doi = {10.1038/NG1482},
+ issn = {10614036},
+ pmid = {15568024}
+}
+
+@misc{TheSociety,
+ title = {{The Clay Minerals Society}},
+ url = {https://www.clays.org/}
+}
+
+@article{Boles2011TheInteins,
+ title = {{The Cyclization of Peptides and Proteins with Inteins}},
+ year = {2011},
+ journal = {Protein Engineering Handbook, Volume 1 {\&} Volume 2},
+ author = {Boles, Blaise R. and Horswill, Alexander R.},
+ pages = {391--407},
+ volume = {1},
+ isbn = {9783527318506},
+ doi = {10.1002/9783527634026.ch15},
+ keywords = {Cyclic peptide, Cyclization, Cyclotide, Intein, Protein splicing, Siclopps}
+}
+
+@article{Berezovsky2011TheInteractions,
+ title = {{The diversity of physical forces and mechanisms in intermolecular interactions}},
+ year = {2011},
+ journal = {Physical Biology},
+ author = {Berezovsky, Igor N.},
+ number = {3},
+ volume = {8},
+ publisher = {Institute of Physics Publishing},
+ doi = {10.1088/1478-3975/8/3/035002},
+ issn = {14783975},
+ pmid = {21572170}
+}
+
+@article{Kavanaugh2011TheRepair,
+ title = {{The human DEK oncogene regulates DNA damage response signaling and repair}},
+ year = {2011},
+ journal = {Nucleic Acids Research},
+ author = {Kavanaugh, Gina M. and Wise-Draper, Trisha M. and Morreale, Richard J. and Morrison, Monique A. and Gole, Boris and Schwemberger, Sandy and Tichy, Elisia D. and Lu, Lu and Babcock, George F. and Wells, James M. and Drissi, Rachid and Bissler, John J. and Stambrook, Peter J. and Andreassen, Paul R. and Wiesm{\"{u}}ller, Lisa and Wells, Susanne I.},
+ number = {17},
+ pages = {7465--7476},
+ volume = {39},
+ isbn = {1362-4962},
+ doi = {10.1093/nar/gkr454},
+ issn = {03051048},
+ pmid = {21653549}
+}
+
+@article{Splinter2011TheRNA,
+ title = {{The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA}},
+ year = {2011},
+ journal = {Genes and Development},
+ author = {Splinter, Erik and de Wit, Elzo and Nora, Elphège P. and Klous, Petra and van de Werken, Harmen J.G. and Zhu, Yun and Kaaij, Lucas J.T. and van Ijcken, Wilfred and Gribnau, Joost and Heard, Edith and de Laat, Wouter},
+ number = {13},
+ pages = {1371--1383},
+ volume = {25},
+ isbn = {1549-5477 (Electronic){\textbackslash}n0890-9369 (Linking)},
+ doi = {10.1101/gad.633311},
+ issn = {08909369},
+ pmid = {21690198},
+ keywords = {4C technology, Gene regulation, Nuclear organization, Transcription, X-chromosome inactivation}
+}
+
+@article{Bishop2002TheSmectites,
+ title = {{The influence of structural Fe, Al and Mg on the infrared OH bands in spectra of dioctahedral smectites}},
+ year = {2002},
+ journal = {Clay Minerals},
+ author = {Bishop, J. and Madejov{\'{a}}, J . and Komadel, P. and Fr{\"{o}}schl, H.},
+ number = {4},
+ month = {12},
+ pages = {607--616},
+ volume = {37},
+ publisher = {Mineralogical Society},
+ doi = {10.1180/0009855023740063},
+ issn = {0009-8558}
+}
+
+@article{Wadsworth2017TheMars,
+ title = {{The Janus face of iron on anoxic worlds: iron oxides are both protective and destructive to life on the early Earth and present-day Mars}},
+ year = {2017},
+ journal = {FEMS Microbiology Ecology},
+ author = {Wadsworth, Jennifer and Cockell, Charles S},
+ pages = {56},
+ volume = {93},
+ url = {https://academic.oup.com/femsec/article/93/5/fix056/3778240},
+ doi = {10.1093/femsec/fix056},
+ keywords = {Editor: Tillmann Lueders Keywords: UV radiation, Mars, Photo-Fenton, habitability, iron oxide, reactive oxygen species}
+}
+
+@article{Rotelli2016TheEnvironment,
+ title = {{The key role of meteorites in the formation of relevant prebiotic molecules in a formamide/water environment}},
+ year = {2016},
+ journal = {Scientific Reports 2016 6:1},
+ author = {Rotelli, Luca and Trigo-Rodr{\'{i}}guez, Josep M. and Moyano-Cambero, Carles E. and Carota, Eleonora and Botta, Lorenzo and Di Mauro, Ernesto and Saladino, Raffaele},
+ number = {1},
+ month = {12},
+ pages = {1--7},
+ volume = {6},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/srep38888},
+ doi = {10.1038/srep38888},
+ issn = {2045-2322},
+ pmid = {27958316},
+ keywords = {Carbon cycle, Chemical origin of life}
+}
+
+@article{Chipot1898The3,
+ title = {{The Library World Volume 1 Issue 3}},
+ year = {1898},
+ journal = {New Library World},
+ author = {Chipot, Christophe},
+ number = {3},
+ month = {3},
+ pages = {33--50},
+ volume = {1},
+ url = {https://www.emerald.com/insight/content/doi/10.1108/eb008799/full/html},
+ isbn = {9783540384472},
+ doi = {10.1108/eb008799},
+ issn = {0307-4803}
+}
+
+@misc{TheVictoria,
+ title = {{The Murchison meteorite - Museums Victoria}},
+ url = {https://museumsvictoria.com.au/article/the-murchison-meteorite/}
+}
+
+@article{Bernal1949TheLife,
+ title = {{The Physical Basis of Life}},
+ year = {1949},
+ journal = {Proceedings of the Physical Society. Section A},
+ author = {Bernal, J. D.},
+ number = {9},
+ month = {9},
+ pages = {537--558},
+ volume = {62},
+ publisher = {IOP Publishing},
+ url = {https://iopscience.iop.org/article/10.1088/0370-1298/62/9/301 https://iopscience.iop.org/article/10.1088/0370-1298/62/9/301/meta},
+ doi = {10.1088/0370-1298/62/9/301},
+ issn = {0370-1298}
+}
+
+@book{Dohrmann2013TheWaste,
+ title = {{The Role of Clays for Safe Storage of Nuclear Waste}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Dohrmann, R. and Kaufhold, S. and Lundqvist, B.},
+ edition = {1},
+ number = {C},
+ pages = {677--710},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00024-X},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00024-X},
+ issn = {15724352},
+ keywords = {Argillaceous host rock, Bentonite buffer, Long-term safety, Multi-barrier system}
+}
+
+@misc{TheReader,
+ title = {{The role of montmorillonite in its catalysis of RNA synthesis | Elsevier Enhanced Reader}},
+ url = {https://reader.elsevier.com/reader/sd/pii/S0169131711002201?token=70B15D2C484A14D63C6C0C9A99B2E0AA70E5245830756C245A7BD0F4BBA66C477E7B5F584427017112C4FB23F658DFAF&originRegion=eu-west-1&originCreation=20210531105438}
+}
+
+@article{Jin2011TheChemists,
+ title = {{The selective addition of water to CQC bonds; enzymes are the best chemists}},
+ year = {2011},
+ journal = {Chem. Commun. Chem. Commun},
+ author = {Jin, Jianfeng and Hanefeld, Ulf},
+ number = {47},
+ pages = {2502--2510},
+ volume = {47},
+ url = {http://pubs.rsc.org/en/content/articlepdf/2011/cc/c0cc04153j},
+ doi = {10.1039/c0cc04153j}
+}
+
+@article{Jin2011TheChemistsb,
+ title = {{The selective addition of water to CC bonds; enzymes are the best chemists}},
+ year = {2011},
+ journal = {Chemical Communications},
+ author = {Jin, Jianfeng and Hanefeld, Ulf},
+ number = {9},
+ pages = {2502},
+ volume = {47},
+ url = {http://xlink.rsc.org/?DOI=c0cc04153j},
+ isbn = {1359-7345},
+ doi = {10.1039/c0cc04153j},
+ issn = {1359-7345},
+ pmid = {21243161}
+}
+
+@misc{TheJSTOR,
+ title = {{The Significance of Clays in Agriculture and Soils on JSTOR}},
+ url = {https://www.jstor.org/stable/37331?seq=1#metadata_info_tab_contents}
+}
+
+@article{Akiva2014TheDatabase,
+ title = {{The Structure-Function Linkage Database}},
+ year = {2014},
+ journal = {Nucleic Acids Research},
+ author = {Akiva, Eyal and Brown, Shoshana and Almonacid, Daniel E. and Barber, Alan E. and Custer, Ashley F. and Hicks, Michael A. and Huang, Conrad C. and Lauck, Florian and Mashiyama, Susan T. and Meng, Elaine C. and Mischel, David and Morris, John H. and Ojha, Sunil and Schnoes, Alexandra M. and Stryke, Doug and Yunes, Jeffrey M. and Ferrin, Thomas E. and Holliday, Gemma L. and Babbitt, Patricia C.},
+ number = {D1},
+ month = {1},
+ volume = {42},
+ doi = {10.1093/NAR/GKT1130},
+ issn = {03051048},
+ pmid = {24271399}
+}
+
+@article{Albarede2009TheLife,
+ title = {{The terrestrial craddle of life}},
+ year = {2009},
+ author = {Albar{\`{e}}de, F. and Blichert-Toft, J.},
+ pages = {1--12},
+ publisher = {EDP Sciences},
+ doi = {10.1051/ORVIE/2009001}
+}
+
+@article{Balan2017TheoreticalSpectroscopies,
+ title = {{Theoretical Aspects of Infrared and Raman Spectroscopies}},
+ year = {2017},
+ journal = {Developments in Clay Science},
+ author = {Balan, E. and Kloprogge, J. T.},
+ pages = {6--33},
+ volume = {8},
+ publisher = {Elsevier B.V.},
+ doi = {10.1016/B978-0-08-100355-8.00002-3},
+ issn = {15724352},
+ keywords = {Anharmonic properties, Clay mineral, Effective medium theory, Harmonic approximation, IR, IR spectroscopy, Lattice dynamics, Powder spectra, Quantum-mechanical description, Raman, Raman spectroscopy, Vibrational modes}
+}
+
+@book{Rouquerol2013ThermalAnalysis,
+ title = {{Thermal Analysis}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Rouquerol, F. and Rouquerol, J. and Llewellyn, P.},
+ edition = {2},
+ pages = {361--379},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00014-7},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00014-7},
+ issn = {15724352},
+ keywords = {Conventional thermal analysis, Differential thermal analysis, Evolved gas detection, Sample-controlled thermal analysis, Thermodilatometry, Thermogravimetry}
+}
+
+@article{Karathanasis2015ThermalMinerals,
+ title = {{Thermal analysis of soil minerals}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Karathanasis, A. D.},
+ month = {10},
+ pages = {117--160},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C5},
+ keywords = {Combined thermal analysis techniques, Differential scanning calorimetry, Differential thermal analysis, Qualitative interpretations, Quantitative interpretations, Soil mineral studies, Thermogravimetry}
+}
+
+@book{Heller-Kallai2013ThermallyMinerals,
+ title = {{Thermally modified clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Heller-Kallai, L.},
+ edition = {2},
+ pages = {411--433},
+ volume = {5},
+ publisher = {Elsevier Ltd.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00014-6},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00014-6},
+ issn = {15724352},
+ keywords = {Freezing, acidity, de- and rehydration, dehydroxylation, porosity, structural changes, texture}
+}
+
+@article{Darve2007ThermodynamicDynamics,
+ title = {{Thermodynamic integration using constrained and unconstrained dynamics}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Darve, Eric},
+ pages = {119--170},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}4},
+ issn = {01726218}
+}
+
+@book{Blanc2013ThermodynamicsMinerals,
+ title = {{Thermodynamics of clay minerals}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Blanc, P. and Vieillard, P. and Gailhanou, H. and Gaboreau, S.},
+ edition = {1},
+ pages = {173--210},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098258-8.00006-7},
+ isbn = {9780080982588},
+ doi = {10.1016/B978-0-08-098258-8.00006-7},
+ issn = {15724352},
+ keywords = {Calorimetry, Clay minerals, Equilibrium, Models, Thermodynamic}
+}
+
+@article{Kulig2015TopologiesCholesterol,
+ title = {{Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol}},
+ year = {2015},
+ journal = {Data in Brief},
+ author = {Kulig, Waldemar and Pasenkiewicz-Gierula, Marta and R{\'{o}}g, Tomasz},
+ month = {12},
+ pages = {333--336},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ doi = {10.1016/j.dib.2015.09.013},
+ issn = {23523409}
+}
+
+@article{Czimerova2006TraditionalSmectites,
+ title = {{Traditional and novel methods for estimating the layer charge of smectites}},
+ year = {2006},
+ journal = {Applied Clay Science},
+ author = {Cz{\'{i}}merov{\'{a}}, A. and Bujd{\'{a}}k, J. and Dohrmann, R.},
+ number = {1-4},
+ month = {10},
+ pages = {2--13},
+ volume = {34},
+ publisher = {Elsevier},
+ doi = {10.1016/J.CLAY.2006.02.008},
+ issn = {0169-1317},
+ keywords = {Alkylammonium method, Cation exchange capacity, Layer charge, Methylene blue, Smectites, Structural formulae}
+}
+
+@article{Dellago2007TransitionEnergies,
+ title = {{Transition path sampling and the calculation of free energies}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Dellago, Christoph},
+ pages = {249--276},
+ volume = {86},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}7},
+ issn = {01726218}
+}
+
+@article{Elsass2015TransmissionUse,
+ title = {{Transmission electron microscopy for soil samples: Preparation methods and use}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Elsass, Françoise and Chenu, Claire and Tessier, Daniel},
+ month = {10},
+ pages = {235--268},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C9},
+ keywords = {Clay minerals, Clay-organic matter associations, Microstructures, Optical principles, Sample preparation methods, Soil component associations, Soil samples, Surface properties, Transmission electron microscopy}
+}
+
+@article{The2005UltravioletAbsorbance,
+ title = {{ultraviolet absorbance}},
+ year = {2005},
+ author = {The, A and Uvr-induced, The},
+ pages = {275--276},
+ volume = {39}
+}
+
+@article{Lu2007UnderstandingMethods,
+ title = {{Understanding and improving free energy calculations in molecular simulations: Error analysis and reduction methods}},
+ year = {2007},
+ journal = {Springer Series in Chemical Physics},
+ author = {Lu, Nandou and Woolf, Thomas B.},
+ pages = {199--247},
+ volume = {86},
+ publisher = {Springer New York},
+ isbn = {9783540736172},
+ doi = {10.1007/978-3-540-38448-9{\_}6},
+ issn = {01726218}
+}
+
+@article{Hynek2012UninhabitableClays,
+ title = {{Uninhabitable martian clays?}},
+ year = {2012},
+ journal = {Nature Geoscience 2012 5:10},
+ author = {Hynek, Brian},
+ number = {10},
+ month = {9},
+ pages = {683--684},
+ volume = {5},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/ngeo1560},
+ doi = {10.1038/ngeo1560},
+ issn = {1752-0908},
+ keywords = {Inner planets, Mineralogy}
+}
+
+@article{Maurice2015UseInteractions,
+ title = {{Use of atomic force microscopy to study soil particle properties and interactions}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Maurice, Patricia A. and Lower, Steven K.},
+ month = {10},
+ pages = {299--333},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C11},
+ keywords = {Atomic force microscopy imaging, Field-dissolved samples, Force measurements, Microbially mediated mineral dissolution, Operating principles, Soil microbiology, Soil mineralogy, Soil organic matter}
+}
+
+@article{Horswill2004UsingEnzymes,
+ title = {{Using incremental truncation to create libraries of hybrid enzymes}},
+ year = {2004},
+ journal = {Methods in Enzymology},
+ author = {Horswill, Alexander R. and Naumann, Todd A. and Benkovic, Stephen J.},
+ number = {1999},
+ pages = {50--60},
+ volume = {388},
+ isbn = {9780121827939},
+ doi = {10.1016/S0076-6879(04)88006-6},
+ issn = {00766879},
+ pmid = {15289061}
+}
+
+@article{Bussi2020UsingLandscapes,
+ title = {{Using metadynamics to explore complex free-energy landscapes}},
+ year = {2020},
+ journal = {Nature Reviews Physics 2020 2:4},
+ author = {Bussi, Giovanni and Laio, Alessandro},
+ number = {4},
+ month = {3},
+ pages = {200--212},
+ volume = {2},
+ publisher = {Nature Publishing Group},
+ url = {https://www.nature.com/articles/s42254-020-0153-0},
+ isbn = {4225402001530},
+ doi = {10.1038/s42254-020-0153-0},
+ issn = {2522-5820},
+ keywords = {Computational science, Molecular dynamics}
+}
+
+@article{Fornaro2020UVSamples,
+ title = {{UV Irradiation and Near Infrared Characterization of Laboratory Mars Soil Analog Samples}},
+ year = {2020},
+ journal = {Frontiers in Astronomy and Space Sciences},
+ author = {Fornaro, Teresa and Brucato, John R. and Poggiali, Giovanni and Corazzi, Maria Angela and Biczysko, Malgorzata and Jaber, Maguy and Foustoukos, Dionysis I. and Hazen, Robert M. and Steele, Andrew},
+ month = {11},
+ pages = {91},
+ volume = {7},
+ publisher = {Frontiers Media S.A.},
+ doi = {10.3389/FSPAS.2020.539289/BIBTEX},
+ issn = {2296987X},
+ keywords = {Mars, UV irradiation, infrared spectroscopy, life detection, molecular biosignatures}
+}
+
+@article{MicrobiolVFactor,
+ title = {{V factor}},
+ author = {Microbiol, B M C and Microbiol, Clin and Ca, La Jolla},
+ number = {1},
+ pages = {277--280}
+}
+
+@inproceedings{deGroot2011VirusCoronaviridae.,
+ title = {{Virus Taxonomy Classification and Nomenclature of Viruses. Family Coronaviridae.}},
+ year = {2011},
+ author = {de Groot, R. J.},
+ editor = {King, Andrew M Q and Adams, Michael J and Carstens, Eric B and Lefkowitz, Elliot J},
+ pages = {806–828},
+ publisher = {Elsevier},
+ organization = {International Union of Microbiological Societies Virology Division},
+ address = {Oxford},
+ keywords = {CA. ISBN 978-0-12-384684-6., E.B. Carstens, E.J. Lefkowitz. Elsevier, Eds. A.M.Q. King, M.J. Adams, San Diego}
+}
+
+@article{Microbiol2005W-BeijingStrain,
+ title = {{W-Beijing strain}},
+ year = {2005},
+ author = {Microbiol, Clin and Pcr-based, Rapid and Microbiol, Clin and Microbiol, Clin},
+ number = {1},
+ pages = {281--282}
+}
+
+@article{Hughes2015WhatInterfaces,
+ title = {{What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces}},
+ year = {2015},
+ journal = {Journal of Materials Chemistry B},
+ author = {Hughes, Zak E. and Walsh, Tiffany R.},
+ number = {16},
+ month = {4},
+ pages = {3211--3221},
+ volume = {3},
+ publisher = {Royal Society of Chemistry},
+ url = {https://pubs.rsc.org/en/content/articlehtml/2015/tb/c5tb00004a https://pubs.rsc.org/en/content/articlelanding/2015/tb/c5tb00004a},
+ doi = {10.1039/C5TB00004A},
+ issn = {2050750X}
+}
+
+@article{Zheng2011WholeDiagnosis,
+ title = {{Whole genome amplification in preimplantation genetic diagnosis}},
+ year = {2011},
+ journal = {Journal of Zhejiang University SCIENCE B},
+ author = {Zheng, Ying-ming and Wang, Ning and Li, Lei and Jin, Fan},
+ number = {1},
+ pages = {1--11},
+ volume = {12},
+ url = {http://www.springerlink.com/index/10.1631/jzus.B1000196},
+ isbn = {1673-1581},
+ doi = {10.1631/jzus.B1000196},
+ issn = {1673-1581},
+ pmid = {21194180}
+}
+
+@misc{WO2012142302A2_LKlica.pdf,
+ title = {{WO2012142302A2{\_}LKlica.pdf}}
+}
+
+@article{XChromatin,
+ title = {{X chromatin}},
+ pages = {283}
+}
+
+@article{Harris2015X-rayIdentification,
+ title = {{X-ray diffraction techniques for soil mineral identification}},
+ year = {2015},
+ journal = {Methods of Soil Analysis, Part 5: Mineralogical Methods},
+ author = {Harris, Willie and White, G. Norman},
+ month = {10},
+ pages = {81--115},
+ volume = {5},
+ publisher = {wiley},
+ isbn = {9780891188575},
+ doi = {10.2136/SSSABOOKSER5.5.C4},
+ keywords = {Atomic crystal planes, Sample preparation, Soil mineral identification, X-ray diffraction techniques, X-ray diffractometer, XRD powder camera}
+}
+
+@book{Sakharov2013X-rayEffects,
+ title = {{X-ray Identification of Mixed-Layer Structures: Modelling of Diffraction Effects}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Sakharov, B. A. and Lanson, B.},
+ edition = {2},
+ number = {C},
+ pages = {51--135},
+ volume = {5},
+ publisher = {Copyright {\&}copy; 2013, 2006 Elsevier Ltd. All rights reserved.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00005-6},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00005-6},
+ issn = {15724352},
+ keywords = {Defective lamellar structures, Interstratification, Mixed layer structures, X-ray diffraction}
+}
+
+@book{Seyama2013X-RaySpectroscopy,
+ title = {{X-Ray Photoelectron Spectroscopy}},
+ year = {2013},
+ booktitle = {Developments in Clay Science},
+ author = {Seyama, H. and Soma, M. and Theng, B. K.G.},
+ edition = {1},
+ number = {C},
+ pages = {161--176},
+ volume = {5},
+ publisher = {Elsevier Inc.},
+ url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00007-X},
+ isbn = {9780080982595},
+ doi = {10.1016/B978-0-08-098259-5.00007-X},
+ issn = {15724352},
+ keywords = {Auger parameter, Chemical bonding state, Chemical-state plot, Photoelectron microscopy, X-ray photoelectron diffraction, X-ray photoelectron spectroscopy (XPS)}
+}
+
+@article{Fungi2006YBases,
+ title = {{Y bases}},
+ year = {2006},
+ journal = {Amino Acids},
+ author = {Fungi, Dimorphic and Bodies, Councilman},
+ number = {1},
+ pages = {0--2},
+ volume = {103},
+ isbn = {0470035455}
+}
+
+@article{Hackel2008YeastAnalysis,
+ title = {{Yeast Surface Display in Protein Engineering and Analysis}},
+ year = {2008},
+ journal = {Protein Engineering Handbook},
+ author = {Hackel, Benjamin J and Wittrup, Dane},
+ pages = {621--648},
+ volume = {2},
+ url = {http://dx.doi.org/10.1002/9783527634026.ch26},
+ isbn = {9783527634026},
+ doi = {10.1002/9783527634026.ch26},
+ keywords = {affinity maturation, antibody engineering, directed evolution, flow cytometry, protein analysis, protein engineering, yeast surface display}
+}
+
+@article{Pair2006ZRing,
+ title = {{Z ring}},
+ year = {2006},
+ journal = {Most},
+ author = {Pair, Base and Value, D and Reverse, Nucleoside and Inhibitors, Transcriptase and Spoilage, Textile and Zoster, Herpes and Compounds, Quaternary Ammonium},
+ pages = {289--291},
+ volume = {3},
+ isbn = {0470035455}
+}
+
+@article{Fusion2013Z-DNASome,
+ title = {{Z-DNA Left-handed helical dsDNA, with {\~{}}12 bases/turn, fi rst observed in sequences such as ...GCGCGCGC... under some}},
+ year = {2013},
+ author = {Fusion, Gene},
+ doi = {10.1101/gad.1998111.}
+}
+
+@book{Ferguson2008-ValueStates,
+ title = {{{$\Phi$}-Value Analysis of Protein Folding Transition States}},
+ year = {2008},
+ booktitle = {Protein Engineering Handbook},
+ author = {Ferguson, Neil and Fersht, Alan R},
+ pages = {81--120},
+ url = {http://dx.doi.org/10.1002/9783527634026.ch4},
+ isbn = {9783527634026},
+ doi = {10.1002/9783527634026.ch4},
+ keywords = {cooperativity, energy diagram, folding mechanism, free energy, nondisruptive mutations, phi-value, protein engineering, transition state}
+}
+
+@book{Bergaya2013,
+author = {Bergaya, F. and Lagaly, G.},
+title = {Handbook of Clay Science},
+edition = {2},
+keywords = {Aggregate,Anionic clay,Associated mineral,Associated phase,Clay minerals,Clay science,Clays,Delamination,Exfoliation,Hydrotalcite,LDH,Particle,Tactoid},
+mendeley-groups = {PhD},
+publisher = {Elsevier Ltd.},
+url = {http://dx.doi.org/10.1016/B978-0-08-098259-5.00001-9 https://linkinghub.elsevier.com/retrieve/pii/B9780080982595000019},
+volume = {5},
+year = {2013}
+}
+@misc{mindat,
+url="https://www.mindat.org/"}
+
+@article{Jo2008,
+author = {Jo, Sunhwan and Kim, Taehoon and Iyer, Vidyashankara G. and Im, Wonpil},
+
+journal = {Journal of Computational Chemistry},
+
+number = {11},
+pages = {1859--1865},
+title = {{CHARMM-GUI: A web-based graphical user interface for CHARMM}},
+volume = {29},
+year = {2008}
+}
+
+@techreport{SSAPharmacopeia2004,
+booktitle = {Pharmacopeial Forum},
+file = {::},
+keywords = {SSA2004},
+mendeley-groups = {PhD},
+mendeley-tags = {SSA2004},
+number = {4},
+pages = {1465},
+publisher = {The United States Pharmacopeial Convention, Inc.},
+title = {{SPECIFIC SURFACE AREA}},
+volume = {30},
+year = {2004}
+}
+
+@article{clayff,
+author = {Cygan, Randall T. and Greathouse, Jeffery A. and Kalinichev, Andrey G.},
+title = {Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces},
+journal = {The Journal of Physical Chemistry C},
+volume = {125},
+number = {32},
+pages = {17573--17589},
+year = {2021},
+
+}
+
+
+@article{gromacs,
+author = {Berendsen, H J C and van der Spoel, D and van Drunen, R},
+
+
+journal = {Computer Physics Communications},
+number = {1},
+pages = {43--56},
+title = {{GROMACS: A message-passing parallel molecular dynamics implementation}},
+volume = {91},
+year = {1995}
+}
+
+@book{Bergaya2013,
+author = {Bergaya, F. and Lagaly, G.},
+booktitle = {Handbook of Clay Science},
+edition = {2},
+
+
+keywords = {Aggregate,Anionic clay,Associated mineral,Associated phase,Clay minerals,Clay science,Clays,Delamination,Exfoliation,Hydrotalcite,LDH,Particle,Tactoid},
+mendeley-groups = {PhD},
+publisher = {Elsevier Ltd.},
+title = {{Introduction to Clay Science}},
+volume = {5},
+year = {2013}
+}
+
+@inproceedings{Gowers2016,
+abstract = {MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed. MDAnalysis addresses this problem by abstracting access to the raw simulation data and presenting a uniform object-oriented Python interface to the user. It thus enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities. The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks, especially together with molecular visualization provided by nglview and time series analysis with pandas. MDAnalysis is written in Python and Cython and uses NumPy arrays for easy interoperability with the wider scientific Python ecosystem. It is widely used and forms the foundation for more specialized biomolecular simulation tools. MDAnalysis is available under the GNU General Public License v2.},
+author = {Gowers, Richard and Linke, Max and Barnoud, Jonathan and Reddy, Tyler and Melo, Manuel and Seyler, Sean and Doma{\'{n}}ski, Jan and Dotson, David and Buchoux, S{\'{e}}bastien and Kenney, Ian and Beckstein, Oliver},
+booktitle = {Proceedings of the 15th Python in Science Conference},
+
+file = {::},
+keywords = {Index Terms-molecular dynamics simulations,biology,chemistry,physics,science},
+mendeley-groups = {PhD},
+pages = {98--105},
+publisher = {SciPy},
+title = {{MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations}},
+url = {https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html},
+year = {2016}
+}
+
+
+@article{Michaud-Agrawal2011,
+author = {Michaud-Agrawal, Naveen and Denning, Elizabeth J. and Woolf, Thomas B. and Beckstein, Oliver},
+journal = {Journal of Computational Chemistry},
+mendeley-groups = {old/Master/MDAnalysis},
+number = {10},
+pages = {2319--2327},
+title = {{MDAnalysis: A toolkit for the analysis of molecular dynamics simulations}},
+volume = {32},
+year = {2011}
+}
+
+@software{reback2020pandas,
+ author = {The pandas development team},
+ title = {pandas-dev/pandas: Pandas},
+ year = 2020,
+ publisher = {Zenodo},
+ version = {latest},
+ doi = {10.5281/zenodo.3509134},
+}
+
+@article{Zheng2010,
+abstract = {The evolution of the interlayer space of different hydrated, Wyoming-type montmorillonite under the influence of temperature was investigated by means of Monte Carlo molecular modeling simulation methods. Calculations were performed on montmorillonite with monovalent and divalent counterions including Li +, Na+, K+, Rb+, Cs+, Ca2+, Ni2+, Zn2+, and Pb2+. For each of these clays we have conducted a series of 16 simulations in which the temperature is increased systematically from 300 to 400 K, then decreased to 260 K, and finally increased to 300 K. SPC/E water model is used to describe the water and hydroxyl behavior. From these simulations we found that the variation in the interlayer spacing of 3-layer hydrated montmorillonite is much greater than that of 2- and 1-layer hydrated montmorillonite. Hysteresis phenomena have been found in the interlayer spacing-temperature curves, especially at high temperature. The influence of temperature on the swelling behaviors of montmorillonite is different in that it depends on the counterions contained in the clay.},
+author = {Zheng, Y. and Zaoui, A. and Shahrour, I.},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zheng, Zaoui, Shahrour - 2010 - Evolution of the interlayer space of hydrated montmorillonite as a function of temperature.pdf:pdf;:home/hannahpollak/Downloads/10.2138_am.2010.3541.pdf:pdf},
+issn = {0003-004X},
+journal = {American Mineralogist},
+keywords = {Interlayer space,Light and heavy cations,Molecular dynamics,Montmorillonite clay},
+mendeley-tags = {Interlayer space,Light and heavy cations,Molecular dynamics,Montmorillonite clay},
+
+number = {10},
+pages = {1493--1499},
+publisher = {Walter de Gruyter GmbH},
+title = {{Evolution of the interlayer space of hydrated montmorillonite as a function of temperature}},
+url = {https://www.degruyter.com/document/doi/10.2138/am.2010.3541/html},
+volume = {95},
+year = {2010}
+}
+@article{Chang1998,
+abstract = {Monte Carlo and molecular dynamics simulations of interlayer molecular structure in the one-, two-, and (hypothetical) three-layer hydrates of K-montmorillonite were performed concurrently in order to elucidate counterion speciation and water structure in the electrical double layer of this clay mineral. Calculated layer spacings, interlayer water potential energies, and counterion mobilities were in agreement with available experimental data. In the one-layer hydrate, both outer-sphere and inner-sphere surface complexes of K+ were observed, the latter always near sites of tetrahedral charge substitution, with the counterion species exchanging readily on the simulation time scale (up to 200 ps). In the two- and threelayer hydrates, the surface complexes persisted, but an incipient diffuse layer of counterions also was observed, with all three types of surface species engaging in sluggish exchange. Water molecules in the one-layer hydrate resided at the interlayer midplane, whereas in the two-layer hydrate they lay in two planes between outer- and inner-sphere K+ surface complexes, as well as at the midplane. Hydrogen bonds in the one-layer hydrate were longer and more bent than in bulk liquid water. For all three hydrates, water and cation interlayer mobilities remained below those observed in bulk solution, principally because of the restricted geometry and the retarding effect of clay layer surface charge. Most of our results can be understood in terms of the weak solvation of the counterions by water molecules, which permits significant competition between K+ and water protons for negatively charged sites in the clay mineral layer.},
+author = {Chang, Fang Ru Chou and Skipper, N. T. and Sposito, Garrison},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Chang, Skipper, Sposito - 1998 - Monte Carlo and molecular dynamics simulations of electrical double-layer structure in potassium-montmo.pdf:pdf},
+issn = {07437463},
+journal = {Langmuir},
+mendeley-groups = {PhD},
+
+number = {5},
+pages = {1201--1207},
+publisher = {American Chemical Society},
+title = {{Monte Carlo and molecular dynamics simulations of electrical double-layer structure in potassium-montmorillonite hydrates}},
+volume = {14},
+year = {1998}
+}
+@article{Zhou2014,
+abstract = {The interlayer structure of wet organoclays has attracted great interest due to its close relation with adsorption process but still remains ambiguous at the atomic level. In this study, the structure and dynamics of cetyltrimethylammonium (CTMA+) intercalated montmorillonite (Mt) in the water saturated condition were investigated by molecular dynamics (MD) simulations. Two Mt models with different cation exchange capacity (CEC) were selected and various amounts of CTMA+ were added to achieve different loading levels based on experiments. The simulation results show that as the surfactant loading level increases, the arrangement of CTMA+ transforms from bilayer to inclined paraffin-type with a large amount of water in the interlayer space, indicating a different configuration from dry systems. The conformations of CTMA+ are influenced by water molecules and surfactant loading level. Compared to the dry models, the percentage of gauche conformations of CTMA+ decreases in the water saturated condition. In the cases of incomplete cation exchange, the confinement from silicate surface may lead to more ordered structure of alkyl chains. In the cases of excessive surfactant loading, the percentage of gauche conformation decreases due to the steric hindrance. Moreover, the ammonium head groups of CTMA+ are found to locate close to the center of six-member ring of silicate surface and coordinated with 4-6 water molecules. Their mobility is low due to the electrostatic interactions while the alkyl chains show higher mobility. Mt with a higher CEC has a stronger confining effect on both alkylammonium and water, which then reduces the mobility of alkyl chains and water molecules within the interlayer space. {\textcopyright} 2014 Elsevier B.V.},
+author = {Zhou, Qing and Shen, Wei and Zhu, Jianxi and Zhu, Runliang and He, Hongping and Zhou, Jinhong and Yuan, Peng},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zhou et al. - 2014 - Structure and dynamic properties of water saturated CTMA-montmorillonite molecular dynamics simulations.pdf:pdf},
+issn = {01691317},
+journal = {Applied Clay Science},
+keywords = {Confining effect,Interlayer structures,Mobility,Molecular dynamic,Organo-montmorillonite,Water saturated condition},
+mendeley-groups = {PhD},
+
+pages = {62--71},
+publisher = {Elsevier Ltd},
+title = {{Structure and dynamic properties of water saturated CTMA-montmorillonite: molecular dynamics simulations}},
+url = {https://linkinghub.elsevier.com/retrieve/pii/S0169131714001938},
+volume = {97-98},
+year = {2014}
+}
+@article{Smith1998,
+abstract = {The crystalline swelling properties and interlayer structure of a cesium montmorillonite clay were investigated using molecular computer simulations. Two classes of dry-clay structures, proposed previously to explain X-ray diffraction and NMR experiments, were identified using Monte Carlo annealing calculations. Hydrated clays with water contents ranging from 0.044 to 0.440 gH2O/gclay were investigated using molecular dynamics simulations. Layer spacings calculated as a function of water content were found to be similar to experimental swelling curves, showing a distinct plateau at the monolayer-hydrate spacing. Hydration energies were calculated as a function of water content and expressed in three complementary forms. The immersion energy form was found to be most useful, revealing an apparently global minimum in the swelling-coordinate energy that corresponds to the monolayer hydrate. This is in agreement with experimental measurements and may help clarify the energetic origins of discrete, crystalline swelling processes in clay minerals. For two- and four-layer hydrates, cesium ions readily formed two different types of inner-sphere complexes with the clay surface. Ions associated with negatively charged tetrahedral substitution sites formed exclusively inner-sphere complexes and occupied hexagonal cavities adjacent to the substitutions. Other cesium ions occupied both inner-sphere and outer-sphere configurations with roughly equal probability. The ease with which cesium associates with the clay surface may be responsible for the formation of monolayer hydrates in cesium-substituted clays and for selective binding of cesium to many clay minerals.},
+author = {Smith, David E.},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Smith - 1998 - Molecular computer simulations of the swelling properties and interlayer structure of cesium montmorillonite.pdf:pdf},
+issn = {0743-7463},
+journal = {Langmuir},
+mendeley-groups = {PhD},
+
+number = {20},
+pages = {5959--5967},
+publisher = {American Chemical Society},
+title = {{Molecular Computer Simulations of the Swelling Properties and Interlayer Structure of Cesium Montmorillonite}},
+url = {https://pubs.acs.org/doi/10.1021/la980015z},
+volume = {14},
+year = {1998}
+}
+@article{Zhang2014,
+abstract = {In most of natural montmorillonites, Na+ and Ca2+ ions commonly coexist in the interlayer space as compensation ions. Molecular dynamics simulations have been performed to investigate the swelling properties, hydration behaviors, and mobility of the interlayer species of (Nax, Cay)-montmorillonites with different water contents. Nine montmorillonites with different Na+/Ca2+ ratio were selected as model clay frameworks, and the content of interlayer water was set within a range from 0 to 486 mgwater/gclay. The results show that the montmorillonites with coexisting of Na+ and Ca2+ present slightly different swelling curves, hydration energies, and immersion energies from Na- or Ca-montmorillonite. The double-layered hydrates are the thermodynamically stable states for all montmorillonites in the regime of crystalline swelling. A total of 170 mgwater/gclay is found as the threshold water content for the complexing modes of interlayer Ca2+ and Na+ ions switching from inner-sphere complexes to outer-sphere ones. The self-confusion coefficient of interlayer species obviously reveals the confining effects of clay surfaces. In all montmorillonites, the mobility of Na+ is always much greater than that of Ca2+ due to their different hydration shells. According to the water residence time in typical Na+ and Ca2+ hydration complexes, Ca2+ hydration complexes is pronounced more stable than those of Na+, and in montmorillonites with high Ca2+/Na+ ratio, the inhibitory effects of Ca2+ hydration complexes on the mobility of Na+ is clearly revealed.},
+author = {Zhang, Lihu and Lu, Xiancai and Liu, Xiandong and Zhou, Jinhong and Zhou, Huiqun},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zhang et al. - 2014 - Hydration and Mobility of Interlayer Ions of (Na x , Ca y )-Montmorillonite A Molecular Dynamics Study.pdf:pdf},
+issn = {1932-7447},
+journal = {The Journal of Physical Chemistry C},
+keywords = {MD,calcium,interlayer ions,self diffusion,sodium},
+mendeley-groups = {PhD},
+mendeley-tags = {MD,calcium,interlayer ions,self diffusion,sodium},
+
+number = {51},
+pages = {29811--29821},
+publisher = {American Chemical Society},
+title = {{Hydration and Mobility of Interlayer Ions of (Na x , Ca y )-Montmorillonite: A Molecular Dynamics Study}},
+url = {https://pubs.acs.org/doi/10.1021/jp508427c},
+volume = {118},
+year = {2014}
+}
+@article{Teich-McGoldrick2015,
+abstract = {The swelling properties of smectite clay minerals are relevant to many engineering applications including environmental remediation, repository design for nuclear waste disposal, borehole stability in drilling operations, and additives for numerous industrial processes and commercial products. We used molecular dynamics and grand canonical Monte Carlo simulations to study the effects of layer charge location, interlayer cation, and temperature on intracrystalline swelling of montmorillonite and beidellite clay minerals. For a beidellite model with layer charge exclusively in the tetrahedral sheet, strong ion-surface interactions shift the onset of the two-layer hydrate to higher water contents. In contrast, for a montmorillonite model with layer charge exclusively in the octahedral sheet, weaker ion-surface interactions result in the formation of fully hydrated ions (two-layer hydrate) at much lower water contents. Clay hydration enthalpies and interlayer atomic density profiles are consistent with the swelling results. Water adsorption isotherms from grand canonical Monte Carlo simulations are used to relate interlayer hydration states to relative humidity, in good agreement with experimental findings.},
+author = {Teich-McGoldrick, Stephanie L. and Greathouse, Jeffery A. and Jov{\'{e}}-Col{\'{o}}n, Carlos F. and Cygan, Randall T.},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Teich-Mcgoldrick et al. - 2015 - Swelling Properties of Montmorillonite and Beidellite Clay Minerals from Molecular Simulation Compariso.pdf:pdf;::},
+issn = {1932-7447},
+journal = {The Journal of Physical Chemistry C},
+keywords = {MMT,charge solation,swelling},
+mendeley-groups = {PhD,PhD/swelling},
+mendeley-tags = {MMT,charge solation,swelling},
+
+number = {36},
+pages = {20880--20891},
+publisher = {American Chemical Society},
+title = {{Swelling Properties of Montmorillonite and Beidellite Clay Minerals from Molecular Simulation: Comparison of Temperature, Interlayer Cation, and Charge Location Effects}},
+url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acs.jpcc.5b03253},
+volume = {119},
+year = {2015}
+}
+@article{Chang1995,
+abstract = {Molecular structure in the interlayers of sodium Wyoming montmorillonite with one, two, or three water monolayers was investigated by Monte Carlo and molecular dynamics simulation, based on tested water-water, water-counterion, clay-water, and clay-counterion potential functions. Calculated layer spacings and thermodynamic properties, as well as interlayer water configurations and interlayer-species self-diffusion coefficients, weee in good agreement with available experimental data. Inner-sphere surface complexes of Na+ with tetrahedral charge sites persisted in all hydrates, whereas the outer-sphere surface complexes with octahedral charge sites found in the one-layer hydrate dissociated partially into an incipient diffuse layer in the two- and three-layer hydrates. Even in the three-layer hydrate, interlayer water molecules did not replicate their structure or mobility in bulk aqueous solution. Improved diffraction and spectroscopic data on interlayer water are needed to guide future simulation studies. {\textcopyright} 1995, American Chemical Society. All rights reserved.},
+author = {Chang, Fang-Ru Chou and Skipper, N. T. and Sposito, Garrison},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Chang, Skipper, Sposito - 1995 - Computer Simulation of Interlayer Molecular Structure in Sodium Montmorillonite Hydrates.pdf:pdf;::},
+issn = {0743-7463},
+journal = {Langmuir},
+mendeley-groups = {PhD},
+
+number = {7},
+pages = {2734--2741},
+title = {{Computer Simulation of Interlayer Molecular Structure in Sodium Montmorillonite Hydrates}},
+url = {https://pubs.acs.org/doi/abs/10.1021/la00007a064},
+volume = {11},
+year = {1995}
+}
+@article{Boek1995,
+abstract = {Monte Carlo molecular modeling simulations have been performed to investigate some of the microscopic mechanisms underlying smectite clay swelling. The systems we have studied represent hydrated Wyoming montmorillonites in which the counterions are Li+, Na+, or K+. For each of these three counterions we have conducted a series of 15 simulations in which the water content is increased systematically from 0 to 300 mg/g of clay. In this paper we introduce a new set of interaction potentials that can be used to study clay–water–cation systems and which lend themselves to future studies of intercalated organic molecules. We compare simulation data for the clay layer spacing with experimental swelling curves and find that the level of agreement is striking. Interestingly, in regions where the experimental curves exhibit hysteresis for adsorption/desorption, these loops enclose our calculated data. This indicates that our simulations indeed represent states of thermodynamic equilibrium, conditions which are harder to achieve experimentally. We are therefore content with our choice of atomistic interaction potentials for the current work. Analysis of the microscopic interlayer structure reveals a qualitative difference between Li+and Na+ on the one hand and K+ on the other. We find that as the water content is increased, both Li+and Na+ are able to hydrate, thereby becoming detached from the clay surface. In contrast, we find that K+ ions migrate to and bind to the clay surface during our simulations. Therefore K+ ions screen the negatively charged, mutually repelling clay surfaces more effectively than Na+ and Li+ ions do. The reluctance of K+ ions to fully hydrate will reduce the tendency of K+-saturated clays to expand. Our simulations therefore provide a qualitatively satisfying insight into the role of K+ ions as a clay swelling inhibitor. Indeed, the differences between Na+ and K+ ions displayed in these simulations may also be of more general relevance to colloid chemistry and physiology. {\textcopyright} 1995, American Chemical Society. All rights reserved.},
+author = {Boek, E. S. and Coveney, P. V. and Skipper, N. T.},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Boek, Coveney, Skipper - 1995 - Monte Carlo Molecular Modeling Studies of Hydrated Li-, Na-, and K-Smectites Understanding the Role of P.pdf:pdf},
+issn = {0002-7863},
+journal = {Journal of the American Chemical Society},
+mendeley-groups = {PhD},
+
+number = {50},
+pages = {12608--12617},
+title = {{Monte Carlo Molecular Modeling Studies of Hydrated Li-, Na-, and K-Smectites: Understanding the Role of Potassium as a Clay Swelling Inhibitor}},
+url = {https://pubs.acs.org/doi/abs/10.1021/ja00155a025},
+volume = {117},
+year = {1995}
+}
+@article{Marry2010,
+abstract = {We report a molecular simulation study of aqueous solutions at montmorillonite clay surfaces. Unlike most previous studies, we do not focus on the interlayer nanopores, but on both types of external surfaces of clay particles: basal surfaces along the clay layers, and lateral surfaces through which interlayer and larger interparticle pores are linked. We present results on structural, dynamic and thermodynamic properties, such as hydration complexes of ions, H-bonding network, modification of water dynamics with respect to bulk, role of water on cation exchange between interlayer and interparticle pores.},
+author = {Marry, Virginie and Malikova, Natalie and Turq, Pierre},
+
+file = {:home/hannahpollak/Downloads/Rotenberg et al. - 2010 - Molecular simulation of aqueous solutions at clay .pdf:pdf},
+journal = {Journal of Physics: Condensed Matter},
+mendeley-groups = {PhD},
+number = {28},
+pages = {284114},
+publisher = {IOP Publishing},
+title = {{Molecular simulation of aqueous solutions at clay surfaces}},
+url = {https://hal.archives-ouvertes.fr/hal-00531718},
+year = {2010}
+}
+@article{Rahromostaqim2018,
+abstract = {Swelling of clay minerals is important to a broad class of problems in science and engineering. While the problem has been extensively studied experimentally, past molecular modeling of the phenomenon was focused on pure clays of one type or another. In practice, however, there is a diverse class of mixed-layer clays (MLCs) in sedimentary rock with intermixed stacking sequence of two or more types of distinct layers within a single crystal. In fact, more than 60\% of sedimentary rocks in the U.S. contain various types of MLCs. We present the results, to our knowledge, of the first molecular dynamics simulation of hydration energetics and swelling of illite-montmorillonite (I-MMT) MLCs, the most common type of mixed clays. The swelling is studied as a function of the water concentration with three combinations of interlayer cations, namely, Na+ and K+. The hydration energies, the radial distribution functions, and the density profiles in the interlayer region are computed. For regular Na-MMT with layer charge concentrated in the octahedral sheet, weak cation-surface interaction results in fully hydrated ions and significant swelling. In the asymmetric interlayer of the MLC, however, the illite sheet with stronger interaction of surface and ions causes adsorption of the cations deep in the ditrigonal cavities of the siloxane surface. Given that the hydration enthalpy of K+ is smaller than that of Na+, its hydration shell is quite unstable compared with that of Na+. Therefore, swelling is inhibited as the ratio K+/Na+ increases. The results demonstrate the significant differences between the hydration and swelling properties of pure clays and the mixed ones, which have important implications in practice, particularly for sequestration of CO2 in sedimentary rock.},
+author = {Rahromostaqim, Mahsa and Sahimi, Muhammad},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Rahromostaqim, Sahimi - 2018 - Molecular Dynamics Simulation of Hydration and Swelling of Mixed-Layer Clays.pdf:pdf},
+issn = {1932-7447},
+journal = {The Journal of Physical Chemistry C},
+mendeley-groups = {PhD},
+
+number = {26},
+pages = {14631--14639},
+publisher = {American Chemical Society},
+title = {{Molecular Dynamics Simulation of Hydration and Swelling of Mixed-Layer Clays}},
+url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.8b03693},
+volume = {122},
+year = {2018}
+}
+@article{Rotenberg2010,
+abstract = {We report a molecular simulation study of aqueous solutions at montmorillonite clay surfaces. Unlike most previous studies, ours does not focus on the interlayer nanopores, but looks at both kinds of external surfaces of clay particles: basal surfaces along the clay layers, and lateral surfaces through which interlayer and larger interparticle pores are linked. We present results on structural, dynamic and thermodynamic properties and phenomena, including hydration complexes of ions, H bonding networks, modification of the water dynamics with respect to the bulk, and the role of water in the cation exchange between interlayer and interparticle pores. {\textcopyright} 2010 IOP Publishing Ltd.},
+author = {Rotenberg, B. and Marry, V. and Malikova, N. and Turq, P.},
+
+file = {:home/hannahpollak/Downloads/Rotenberg_2010_J._Phys. _Condens._Matter_22_284114.pdf:pdf},
+issn = {0953-8984},
+journal = {Journal of Physics: Condensed Matter},
+mendeley-groups = {PhD},
+
+number = {28},
+pages = {284114},
+pmid = {21399286},
+title = {{Molecular simulation of aqueous solutions at clay surfaces}},
+url = {https://iopscience.iop.org/article/10.1088/0953-8984/22/28/284114},
+volume = {22},
+year = {2010}
+}
+@article{Tambach2004,
+abstract = {We have carried out molecular simulations in the grand-canonical ensemble of water and cations in Wyoming and Arizona montmorillonite clay minerals, with varying relative humidity. Several water models and cations are used to investigate the swelling of these clays. We show how the water content depends on the type of clay, type of cation, the basal spacing, and the relative humidity. Related to the layering of water molecules in the interlayer space, the pressure normal to the clay sheets oscillates as a function of the basal spacing. Minima in corresponding free energy curves indicate the presence of dehydrated states and layered hydrates. The development of these stable states and the corresponding basal spacings are in agreement with experimental data. Density profiles show significantly different interlayer structures depending on the type of clay and models used. We show a relation between formation of two-layer hydrates and the position of the cations. The simulations with the MCY water model underestimate the spacings of two-and three-layer hydrates, whereas our simulations with the TIP4P model produce a better agreement. Therefore, we recommend the TIP4P model for simulating clay minerals. In addition, we report remarkable ordering of cations and water molecules in a one-layer Arizona montmorillonite hydrate.},
+author = {Tambach, Tim J. and Hensen, Emiel J.M. M. and Smit, Berend},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Tambach, Hensen, Smit - 2004 - Molecular Simulations of Swelling Clay Minerals.pdf:pdf},
+issn = {15206106},
+journal = {Journal of Physical Chemistry B},
+mendeley-groups = {PhD},
+
+number = {23},
+pages = {7586--7596},
+title = {{Molecular Simulations of Swelling Clay Minerals}},
+url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/jp049799h},
+volume = {108},
+year = {2004}
+}
+@article{Rotenberg2009,
+abstract = {We study the origin of the ionic exchange enthalpy in montmorillonite clays using microcalorimetry measurements and molecular simulation. We first determine the standard reaction enthalpy for well-defined interlayer water contents. We then show by a detailed analysis based on thermodynamic cycles that replacing Na+ ions by Cs+ in the interlayer of montmorillonite clays is an endothermic process, and that the overall exchange is exothermic only because it is dominated by the exothermic replacement of Cs+ by Na+ in the aqueous phase. This conclusion from ionic exchange enthalpies supports the one of a recent study of the ionic exchange free energy by Teppen and Miller [Teppen B. J. and Miller D. M. (2006) Hydration energy determines isovalent cation exchange selectivity by clay minerals. Soil Sci. Soc. Am. J. 70(1), 31-40] and contradicts long-held views on the role of ion-clay interactions in determining the ionic exchange thermodynamics. This calls for a paradigm shift for the origin of this exchange: The driving force is the "hydrophobicity" of Cs+ compared to Na+ and not its affinity for clay surfaces. {\textcopyright} 2009 Elsevier Ltd. All rights reserved.},
+author = {Rotenberg, Benjamin and Morel, Jean Pierre and Marry, Virginie and Turq, Pierre and Morel-Desrosiers, Nicole},
+
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Rotenberg et al. - 2009 - On the driving force of cation exchange in clays Insights from combined microcalorimetry experiments and molec.pdf:pdf},
+issn = {00167037},
+journal = {Geochimica et Cosmochimica Acta},
+mendeley-groups = {PhD},
+
+number = {14},
+pages = {4034--4044},
+title = {{On the driving force of cation exchange in clays: Insights from combined microcalorimetry experiments and molecular simulation}},
+volume = {73},
+year = {2009}
+}
+@article{VirginiaA.Colten-Bradley21987,
+author = {{Virginia A. Colten-Bradley (2)}},
+doi = {10.1306/703C8092-1707-11D7-8645000102C1865D},
+file = {::},
+issn = {0149-1423},
+journal = {AAPG Bulletin},
+month = {nov},
+number = {11},
+pages = {1414--1427},
+publisher = {GeoScienceWorld},
+title = {{Role of Pressure in Smectite Dehydration--Effects on Geopressure and Smectite-to-Illite Transformation}},
+url = {http://search.datapages.com/data/doi/10.1306/703C8092-1707-11D7-8645000102C1865D},
+volume = {71},
+year = {1987}
+}
+@article{Hensen2002,
+author = {Hensen, Emiel J. M. and Smit, Berend},
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hensen, Smit - 2002 - Why Clays Swell.pdf:pdf},
+issn = {1520-6106},
+journal = {The Journal of Physical Chemistry B},
+mendeley-groups = {PhD},
+month = {dec},
+number = {49},
+pages = {12664--12667},
+title = {{Why Clays Swell}},
+url = {https://pubs.acs.org/doi/10.1021/jp0264883},
+volume = {106},
+year = {2002}
+}
+@article{Gates2002,
+author = {Gates, W. P. and Slade, P. G. and Manceau, A. and Lanson, B.},
+doi = {10.1346/000986002760832829},
+file = {:home/hannahpollak/Downloads/Gates2002_Article_SiteOccupanciesByIronInNontron(1).pdf:pdf},
+issn = {00000000},
+journal = {Clays and Clay Minerals},
+mendeley-groups = {PhD},
+month = {apr},
+number = {2},
+pages = {223--239},
+title = {{Site Occupancies by Iron in Nontronites}},
+url = {http://link.springer.com/10.1346/000986002760832829},
+volume = {50},
+year = {2002}
+}
+
+@article{Jordan2021,
+abstract = {Iron-sulfur (FeS) proteins are ancient and fundamental to life, being involved in electron transfer and CO 2 fixation. FeS clusters have structures similar to the unit-cell of FeS minerals such as greigite, found in hydrothermal systems linked with the origin of life. However, the prebiotic pathway from mineral surfaces to biological clusters is unknown. Here we show that FeS clusters form spontaneously through interactions of inorganic Fe 2+ /Fe 3+ and S 2− with micromolar concentrations of the amino acid cysteine in water at alkaline pH. Bicarbonate ions stabilize the clusters and even promote cluster formation alone at concentrations >10 mM, probably through salting-out effects. We demonstrate robust, concentration-dependent formation of [4Fe4S], [2Fe2S] and mononuclear iron clusters using UV-Vis spectroscopy, 57 Fe-M{\"{o}}ssbauer spectroscopy and 1 H-NMR. Cyclic voltammetry shows that the clusters are redox-active. Our findings reveal that the structures responsible for biological electron transfer and CO 2 reduction could have formed spontaneously from monomers at the origin of life.},
+author = {Jordan, Sean F. and Ioannou, Ioannis and Rammu, Hanadi and Halpern, Aaron and Bogart, Lara K. and Ahn, Minkoo and Vasiliadou, Rafaela and Christodoulou, John and Mar{\'{e}}chal, Amandine and Lane, Nick},
+doi = {10.1038/s41467-021-26158-2},
+file = {:home/hannahpollak/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Jordan et al. - 2021 - Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine.pdf:pdf},
+issn = {2041-1723},
+journal = {Nature Communications},
+keywords = {Biogeochemistry,Biophysical chemistry,Carbon cycle},
+mendeley-groups = {PhD,PhD/Fe-S},
+month = {dec},
+number = {1},
+pages = {5925},
+pmid = {34635654},
+publisher = {Nature Publishing Group},
+title = {{Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine}},
+url = {https://www.nature.com/articles/s41467-021-26158-2},
+volume = {12},
+year = {2021}
+}
diff --git a/refs.bib b/refs.bib
new file mode 100644
index 00000000..5a1bfca1
--- /dev/null
+++ b/refs.bib
@@ -0,0 +1,130 @@
+@article{Gates2002,
+ title = {{Site Occupancies by Iron in Nontronites}},
+ year = {2002},
+ journal = {Clays and Clay Minerals},
+ author = {Gates, W. P. and Slade, P. G. and Manceau, A. and Lanson, B.},
+ number = {2},
+ month = {4},
+ pages = {223--239},
+ volume = {50},
+ doi = {10.1346/000986002760832829},
+ issn = {00000000}
+}
+
+@article{Frost2002,
+ title = {{The Garfield and Uley nontronites - An infrared spectroscopic comparison}},
+ year = {2002},
+ journal = {Spectrochimica Acta - Part A Molecular and Biomolecular Spectroscopy},
+ author = {Frost, Ray L. and Kloprogge, J. Theo and Ding, Zhe},
+ number = {9},
+ month = {7},
+ pages = {1881--1894},
+ volume = {58},
+ publisher = {Spectrochim Acta A Mol Biomol Spectrosc},
+ doi = {10.1016/S1386-1425(01)00638-2},
+ issn = {13861425},
+ pmid = {12164487},
+ keywords = {Dehydroxylation, FT-IR, Infrared emission spectroscopy, Montmorillonite, Nontronite, Smectite}
+}
+
+
+@article{Decarreau2014,
+ title = {{Fe 3+ /Al 3+ partitioning between tetrahedral and octahedral sites in dioctahedral smectites}},
+ year = {2014},
+ journal = {Clay Minerals},
+ author = {Decarreau, A. and Petit, S.},
+ number = {5},
+ month = {12},
+ pages = {657--665},
+ volume = {49},
+ publisher = {Mineralogical Society},
+ doi = {10.1180/claymin.2014.049.5.03},
+ issn = {0009-8558}
+}
+
+ @article{Baron2017,
+ title = {{Revisiting the nontronite M{\"{o}}ssbauer spectra}},
+ year = {2017},
+ journal = {American Mineralogist},
+ author = {Baron, Fabien and Petit, Sabine and Pentr{\'{a}}k, Martin and Decarreau, Alain and Stucki, Joseph W.},
+ number = {7},
+ month = {7},
+ pages = {1501--1515},
+ volume = {102},
+ publisher = {Walter de Gruyter GmbH},
+ doi = {10.2138/am-2017-1501x},
+ issn = {0003-004X},
+ keywords = {Clay minerals, M{\"{o}}ssbauer spectroscopy, iron, nontronite, smectites, tetrahedral iron}
+}
+
+@article{Ding2002,
+ title = {{Controlled rate thermal analysis of nontronite}},
+ year = {2002},
+ booktitle = {Thermochimica Acta},
+ author = {Ding, Z and Frost, R L},
+ number = {2},
+ pages = {185--193},
+ volume = {389},
+ doi = {10.1016/S0040-6031(02)00059-X},
+ keywords = {controlled rate thermal analysis, differential thermogravimetric analysis, ferruginous smectite, nontronite}
+}
+
+
+@article{Cygan2021,
+ title = {{Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces}},
+ year = {2021},
+ journal = {Journal of Physical Chemistry C},
+ author = {Cygan, Randall T. and Greathouse, Jeffery A. and Kalinichev, Andrey G.},
+ number = {32},
+ month = {8},
+ pages = {17573--17589},
+ volume = {125},
+ publisher = {American Chemical Society},
+ doi = {10.1021/ACS.JPCC.1C04600},
+ issn = {19327455}
+}
+
+
+@article{Cygan2004,
+ title = {{Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field}},
+ year = {2004},
+ journal = {Journal of Physical Chemistry B},
+ author = {Cygan, Randall T. and Liang, Jian Jie and Kalinichev, Andrey G.},
+ number = {4},
+ month = {1},
+ pages = {1255--1266},
+ volume = {108},
+ publisher = {American Chemical Society},
+ doi = {10.1021/JP0363287},
+}
+
+@book{li2016advances,
+ title={Advances in metal ion modeling},
+ author={Li, Pengfei},
+ year={2016},
+ publisher={Michigan State University}
+}
+
+@article{smith2023consequences,
+ title={Consequences of Overfitting the van der Waals Radii of Ions},
+ author={Smith, Madelyn and Li, Zhen and Landry, Luke and Merz Jr, Kenneth M and Li, Pengfei},
+ journal={Journal of Chemical Theory and Computation},
+ volume={19},
+ number={7},
+ pages={2064--2074},
+ year={2023},
+ publisher={ACS Publications},
+ doi={10.1021/acs.jctc.2c01255}
+}
+
+@article{hanwell2012avogadro,
+ title={Avogadro: an advanced semantic chemical editor, visualization, and analysis platform},
+ author={Hanwell, Marcus D and Curtis, Donald E and Lonie, David C and Vandermeersch, Tim and Zurek, Eva and Hutchison, Geoffrey R},
+ journal={Journal of cheminformatics},
+ volume={4},
+ number={1},
+ pages={1--17},
+ year={2012},
+ publisher={BioMed Central},
+ doi={10.1186/1758-2946-4-17}
+}
diff --git a/search.html b/search.html
new file mode 100644
index 00000000..aee01e8f
--- /dev/null
+++ b/search.html
@@ -0,0 +1,174 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Search Results
+ + + +
+ Searching...
+
+
+
+
+
+
+
+ ClayCode
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/search/lunr.js b/search/lunr.js
new file mode 100644
index 00000000..aca0a167
--- /dev/null
+++ b/search/lunr.js
@@ -0,0 +1,3475 @@
+/**
+ * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9
+ * Copyright (C) 2020 Oliver Nightingale
+ * @license MIT
+ */
+
+;(function(){
+
+/**
+ * A convenience function for configuring and constructing
+ * a new lunr Index.
+ *
+ * A lunr.Builder instance is created and the pipeline setup
+ * with a trimmer, stop word filter and stemmer.
+ *
+ * This builder object is yielded to the configuration function
+ * that is passed as a parameter, allowing the list of fields
+ * and other builder parameters to be customised.
+ *
+ * All documents _must_ be added within the passed config function.
+ *
+ * @example
+ * var idx = lunr(function () {
+ * this.field('title')
+ * this.field('body')
+ * this.ref('id')
+ *
+ * documents.forEach(function (doc) {
+ * this.add(doc)
+ * }, this)
+ * })
+ *
+ * @see {@link lunr.Builder}
+ * @see {@link lunr.Pipeline}
+ * @see {@link lunr.trimmer}
+ * @see {@link lunr.stopWordFilter}
+ * @see {@link lunr.stemmer}
+ * @namespace {function} lunr
+ */
+var lunr = function (config) {
+ var builder = new lunr.Builder
+
+ builder.pipeline.add(
+ lunr.trimmer,
+ lunr.stopWordFilter,
+ lunr.stemmer
+ )
+
+ builder.searchPipeline.add(
+ lunr.stemmer
+ )
+
+ config.call(builder, builder)
+ return builder.build()
+}
+
+lunr.version = "2.3.9"
+/*!
+ * lunr.utils
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A namespace containing utils for the rest of the lunr library
+ * @namespace lunr.utils
+ */
+lunr.utils = {}
+
+/**
+ * Print a warning message to the console.
+ *
+ * @param {String} message The message to be printed.
+ * @memberOf lunr.utils
+ * @function
+ */
+lunr.utils.warn = (function (global) {
+ /* eslint-disable no-console */
+ return function (message) {
+ if (global.console && console.warn) {
+ console.warn(message)
+ }
+ }
+ /* eslint-enable no-console */
+})(this)
+
+/**
+ * Convert an object to a string.
+ *
+ * In the case of `null` and `undefined` the function returns
+ * the empty string, in all other cases the result of calling
+ * `toString` on the passed object is returned.
+ *
+ * @param {Any} obj The object to convert to a string.
+ * @return {String} string representation of the passed object.
+ * @memberOf lunr.utils
+ */
+lunr.utils.asString = function (obj) {
+ if (obj === void 0 || obj === null) {
+ return ""
+ } else {
+ return obj.toString()
+ }
+}
+
+/**
+ * Clones an object.
+ *
+ * Will create a copy of an existing object such that any mutations
+ * on the copy cannot affect the original.
+ *
+ * Only shallow objects are supported, passing a nested object to this
+ * function will cause a TypeError.
+ *
+ * Objects with primitives, and arrays of primitives are supported.
+ *
+ * @param {Object} obj The object to clone.
+ * @return {Object} a clone of the passed object.
+ * @throws {TypeError} when a nested object is passed.
+ * @memberOf Utils
+ */
+lunr.utils.clone = function (obj) {
+ if (obj === null || obj === undefined) {
+ return obj
+ }
+
+ var clone = Object.create(null),
+ keys = Object.keys(obj)
+
+ for (var i = 0; i < keys.length; i++) {
+ var key = keys[i],
+ val = obj[key]
+
+ if (Array.isArray(val)) {
+ clone[key] = val.slice()
+ continue
+ }
+
+ if (typeof val === 'string' ||
+ typeof val === 'number' ||
+ typeof val === 'boolean') {
+ clone[key] = val
+ continue
+ }
+
+ throw new TypeError("clone is not deep and does not support nested objects")
+ }
+
+ return clone
+}
+lunr.FieldRef = function (docRef, fieldName, stringValue) {
+ this.docRef = docRef
+ this.fieldName = fieldName
+ this._stringValue = stringValue
+}
+
+lunr.FieldRef.joiner = "/"
+
+lunr.FieldRef.fromString = function (s) {
+ var n = s.indexOf(lunr.FieldRef.joiner)
+
+ if (n === -1) {
+ throw "malformed field ref string"
+ }
+
+ var fieldRef = s.slice(0, n),
+ docRef = s.slice(n + 1)
+
+ return new lunr.FieldRef (docRef, fieldRef, s)
+}
+
+lunr.FieldRef.prototype.toString = function () {
+ if (this._stringValue == undefined) {
+ this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef
+ }
+
+ return this._stringValue
+}
+/*!
+ * lunr.Set
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A lunr set.
+ *
+ * @constructor
+ */
+lunr.Set = function (elements) {
+ this.elements = Object.create(null)
+
+ if (elements) {
+ this.length = elements.length
+
+ for (var i = 0; i < this.length; i++) {
+ this.elements[elements[i]] = true
+ }
+ } else {
+ this.length = 0
+ }
+}
+
+/**
+ * A complete set that contains all elements.
+ *
+ * @static
+ * @readonly
+ * @type {lunr.Set}
+ */
+lunr.Set.complete = {
+ intersect: function (other) {
+ return other
+ },
+
+ union: function () {
+ return this
+ },
+
+ contains: function () {
+ return true
+ }
+}
+
+/**
+ * An empty set that contains no elements.
+ *
+ * @static
+ * @readonly
+ * @type {lunr.Set}
+ */
+lunr.Set.empty = {
+ intersect: function () {
+ return this
+ },
+
+ union: function (other) {
+ return other
+ },
+
+ contains: function () {
+ return false
+ }
+}
+
+/**
+ * Returns true if this set contains the specified object.
+ *
+ * @param {object} object - Object whose presence in this set is to be tested.
+ * @returns {boolean} - True if this set contains the specified object.
+ */
+lunr.Set.prototype.contains = function (object) {
+ return !!this.elements[object]
+}
+
+/**
+ * Returns a new set containing only the elements that are present in both
+ * this set and the specified set.
+ *
+ * @param {lunr.Set} other - set to intersect with this set.
+ * @returns {lunr.Set} a new set that is the intersection of this and the specified set.
+ */
+
+lunr.Set.prototype.intersect = function (other) {
+ var a, b, elements, intersection = []
+
+ if (other === lunr.Set.complete) {
+ return this
+ }
+
+ if (other === lunr.Set.empty) {
+ return other
+ }
+
+ if (this.length < other.length) {
+ a = this
+ b = other
+ } else {
+ a = other
+ b = this
+ }
+
+ elements = Object.keys(a.elements)
+
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i]
+ if (element in b.elements) {
+ intersection.push(element)
+ }
+ }
+
+ return new lunr.Set (intersection)
+}
+
+/**
+ * Returns a new set combining the elements of this and the specified set.
+ *
+ * @param {lunr.Set} other - set to union with this set.
+ * @return {lunr.Set} a new set that is the union of this and the specified set.
+ */
+
+lunr.Set.prototype.union = function (other) {
+ if (other === lunr.Set.complete) {
+ return lunr.Set.complete
+ }
+
+ if (other === lunr.Set.empty) {
+ return this
+ }
+
+ return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))
+}
+/**
+ * A function to calculate the inverse document frequency for
+ * a posting. This is shared between the builder and the index
+ *
+ * @private
+ * @param {object} posting - The posting for a given term
+ * @param {number} documentCount - The total number of documents.
+ */
+lunr.idf = function (posting, documentCount) {
+ var documentsWithTerm = 0
+
+ for (var fieldName in posting) {
+ if (fieldName == '_index') continue // Ignore the term index, its not a field
+ documentsWithTerm += Object.keys(posting[fieldName]).length
+ }
+
+ var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)
+
+ return Math.log(1 + Math.abs(x))
+}
+
+/**
+ * A token wraps a string representation of a token
+ * as it is passed through the text processing pipeline.
+ *
+ * @constructor
+ * @param {string} [str=''] - The string token being wrapped.
+ * @param {object} [metadata={}] - Metadata associated with this token.
+ */
+lunr.Token = function (str, metadata) {
+ this.str = str || ""
+ this.metadata = metadata || {}
+}
+
+/**
+ * Returns the token string that is being wrapped by this object.
+ *
+ * @returns {string}
+ */
+lunr.Token.prototype.toString = function () {
+ return this.str
+}
+
+/**
+ * A token update function is used when updating or optionally
+ * when cloning a token.
+ *
+ * @callback lunr.Token~updateFunction
+ * @param {string} str - The string representation of the token.
+ * @param {Object} metadata - All metadata associated with this token.
+ */
+
+/**
+ * Applies the given function to the wrapped string token.
+ *
+ * @example
+ * token.update(function (str, metadata) {
+ * return str.toUpperCase()
+ * })
+ *
+ * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.
+ * @returns {lunr.Token}
+ */
+lunr.Token.prototype.update = function (fn) {
+ this.str = fn(this.str, this.metadata)
+ return this
+}
+
+/**
+ * Creates a clone of this token. Optionally a function can be
+ * applied to the cloned token.
+ *
+ * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.
+ * @returns {lunr.Token}
+ */
+lunr.Token.prototype.clone = function (fn) {
+ fn = fn || function (s) { return s }
+ return new lunr.Token (fn(this.str, this.metadata), this.metadata)
+}
+/*!
+ * lunr.tokenizer
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A function for splitting a string into tokens ready to be inserted into
+ * the search index. Uses `lunr.tokenizer.separator` to split strings, change
+ * the value of this property to change how strings are split into tokens.
+ *
+ * This tokenizer will convert its parameter to a string by calling `toString` and
+ * then will split this string on the character in `lunr.tokenizer.separator`.
+ * Arrays will have their elements converted to strings and wrapped in a lunr.Token.
+ *
+ * Optional metadata can be passed to the tokenizer, this metadata will be cloned and
+ * added as metadata to every token that is created from the object to be tokenized.
+ *
+ * @static
+ * @param {?(string|object|object[])} obj - The object to convert into tokens
+ * @param {?object} metadata - Optional metadata to associate with every token
+ * @returns {lunr.Token[]}
+ * @see {@link lunr.Pipeline}
+ */
+lunr.tokenizer = function (obj, metadata) {
+ if (obj == null || obj == undefined) {
+ return []
+ }
+
+ if (Array.isArray(obj)) {
+ return obj.map(function (t) {
+ return new lunr.Token(
+ lunr.utils.asString(t).toLowerCase(),
+ lunr.utils.clone(metadata)
+ )
+ })
+ }
+
+ var str = obj.toString().toLowerCase(),
+ len = str.length,
+ tokens = []
+
+ for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {
+ var char = str.charAt(sliceEnd),
+ sliceLength = sliceEnd - sliceStart
+
+ if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {
+
+ if (sliceLength > 0) {
+ var tokenMetadata = lunr.utils.clone(metadata) || {}
+ tokenMetadata["position"] = [sliceStart, sliceLength]
+ tokenMetadata["index"] = tokens.length
+
+ tokens.push(
+ new lunr.Token (
+ str.slice(sliceStart, sliceEnd),
+ tokenMetadata
+ )
+ )
+ }
+
+ sliceStart = sliceEnd + 1
+ }
+
+ }
+
+ return tokens
+}
+
+/**
+ * The separator used to split a string into tokens. Override this property to change the behaviour of
+ * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.
+ *
+ * @static
+ * @see lunr.tokenizer
+ */
+lunr.tokenizer.separator = /[\s\-]+/
+/*!
+ * lunr.Pipeline
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr.Pipelines maintain an ordered list of functions to be applied to all
+ * tokens in documents entering the search index and queries being ran against
+ * the index.
+ *
+ * An instance of lunr.Index created with the lunr shortcut will contain a
+ * pipeline with a stop word filter and an English language stemmer. Extra
+ * functions can be added before or after either of these functions or these
+ * default functions can be removed.
+ *
+ * When run the pipeline will call each function in turn, passing a token, the
+ * index of that token in the original list of all tokens and finally a list of
+ * all the original tokens.
+ *
+ * The output of functions in the pipeline will be passed to the next function
+ * in the pipeline. To exclude a token from entering the index the function
+ * should return undefined, the rest of the pipeline will not be called with
+ * this token.
+ *
+ * For serialisation of pipelines to work, all functions used in an instance of
+ * a pipeline should be registered with lunr.Pipeline. Registered functions can
+ * then be loaded. If trying to load a serialised pipeline that uses functions
+ * that are not registered an error will be thrown.
+ *
+ * If not planning on serialising the pipeline then registering pipeline functions
+ * is not necessary.
+ *
+ * @constructor
+ */
+lunr.Pipeline = function () {
+ this._stack = []
+}
+
+lunr.Pipeline.registeredFunctions = Object.create(null)
+
+/**
+ * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token
+ * string as well as all known metadata. A pipeline function can mutate the token string
+ * or mutate (or add) metadata for a given token.
+ *
+ * A pipeline function can indicate that the passed token should be discarded by returning
+ * null, undefined or an empty string. This token will not be passed to any downstream pipeline
+ * functions and will not be added to the index.
+ *
+ * Multiple tokens can be returned by returning an array of tokens. Each token will be passed
+ * to any downstream pipeline functions and all will returned tokens will be added to the index.
+ *
+ * Any number of pipeline functions may be chained together using a lunr.Pipeline.
+ *
+ * @interface lunr.PipelineFunction
+ * @param {lunr.Token} token - A token from the document being processed.
+ * @param {number} i - The index of this token in the complete list of tokens for this document/field.
+ * @param {lunr.Token[]} tokens - All tokens for this document/field.
+ * @returns {(?lunr.Token|lunr.Token[])}
+ */
+
+/**
+ * Register a function with the pipeline.
+ *
+ * Functions that are used in the pipeline should be registered if the pipeline
+ * needs to be serialised, or a serialised pipeline needs to be loaded.
+ *
+ * Registering a function does not add it to a pipeline, functions must still be
+ * added to instances of the pipeline for them to be used when running a pipeline.
+ *
+ * @param {lunr.PipelineFunction} fn - The function to check for.
+ * @param {String} label - The label to register this function with
+ */
+lunr.Pipeline.registerFunction = function (fn, label) {
+ if (label in this.registeredFunctions) {
+ lunr.utils.warn('Overwriting existing registered function: ' + label)
+ }
+
+ fn.label = label
+ lunr.Pipeline.registeredFunctions[fn.label] = fn
+}
+
+/**
+ * Warns if the function is not registered as a Pipeline function.
+ *
+ * @param {lunr.PipelineFunction} fn - The function to check for.
+ * @private
+ */
+lunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {
+ var isRegistered = fn.label && (fn.label in this.registeredFunctions)
+
+ if (!isRegistered) {
+ lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\n', fn)
+ }
+}
+
+/**
+ * Loads a previously serialised pipeline.
+ *
+ * All functions to be loaded must already be registered with lunr.Pipeline.
+ * If any function from the serialised data has not been registered then an
+ * error will be thrown.
+ *
+ * @param {Object} serialised - The serialised pipeline to load.
+ * @returns {lunr.Pipeline}
+ */
+lunr.Pipeline.load = function (serialised) {
+ var pipeline = new lunr.Pipeline
+
+ serialised.forEach(function (fnName) {
+ var fn = lunr.Pipeline.registeredFunctions[fnName]
+
+ if (fn) {
+ pipeline.add(fn)
+ } else {
+ throw new Error('Cannot load unregistered function: ' + fnName)
+ }
+ })
+
+ return pipeline
+}
+
+/**
+ * Adds new functions to the end of the pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.
+ */
+lunr.Pipeline.prototype.add = function () {
+ var fns = Array.prototype.slice.call(arguments)
+
+ fns.forEach(function (fn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(fn)
+ this._stack.push(fn)
+ }, this)
+}
+
+/**
+ * Adds a single function after a function that already exists in the
+ * pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.
+ * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.
+ */
+lunr.Pipeline.prototype.after = function (existingFn, newFn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(newFn)
+
+ var pos = this._stack.indexOf(existingFn)
+ if (pos == -1) {
+ throw new Error('Cannot find existingFn')
+ }
+
+ pos = pos + 1
+ this._stack.splice(pos, 0, newFn)
+}
+
+/**
+ * Adds a single function before a function that already exists in the
+ * pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.
+ * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.
+ */
+lunr.Pipeline.prototype.before = function (existingFn, newFn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(newFn)
+
+ var pos = this._stack.indexOf(existingFn)
+ if (pos == -1) {
+ throw new Error('Cannot find existingFn')
+ }
+
+ this._stack.splice(pos, 0, newFn)
+}
+
+/**
+ * Removes a function from the pipeline.
+ *
+ * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.
+ */
+lunr.Pipeline.prototype.remove = function (fn) {
+ var pos = this._stack.indexOf(fn)
+ if (pos == -1) {
+ return
+ }
+
+ this._stack.splice(pos, 1)
+}
+
+/**
+ * Runs the current list of functions that make up the pipeline against the
+ * passed tokens.
+ *
+ * @param {Array} tokens The tokens to run through the pipeline.
+ * @returns {Array}
+ */
+lunr.Pipeline.prototype.run = function (tokens) {
+ var stackLength = this._stack.length
+
+ for (var i = 0; i < stackLength; i++) {
+ var fn = this._stack[i]
+ var memo = []
+
+ for (var j = 0; j < tokens.length; j++) {
+ var result = fn(tokens[j], j, tokens)
+
+ if (result === null || result === void 0 || result === '') continue
+
+ if (Array.isArray(result)) {
+ for (var k = 0; k < result.length; k++) {
+ memo.push(result[k])
+ }
+ } else {
+ memo.push(result)
+ }
+ }
+
+ tokens = memo
+ }
+
+ return tokens
+}
+
+/**
+ * Convenience method for passing a string through a pipeline and getting
+ * strings out. This method takes care of wrapping the passed string in a
+ * token and mapping the resulting tokens back to strings.
+ *
+ * @param {string} str - The string to pass through the pipeline.
+ * @param {?object} metadata - Optional metadata to associate with the token
+ * passed to the pipeline.
+ * @returns {string[]}
+ */
+lunr.Pipeline.prototype.runString = function (str, metadata) {
+ var token = new lunr.Token (str, metadata)
+
+ return this.run([token]).map(function (t) {
+ return t.toString()
+ })
+}
+
+/**
+ * Resets the pipeline by removing any existing processors.
+ *
+ */
+lunr.Pipeline.prototype.reset = function () {
+ this._stack = []
+}
+
+/**
+ * Returns a representation of the pipeline ready for serialisation.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @returns {Array}
+ */
+lunr.Pipeline.prototype.toJSON = function () {
+ return this._stack.map(function (fn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(fn)
+
+ return fn.label
+ })
+}
+/*!
+ * lunr.Vector
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A vector is used to construct the vector space of documents and queries. These
+ * vectors support operations to determine the similarity between two documents or
+ * a document and a query.
+ *
+ * Normally no parameters are required for initializing a vector, but in the case of
+ * loading a previously dumped vector the raw elements can be provided to the constructor.
+ *
+ * For performance reasons vectors are implemented with a flat array, where an elements
+ * index is immediately followed by its value. E.g. [index, value, index, value]. This
+ * allows the underlying array to be as sparse as possible and still offer decent
+ * performance when being used for vector calculations.
+ *
+ * @constructor
+ * @param {Number[]} [elements] - The flat list of element index and element value pairs.
+ */
+lunr.Vector = function (elements) {
+ this._magnitude = 0
+ this.elements = elements || []
+}
+
+
+/**
+ * Calculates the position within the vector to insert a given index.
+ *
+ * This is used internally by insert and upsert. If there are duplicate indexes then
+ * the position is returned as if the value for that index were to be updated, but it
+ * is the callers responsibility to check whether there is a duplicate at that index
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.positionForIndex = function (index) {
+ // For an empty vector the tuple can be inserted at the beginning
+ if (this.elements.length == 0) {
+ return 0
+ }
+
+ var start = 0,
+ end = this.elements.length / 2,
+ sliceLength = end - start,
+ pivotPoint = Math.floor(sliceLength / 2),
+ pivotIndex = this.elements[pivotPoint * 2]
+
+ while (sliceLength > 1) {
+ if (pivotIndex < index) {
+ start = pivotPoint
+ }
+
+ if (pivotIndex > index) {
+ end = pivotPoint
+ }
+
+ if (pivotIndex == index) {
+ break
+ }
+
+ sliceLength = end - start
+ pivotPoint = start + Math.floor(sliceLength / 2)
+ pivotIndex = this.elements[pivotPoint * 2]
+ }
+
+ if (pivotIndex == index) {
+ return pivotPoint * 2
+ }
+
+ if (pivotIndex > index) {
+ return pivotPoint * 2
+ }
+
+ if (pivotIndex < index) {
+ return (pivotPoint + 1) * 2
+ }
+}
+
+/**
+ * Inserts an element at an index within the vector.
+ *
+ * Does not allow duplicates, will throw an error if there is already an entry
+ * for this index.
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @param {Number} val - The value to be inserted into the vector.
+ */
+lunr.Vector.prototype.insert = function (insertIdx, val) {
+ this.upsert(insertIdx, val, function () {
+ throw "duplicate index"
+ })
+}
+
+/**
+ * Inserts or updates an existing index within the vector.
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @param {Number} val - The value to be inserted into the vector.
+ * @param {function} fn - A function that is called for updates, the existing value and the
+ * requested value are passed as arguments
+ */
+lunr.Vector.prototype.upsert = function (insertIdx, val, fn) {
+ this._magnitude = 0
+ var position = this.positionForIndex(insertIdx)
+
+ if (this.elements[position] == insertIdx) {
+ this.elements[position + 1] = fn(this.elements[position + 1], val)
+ } else {
+ this.elements.splice(position, 0, insertIdx, val)
+ }
+}
+
+/**
+ * Calculates the magnitude of this vector.
+ *
+ * @returns {Number}
+ */
+lunr.Vector.prototype.magnitude = function () {
+ if (this._magnitude) return this._magnitude
+
+ var sumOfSquares = 0,
+ elementsLength = this.elements.length
+
+ for (var i = 1; i < elementsLength; i += 2) {
+ var val = this.elements[i]
+ sumOfSquares += val * val
+ }
+
+ return this._magnitude = Math.sqrt(sumOfSquares)
+}
+
+/**
+ * Calculates the dot product of this vector and another vector.
+ *
+ * @param {lunr.Vector} otherVector - The vector to compute the dot product with.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.dot = function (otherVector) {
+ var dotProduct = 0,
+ a = this.elements, b = otherVector.elements,
+ aLen = a.length, bLen = b.length,
+ aVal = 0, bVal = 0,
+ i = 0, j = 0
+
+ while (i < aLen && j < bLen) {
+ aVal = a[i], bVal = b[j]
+ if (aVal < bVal) {
+ i += 2
+ } else if (aVal > bVal) {
+ j += 2
+ } else if (aVal == bVal) {
+ dotProduct += a[i + 1] * b[j + 1]
+ i += 2
+ j += 2
+ }
+ }
+
+ return dotProduct
+}
+
+/**
+ * Calculates the similarity between this vector and another vector.
+ *
+ * @param {lunr.Vector} otherVector - The other vector to calculate the
+ * similarity with.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.similarity = function (otherVector) {
+ return this.dot(otherVector) / this.magnitude() || 0
+}
+
+/**
+ * Converts the vector to an array of the elements within the vector.
+ *
+ * @returns {Number[]}
+ */
+lunr.Vector.prototype.toArray = function () {
+ var output = new Array (this.elements.length / 2)
+
+ for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {
+ output[j] = this.elements[i]
+ }
+
+ return output
+}
+
+/**
+ * A JSON serializable representation of the vector.
+ *
+ * @returns {Number[]}
+ */
+lunr.Vector.prototype.toJSON = function () {
+ return this.elements
+}
+/* eslint-disable */
+/*!
+ * lunr.stemmer
+ * Copyright (C) 2020 Oliver Nightingale
+ * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
+ */
+
+/**
+ * lunr.stemmer is an english language stemmer, this is a JavaScript
+ * implementation of the PorterStemmer taken from http://tartarus.org/~martin
+ *
+ * @static
+ * @implements {lunr.PipelineFunction}
+ * @param {lunr.Token} token - The string to stem
+ * @returns {lunr.Token}
+ * @see {@link lunr.Pipeline}
+ * @function
+ */
+lunr.stemmer = (function(){
+ var step2list = {
+ "ational" : "ate",
+ "tional" : "tion",
+ "enci" : "ence",
+ "anci" : "ance",
+ "izer" : "ize",
+ "bli" : "ble",
+ "alli" : "al",
+ "entli" : "ent",
+ "eli" : "e",
+ "ousli" : "ous",
+ "ization" : "ize",
+ "ation" : "ate",
+ "ator" : "ate",
+ "alism" : "al",
+ "iveness" : "ive",
+ "fulness" : "ful",
+ "ousness" : "ous",
+ "aliti" : "al",
+ "iviti" : "ive",
+ "biliti" : "ble",
+ "logi" : "log"
+ },
+
+ step3list = {
+ "icate" : "ic",
+ "ative" : "",
+ "alize" : "al",
+ "iciti" : "ic",
+ "ical" : "ic",
+ "ful" : "",
+ "ness" : ""
+ },
+
+ c = "[^aeiou]", // consonant
+ v = "[aeiouy]", // vowel
+ C = c + "[^aeiouy]*", // consonant sequence
+ V = v + "[aeiou]*", // vowel sequence
+
+ mgr0 = "^(" + C + ")?" + V + C, // [C]VC... is m>0
+ meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$", // [C]VC[V] is m=1
+ mgr1 = "^(" + C + ")?" + V + C + V + C, // [C]VCVC... is m>1
+ s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ var re_mgr0 = new RegExp(mgr0);
+ var re_mgr1 = new RegExp(mgr1);
+ var re_meq1 = new RegExp(meq1);
+ var re_s_v = new RegExp(s_v);
+
+ var re_1a = /^(.+?)(ss|i)es$/;
+ var re2_1a = /^(.+?)([^s])s$/;
+ var re_1b = /^(.+?)eed$/;
+ var re2_1b = /^(.+?)(ed|ing)$/;
+ var re_1b_2 = /.$/;
+ var re2_1b_2 = /(at|bl|iz)$/;
+ var re3_1b_2 = new RegExp("([^aeiouylsz])\\1$");
+ var re4_1b_2 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+
+ var re_1c = /^(.+?[^aeiou])y$/;
+ var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+
+ var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+
+ var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ var re2_4 = /^(.+?)(s|t)(ion)$/;
+
+ var re_5 = /^(.+?)e$/;
+ var re_5_1 = /ll$/;
+ var re3_5 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+
+ var porterStemmer = function porterStemmer(w) {
+ var stem,
+ suffix,
+ firstch,
+ re,
+ re2,
+ re3,
+ re4;
+
+ if (w.length < 3) { return w; }
+
+ firstch = w.substr(0,1);
+ if (firstch == "y") {
+ w = firstch.toUpperCase() + w.substr(1);
+ }
+
+ // Step 1a
+ re = re_1a
+ re2 = re2_1a;
+
+ if (re.test(w)) { w = w.replace(re,"$1$2"); }
+ else if (re2.test(w)) { w = w.replace(re2,"$1$2"); }
+
+ // Step 1b
+ re = re_1b;
+ re2 = re2_1b;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = re_mgr0;
+ if (re.test(fp[1])) {
+ re = re_1b_2;
+ w = w.replace(re,"");
+ }
+ } else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = re_s_v;
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = re2_1b_2;
+ re3 = re3_1b_2;
+ re4 = re4_1b_2;
+ if (re2.test(w)) { w = w + "e"; }
+ else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,""); }
+ else if (re4.test(w)) { w = w + "e"; }
+ }
+ }
+
+ // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)
+ re = re_1c;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = re_2;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = re_mgr0;
+ if (re.test(stem)) {
+ w = stem + step2list[suffix];
+ }
+ }
+
+ // Step 3
+ re = re_3;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = re_mgr0;
+ if (re.test(stem)) {
+ w = stem + step3list[suffix];
+ }
+ }
+
+ // Step 4
+ re = re_4;
+ re2 = re2_4;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = re_mgr1;
+ if (re.test(stem)) {
+ w = stem;
+ }
+ } else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = re_mgr1;
+ if (re2.test(stem)) {
+ w = stem;
+ }
+ }
+
+ // Step 5
+ re = re_5;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = re_mgr1;
+ re2 = re_meq1;
+ re3 = re3_5;
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {
+ w = stem;
+ }
+ }
+
+ re = re_5_1;
+ re2 = re_mgr1;
+ if (re.test(w) && re2.test(w)) {
+ re = re_1b_2;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+
+ if (firstch == "y") {
+ w = firstch.toLowerCase() + w.substr(1);
+ }
+
+ return w;
+ };
+
+ return function (token) {
+ return token.update(porterStemmer);
+ }
+})();
+
+lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')
+/*!
+ * lunr.stopWordFilter
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr.generateStopWordFilter builds a stopWordFilter function from the provided
+ * list of stop words.
+ *
+ * The built in lunr.stopWordFilter is built using this generator and can be used
+ * to generate custom stopWordFilters for applications or non English languages.
+ *
+ * @function
+ * @param {Array} token The token to pass through the filter
+ * @returns {lunr.PipelineFunction}
+ * @see lunr.Pipeline
+ * @see lunr.stopWordFilter
+ */
+lunr.generateStopWordFilter = function (stopWords) {
+ var words = stopWords.reduce(function (memo, stopWord) {
+ memo[stopWord] = stopWord
+ return memo
+ }, {})
+
+ return function (token) {
+ if (token && words[token.toString()] !== token.toString()) return token
+ }
+}
+
+/**
+ * lunr.stopWordFilter is an English language stop word list filter, any words
+ * contained in the list will not be passed through the filter.
+ *
+ * This is intended to be used in the Pipeline. If the token does not pass the
+ * filter then undefined will be returned.
+ *
+ * @function
+ * @implements {lunr.PipelineFunction}
+ * @params {lunr.Token} token - A token to check for being a stop word.
+ * @returns {lunr.Token}
+ * @see {@link lunr.Pipeline}
+ */
+lunr.stopWordFilter = lunr.generateStopWordFilter([
+ 'a',
+ 'able',
+ 'about',
+ 'across',
+ 'after',
+ 'all',
+ 'almost',
+ 'also',
+ 'am',
+ 'among',
+ 'an',
+ 'and',
+ 'any',
+ 'are',
+ 'as',
+ 'at',
+ 'be',
+ 'because',
+ 'been',
+ 'but',
+ 'by',
+ 'can',
+ 'cannot',
+ 'could',
+ 'dear',
+ 'did',
+ 'do',
+ 'does',
+ 'either',
+ 'else',
+ 'ever',
+ 'every',
+ 'for',
+ 'from',
+ 'get',
+ 'got',
+ 'had',
+ 'has',
+ 'have',
+ 'he',
+ 'her',
+ 'hers',
+ 'him',
+ 'his',
+ 'how',
+ 'however',
+ 'i',
+ 'if',
+ 'in',
+ 'into',
+ 'is',
+ 'it',
+ 'its',
+ 'just',
+ 'least',
+ 'let',
+ 'like',
+ 'likely',
+ 'may',
+ 'me',
+ 'might',
+ 'most',
+ 'must',
+ 'my',
+ 'neither',
+ 'no',
+ 'nor',
+ 'not',
+ 'of',
+ 'off',
+ 'often',
+ 'on',
+ 'only',
+ 'or',
+ 'other',
+ 'our',
+ 'own',
+ 'rather',
+ 'said',
+ 'say',
+ 'says',
+ 'she',
+ 'should',
+ 'since',
+ 'so',
+ 'some',
+ 'than',
+ 'that',
+ 'the',
+ 'their',
+ 'them',
+ 'then',
+ 'there',
+ 'these',
+ 'they',
+ 'this',
+ 'tis',
+ 'to',
+ 'too',
+ 'twas',
+ 'us',
+ 'wants',
+ 'was',
+ 'we',
+ 'were',
+ 'what',
+ 'when',
+ 'where',
+ 'which',
+ 'while',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'with',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+])
+
+lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')
+/*!
+ * lunr.trimmer
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr.trimmer is a pipeline function for trimming non word
+ * characters from the beginning and end of tokens before they
+ * enter the index.
+ *
+ * This implementation may not work correctly for non latin
+ * characters and should either be removed or adapted for use
+ * with languages with non-latin characters.
+ *
+ * @static
+ * @implements {lunr.PipelineFunction}
+ * @param {lunr.Token} token The token to pass through the filter
+ * @returns {lunr.Token}
+ * @see lunr.Pipeline
+ */
+lunr.trimmer = function (token) {
+ return token.update(function (s) {
+ return s.replace(/^\W+/, '').replace(/\W+$/, '')
+ })
+}
+
+lunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')
+/*!
+ * lunr.TokenSet
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A token set is used to store the unique list of all tokens
+ * within an index. Token sets are also used to represent an
+ * incoming query to the index, this query token set and index
+ * token set are then intersected to find which tokens to look
+ * up in the inverted index.
+ *
+ * A token set can hold multiple tokens, as in the case of the
+ * index token set, or it can hold a single token as in the
+ * case of a simple query token set.
+ *
+ * Additionally token sets are used to perform wildcard matching.
+ * Leading, contained and trailing wildcards are supported, and
+ * from this edit distance matching can also be provided.
+ *
+ * Token sets are implemented as a minimal finite state automata,
+ * where both common prefixes and suffixes are shared between tokens.
+ * This helps to reduce the space used for storing the token set.
+ *
+ * @constructor
+ */
+lunr.TokenSet = function () {
+ this.final = false
+ this.edges = {}
+ this.id = lunr.TokenSet._nextId
+ lunr.TokenSet._nextId += 1
+}
+
+/**
+ * Keeps track of the next, auto increment, identifier to assign
+ * to a new tokenSet.
+ *
+ * TokenSets require a unique identifier to be correctly minimised.
+ *
+ * @private
+ */
+lunr.TokenSet._nextId = 1
+
+/**
+ * Creates a TokenSet instance from the given sorted array of words.
+ *
+ * @param {String[]} arr - A sorted array of strings to create the set from.
+ * @returns {lunr.TokenSet}
+ * @throws Will throw an error if the input array is not sorted.
+ */
+lunr.TokenSet.fromArray = function (arr) {
+ var builder = new lunr.TokenSet.Builder
+
+ for (var i = 0, len = arr.length; i < len; i++) {
+ builder.insert(arr[i])
+ }
+
+ builder.finish()
+ return builder.root
+}
+
+/**
+ * Creates a token set from a query clause.
+ *
+ * @private
+ * @param {Object} clause - A single clause from lunr.Query.
+ * @param {string} clause.term - The query clause term.
+ * @param {number} [clause.editDistance] - The optional edit distance for the term.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.fromClause = function (clause) {
+ if ('editDistance' in clause) {
+ return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)
+ } else {
+ return lunr.TokenSet.fromString(clause.term)
+ }
+}
+
+/**
+ * Creates a token set representing a single string with a specified
+ * edit distance.
+ *
+ * Insertions, deletions, substitutions and transpositions are each
+ * treated as an edit distance of 1.
+ *
+ * Increasing the allowed edit distance will have a dramatic impact
+ * on the performance of both creating and intersecting these TokenSets.
+ * It is advised to keep the edit distance less than 3.
+ *
+ * @param {string} str - The string to create the token set from.
+ * @param {number} editDistance - The allowed edit distance to match.
+ * @returns {lunr.Vector}
+ */
+lunr.TokenSet.fromFuzzyString = function (str, editDistance) {
+ var root = new lunr.TokenSet
+
+ var stack = [{
+ node: root,
+ editsRemaining: editDistance,
+ str: str
+ }]
+
+ while (stack.length) {
+ var frame = stack.pop()
+
+ // no edit
+ if (frame.str.length > 0) {
+ var char = frame.str.charAt(0),
+ noEditNode
+
+ if (char in frame.node.edges) {
+ noEditNode = frame.node.edges[char]
+ } else {
+ noEditNode = new lunr.TokenSet
+ frame.node.edges[char] = noEditNode
+ }
+
+ if (frame.str.length == 1) {
+ noEditNode.final = true
+ }
+
+ stack.push({
+ node: noEditNode,
+ editsRemaining: frame.editsRemaining,
+ str: frame.str.slice(1)
+ })
+ }
+
+ if (frame.editsRemaining == 0) {
+ continue
+ }
+
+ // insertion
+ if ("*" in frame.node.edges) {
+ var insertionNode = frame.node.edges["*"]
+ } else {
+ var insertionNode = new lunr.TokenSet
+ frame.node.edges["*"] = insertionNode
+ }
+
+ if (frame.str.length == 0) {
+ insertionNode.final = true
+ }
+
+ stack.push({
+ node: insertionNode,
+ editsRemaining: frame.editsRemaining - 1,
+ str: frame.str
+ })
+
+ // deletion
+ // can only do a deletion if we have enough edits remaining
+ // and if there are characters left to delete in the string
+ if (frame.str.length > 1) {
+ stack.push({
+ node: frame.node,
+ editsRemaining: frame.editsRemaining - 1,
+ str: frame.str.slice(1)
+ })
+ }
+
+ // deletion
+ // just removing the last character from the str
+ if (frame.str.length == 1) {
+ frame.node.final = true
+ }
+
+ // substitution
+ // can only do a substitution if we have enough edits remaining
+ // and if there are characters left to substitute
+ if (frame.str.length >= 1) {
+ if ("*" in frame.node.edges) {
+ var substitutionNode = frame.node.edges["*"]
+ } else {
+ var substitutionNode = new lunr.TokenSet
+ frame.node.edges["*"] = substitutionNode
+ }
+
+ if (frame.str.length == 1) {
+ substitutionNode.final = true
+ }
+
+ stack.push({
+ node: substitutionNode,
+ editsRemaining: frame.editsRemaining - 1,
+ str: frame.str.slice(1)
+ })
+ }
+
+ // transposition
+ // can only do a transposition if there are edits remaining
+ // and there are enough characters to transpose
+ if (frame.str.length > 1) {
+ var charA = frame.str.charAt(0),
+ charB = frame.str.charAt(1),
+ transposeNode
+
+ if (charB in frame.node.edges) {
+ transposeNode = frame.node.edges[charB]
+ } else {
+ transposeNode = new lunr.TokenSet
+ frame.node.edges[charB] = transposeNode
+ }
+
+ if (frame.str.length == 1) {
+ transposeNode.final = true
+ }
+
+ stack.push({
+ node: transposeNode,
+ editsRemaining: frame.editsRemaining - 1,
+ str: charA + frame.str.slice(2)
+ })
+ }
+ }
+
+ return root
+}
+
+/**
+ * Creates a TokenSet from a string.
+ *
+ * The string may contain one or more wildcard characters (*)
+ * that will allow wildcard matching when intersecting with
+ * another TokenSet.
+ *
+ * @param {string} str - The string to create a TokenSet from.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.fromString = function (str) {
+ var node = new lunr.TokenSet,
+ root = node
+
+ /*
+ * Iterates through all characters within the passed string
+ * appending a node for each character.
+ *
+ * When a wildcard character is found then a self
+ * referencing edge is introduced to continually match
+ * any number of any characters.
+ */
+ for (var i = 0, len = str.length; i < len; i++) {
+ var char = str[i],
+ final = (i == len - 1)
+
+ if (char == "*") {
+ node.edges[char] = node
+ node.final = final
+
+ } else {
+ var next = new lunr.TokenSet
+ next.final = final
+
+ node.edges[char] = next
+ node = next
+ }
+ }
+
+ return root
+}
+
+/**
+ * Converts this TokenSet into an array of strings
+ * contained within the TokenSet.
+ *
+ * This is not intended to be used on a TokenSet that
+ * contains wildcards, in these cases the results are
+ * undefined and are likely to cause an infinite loop.
+ *
+ * @returns {string[]}
+ */
+lunr.TokenSet.prototype.toArray = function () {
+ var words = []
+
+ var stack = [{
+ prefix: "",
+ node: this
+ }]
+
+ while (stack.length) {
+ var frame = stack.pop(),
+ edges = Object.keys(frame.node.edges),
+ len = edges.length
+
+ if (frame.node.final) {
+ /* In Safari, at this point the prefix is sometimes corrupted, see:
+ * https://github.com/olivernn/lunr.js/issues/279 Calling any
+ * String.prototype method forces Safari to "cast" this string to what
+ * it's supposed to be, fixing the bug. */
+ frame.prefix.charAt(0)
+ words.push(frame.prefix)
+ }
+
+ for (var i = 0; i < len; i++) {
+ var edge = edges[i]
+
+ stack.push({
+ prefix: frame.prefix.concat(edge),
+ node: frame.node.edges[edge]
+ })
+ }
+ }
+
+ return words
+}
+
+/**
+ * Generates a string representation of a TokenSet.
+ *
+ * This is intended to allow TokenSets to be used as keys
+ * in objects, largely to aid the construction and minimisation
+ * of a TokenSet. As such it is not designed to be a human
+ * friendly representation of the TokenSet.
+ *
+ * @returns {string}
+ */
+lunr.TokenSet.prototype.toString = function () {
+ // NOTE: Using Object.keys here as this.edges is very likely
+ // to enter 'hash-mode' with many keys being added
+ //
+ // avoiding a for-in loop here as it leads to the function
+ // being de-optimised (at least in V8). From some simple
+ // benchmarks the performance is comparable, but allowing
+ // V8 to optimize may mean easy performance wins in the future.
+
+ if (this._str) {
+ return this._str
+ }
+
+ var str = this.final ? '1' : '0',
+ labels = Object.keys(this.edges).sort(),
+ len = labels.length
+
+ for (var i = 0; i < len; i++) {
+ var label = labels[i],
+ node = this.edges[label]
+
+ str = str + label + node.id
+ }
+
+ return str
+}
+
+/**
+ * Returns a new TokenSet that is the intersection of
+ * this TokenSet and the passed TokenSet.
+ *
+ * This intersection will take into account any wildcards
+ * contained within the TokenSet.
+ *
+ * @param {lunr.TokenSet} b - An other TokenSet to intersect with.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.prototype.intersect = function (b) {
+ var output = new lunr.TokenSet,
+ frame = undefined
+
+ var stack = [{
+ qNode: b,
+ output: output,
+ node: this
+ }]
+
+ while (stack.length) {
+ frame = stack.pop()
+
+ // NOTE: As with the #toString method, we are using
+ // Object.keys and a for loop instead of a for-in loop
+ // as both of these objects enter 'hash' mode, causing
+ // the function to be de-optimised in V8
+ var qEdges = Object.keys(frame.qNode.edges),
+ qLen = qEdges.length,
+ nEdges = Object.keys(frame.node.edges),
+ nLen = nEdges.length
+
+ for (var q = 0; q < qLen; q++) {
+ var qEdge = qEdges[q]
+
+ for (var n = 0; n < nLen; n++) {
+ var nEdge = nEdges[n]
+
+ if (nEdge == qEdge || qEdge == '*') {
+ var node = frame.node.edges[nEdge],
+ qNode = frame.qNode.edges[qEdge],
+ final = node.final && qNode.final,
+ next = undefined
+
+ if (nEdge in frame.output.edges) {
+ // an edge already exists for this character
+ // no need to create a new node, just set the finality
+ // bit unless this node is already final
+ next = frame.output.edges[nEdge]
+ next.final = next.final || final
+
+ } else {
+ // no edge exists yet, must create one
+ // set the finality bit and insert it
+ // into the output
+ next = new lunr.TokenSet
+ next.final = final
+ frame.output.edges[nEdge] = next
+ }
+
+ stack.push({
+ qNode: qNode,
+ output: next,
+ node: node
+ })
+ }
+ }
+ }
+ }
+
+ return output
+}
+lunr.TokenSet.Builder = function () {
+ this.previousWord = ""
+ this.root = new lunr.TokenSet
+ this.uncheckedNodes = []
+ this.minimizedNodes = {}
+}
+
+lunr.TokenSet.Builder.prototype.insert = function (word) {
+ var node,
+ commonPrefix = 0
+
+ if (word < this.previousWord) {
+ throw new Error ("Out of order word insertion")
+ }
+
+ for (var i = 0; i < word.length && i < this.previousWord.length; i++) {
+ if (word[i] != this.previousWord[i]) break
+ commonPrefix++
+ }
+
+ this.minimize(commonPrefix)
+
+ if (this.uncheckedNodes.length == 0) {
+ node = this.root
+ } else {
+ node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child
+ }
+
+ for (var i = commonPrefix; i < word.length; i++) {
+ var nextNode = new lunr.TokenSet,
+ char = word[i]
+
+ node.edges[char] = nextNode
+
+ this.uncheckedNodes.push({
+ parent: node,
+ char: char,
+ child: nextNode
+ })
+
+ node = nextNode
+ }
+
+ node.final = true
+ this.previousWord = word
+}
+
+lunr.TokenSet.Builder.prototype.finish = function () {
+ this.minimize(0)
+}
+
+lunr.TokenSet.Builder.prototype.minimize = function (downTo) {
+ for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {
+ var node = this.uncheckedNodes[i],
+ childKey = node.child.toString()
+
+ if (childKey in this.minimizedNodes) {
+ node.parent.edges[node.char] = this.minimizedNodes[childKey]
+ } else {
+ // Cache the key for this node since
+ // we know it can't change anymore
+ node.child._str = childKey
+
+ this.minimizedNodes[childKey] = node.child
+ }
+
+ this.uncheckedNodes.pop()
+ }
+}
+/*!
+ * lunr.Index
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * An index contains the built index of all documents and provides a query interface
+ * to the index.
+ *
+ * Usually instances of lunr.Index will not be created using this constructor, instead
+ * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be
+ * used to load previously built and serialized indexes.
+ *
+ * @constructor
+ * @param {Object} attrs - The attributes of the built search index.
+ * @param {Object} attrs.invertedIndex - An index of term/field to document reference.
+ * @param {Object' + noResultsText + '
'); + } +} + +function doSearch () { + var query = document.getElementById('mkdocs-search-query').value; + if (query.length > min_search_length) { + if (!window.Worker) { + displayResults(search(query)); + } else { + searchWorker.postMessage({query: query}); + } + } else { + // Clear results for short queries + displayResults([]); + } +} + +function initSearch () { + var search_input = document.getElementById('mkdocs-search-query'); + if (search_input) { + search_input.addEventListener("keyup", doSearch); + } + var term = getSearchTermFromLocation(); + if (term) { + search_input.value = term; + doSearch(); + } +} + +function onWorkerMessage (e) { + if (e.data.allowSearch) { + initSearch(); + } else if (e.data.results) { + var results = e.data.results; + displayResults(results); + } else if (e.data.config) { + min_search_length = e.data.config.min_search_length-1; + } +} + +if (!window.Worker) { + console.log('Web Worker API not supported'); + // load index in main thread + $.getScript(joinUrl(base_url, "search/worker.js")).done(function () { + console.log('Loaded worker'); + init(); + window.postMessage = function (msg) { + onWorkerMessage({data: msg}); + }; + }).fail(function (jqxhr, settings, exception) { + console.error('Could not load worker.js'); + }); +} else { + // Wrap search in a web worker + var searchWorker = new Worker(joinUrl(base_url, "search/worker.js")); + searchWorker.postMessage({init: true}); + searchWorker.onmessage = onWorkerMessage; +} diff --git a/search/search_index.json b/search/search_index.json new file mode 100644 index 00000000..024288a3 --- /dev/null +++ b/search/search_index.json @@ -0,0 +1 @@ +{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"ClayCode generates clay mineral structures based upon their natural partially ocupied unit cell compositions and assigns ClayFF forecefield parameters, generating all the input files ready for simulation with Gromacs software. Here Quick Start User Guide Tutorials On GitHub GitHub Project Report bugs and give sugestions for future improvements and new features via issues Contribute via branches and pull requests Claycode is published under the MIT License ClayCode is developed by Hannah Pollak, Matteo Degiacomi and Valentina Erastova, University of Edinburgh, 2023 Please CITE us: HP, MTD, VE \"ClayCode: setting up clay structures from simulation in Gromacs\", DOI: XXX","title":"Home"},{"location":"#here","text":"Quick Start User Guide Tutorials","title":"Here"},{"location":"#on-github","text":"GitHub Project Report bugs and give sugestions for future improvements and new features via issues Contribute via branches and pull requests Claycode is published under the MIT License ClayCode is developed by Hannah Pollak, Matteo Degiacomi and Valentina Erastova, University of Edinburgh, 2023 Please CITE us: HP, MTD, VE \"ClayCode: setting up clay structures from simulation in Gromacs\", DOI: XXX","title":"On GitHub"},{"location":"CSV/","text":"Clay stoicheometry in CSV format Including into Input Parameter File The .CSV file must be included into the INPUT .YAML file : the path to the CSV file is specified under CLAY_COMP , target occupancies from the CSV file are given by SYSNAME , corresponding to the clay name. e.g.: CLAY_COMP: /path/to/clay_comp.csv SYSNAME: NAu-1-fe File Structure First column: sheet for tetrahedral ( T ) and octahedral ( O ) occupancies; interlayer ion ( I ) ocupansies, if the total charge ( tot second column) is non-zero; T , O and total ( tot ) average unit cell charge ( C ). Second column with element : Atom names (if atom is not supported by ClayFF.FF, ClayCode.builder will try to assign it to the supported atom of same charge and re-assign the ocupansies); charges for the T layer, O layer and tot total; The oxidation state of clay atoms can be specified by adding the charge after the element name (e.g. Fe2). Rules Occupancies: Total occupancies for each dioctahedral/trioctahedral tetrahedral ( T ) sheet should sum up to 4. For octahedral ( O ) sheets, the total occupancies should amount to 4/3 for dioctahedral/trioctahedral unit cell types, respectively. For example, the occupancies of a dioctahedral 2:1 clay (TOT) should have T occupancies of 8, and O occupancies of 4; Experimental stoichiometries do not necessarily sum up to interger occupancies. ClayCode.builder will first process the target composition such that the occupancies match those expected for the specified unit cell type . Interlayer Ions: Interlayer ions will be added to compensate the total charge imbalance resulting from substitutions. The ratio of these ions can be specified in the I section. The sum of all ion contributions should sum to 1. Only ion species of the opposite sign to the layer charge will be considered. Iron 2+/3+: There is no need to specify how much of the total iron is Fe3+ or Fe2+ if at least two values among the total, T and O unit cell charge are specified. ClayCode.builder can perform the splitting between the two iron species. Supplied CSV file The supplied file within directory Tutorial is exp_clay.csv and contains clay structures corresponding to the Source Clays listed under \"Physical and Chemical Data of Source Clays\" clays.org . 1:1 (TO) dioctohedral smectite: Kaolin KGa-1; 2:1 (TOT) dioctohedral smectite: Na-Montmorillonite (Wyoming) SWy-1, Illite IMt-1, Ferruginous Smectite SWa-1, Nontronite NAu-1-fe, Nontronite NAu-2-fe, Nontronite NG-1; example Al-Mg 3:1 layered double hydroxide (not via clays.org ): LDH31. Example Example from clay_comp.csv file for NAu-1 and NAu-2 nontronite clays: sheet element NAu-1-fe NAu-2-fe T Si 6.98 7.55 T Al 0.95 0.16 T Fe3 0.07 0.29 O Fe 3.61 3.54 O Al 0.36 0.34 O Mg 0.04 0.05 I Ca 0.525 0.36 I Na 0 0 I Mg 0 0 I K 0 0 I Cl 0 0 C T -1.02 -0.45 C O -0.03 -0.27 C tot -1.05 -0.72","title":"CSV"},{"location":"CSV/#clay-stoicheometry-in-csv-format","text":"","title":"Clay stoicheometry in CSV format"},{"location":"CSV/#including-into-input-parameter-file","text":"The .CSV file must be included into the INPUT .YAML file : the path to the CSV file is specified under CLAY_COMP , target occupancies from the CSV file are given by SYSNAME , corresponding to the clay name. e.g.: CLAY_COMP: /path/to/clay_comp.csv SYSNAME: NAu-1-fe","title":"Including into Input Parameter File"},{"location":"CSV/#file-structure","text":"First column: sheet for tetrahedral ( T ) and octahedral ( O ) occupancies; interlayer ion ( I ) ocupansies, if the total charge ( tot second column) is non-zero; T , O and total ( tot ) average unit cell charge ( C ). Second column with element : Atom names (if atom is not supported by ClayFF.FF, ClayCode.builder will try to assign it to the supported atom of same charge and re-assign the ocupansies); charges for the T layer, O layer and tot total; The oxidation state of clay atoms can be specified by adding the charge after the element name (e.g. Fe2).","title":"File Structure"},{"location":"CSV/#rules","text":"","title":"Rules"},{"location":"CSV/#occupancies","text":"Total occupancies for each dioctahedral/trioctahedral tetrahedral ( T ) sheet should sum up to 4. For octahedral ( O ) sheets, the total occupancies should amount to 4/3 for dioctahedral/trioctahedral unit cell types, respectively. For example, the occupancies of a dioctahedral 2:1 clay (TOT) should have T occupancies of 8, and O occupancies of 4; Experimental stoichiometries do not necessarily sum up to interger occupancies. ClayCode.builder will first process the target composition such that the occupancies match those expected for the specified unit cell type .","title":"Occupancies:"},{"location":"CSV/#interlayer-ions","text":"Interlayer ions will be added to compensate the total charge imbalance resulting from substitutions. The ratio of these ions can be specified in the I section. The sum of all ion contributions should sum to 1. Only ion species of the opposite sign to the layer charge will be considered.","title":"Interlayer Ions:"},{"location":"CSV/#iron-23","text":"There is no need to specify how much of the total iron is Fe3+ or Fe2+ if at least two values among the total, T and O unit cell charge are specified. ClayCode.builder can perform the splitting between the two iron species.","title":"Iron 2+/3+:"},{"location":"CSV/#supplied-csv-file","text":"The supplied file within directory Tutorial is exp_clay.csv and contains clay structures corresponding to the Source Clays listed under \"Physical and Chemical Data of Source Clays\" clays.org . 1:1 (TO) dioctohedral smectite: Kaolin KGa-1; 2:1 (TOT) dioctohedral smectite: Na-Montmorillonite (Wyoming) SWy-1, Illite IMt-1, Ferruginous Smectite SWa-1, Nontronite NAu-1-fe, Nontronite NAu-2-fe, Nontronite NG-1; example Al-Mg 3:1 layered double hydroxide (not via clays.org ): LDH31.","title":"Supplied CSV file"},{"location":"CSV/#example","text":"Example from clay_comp.csv file for NAu-1 and NAu-2 nontronite clays: sheet element NAu-1-fe NAu-2-fe T Si 6.98 7.55 T Al 0.95 0.16 T Fe3 0.07 0.29 O Fe 3.61 3.54 O Al 0.36 0.34 O Mg 0.04 0.05 I Ca 0.525 0.36 I Na 0 0 I Mg 0 0 I K 0 0 I Cl 0 0 C T -1.02 -0.45 C O -0.03 -0.27 C tot -1.05 -0.72","title":"Example"},{"location":"YAML/","text":"ClayCode.builder System Specifications YAML file ClayCode.builder reads the parameters specified in this file. Required Parameters The first section contains general parameters that are required for the model construction. OUTPATH - output directory path [str] Directory in which output folder is created. SYSNAME - clay system name [str] Th name for clay type, must to match a column header in the CSV file, the created output folder will also have this name. Avoid spaces and unusual symbols. CLAY_COMP - filename.csv [str] Name of CSV file where the target stoichiometry for the system specified under SYSNAME . CLAY_TYPE - unit cell type [str] Clay unit cell type, available in data/UCS directory. Such as: Dioctahedral 2:1 - D21 Trioctahedral 2:1 - T21 Dioctahedral 1:1 - D11 Trioctahedral 1:1 - T11 layered double hydroxide 3:1 - L31 layered double hydroxide 2:1 - L21 Sepiolite - SEP Note : Only D21, D11 and L31 are supplied with current release. Example: # output directory path OUTPATH: /path/to/output/directory # name of system SYSNAME: NAu-1-fe # name of CSV file with target stoichiometry CLAY_COMP: /path/to/clay_comp.csv # clay type CLAY_TYPE: D21 # Dioctahedral 2:1 - D21 Optional Parameters This is an optional parameter section, if the directives are not given by the user, ClayCode.builder will use default values. Clay Sheet Size X_CELLS - Unit cell number [int] (Default: 7) Number of unit cells in x-direction. Note : Future version will have the option to specify target x-dimensions X_DIM Y_CELLS - Unit cell number [int] (Default: 5) Number of unit cells in y-direction. Note : Future version will have the option to specify target y-dimensions Y_DIM N_SHEETS - Unit cell number [int] (Default: 3) Number of sheets of 1 unit cell thickness to be stacked in z-direction. Example: # number of unit cells in x direction (Default 7) X_CELLS: 7 # number of unit cells in y direction (Default 5) Y_CELLS: 5 # number of unit cells in z direction (Default 3) N_SHEETS: 3 Clay Composition ClayCode.builder calculates the number and type of unit cells necessary to match the desired composition, as given in CSV file. If, instead, the user would like to specify this manually, the following parameters can be used: UC_INDEX_LIST - unit cell list [list] required unit cells, as specified in data/UCS directory, to use for building the system UC_RATIOS_LIST - probabilities [list] probability list for the above unit cells, total probability must be 1.00 Example: The following script will use the dioctohedral 2:1 unit cells, which are both neutral smectite unit cells, with the latter having 1 octohedral Al substitution for the Fe3. This will produce a neutral smectite with the following stoichiometry: \\mathrm{Si_8 \\left[Al_{3.8}Fe_{0.2}\\right]} . # required UCs to builder system as list UC_INDEX_LIST: [D221 D228] # probability list of unit cells in system UC_RATIOS_LIST: [0.8 0.2] Interlayer Solvent and Ions IL_SOLV - interlayer solvent presence [bool] (Default: True ) If True interlayer space should be solvated, otherwise False will produce non-hydrated clay. There are three options to handle interlayer water and interlayer ions, only one should be specified : ION_WATERS - number of waters per ion [int, Dict[str: int]] Number of water molecules that should be added per ion. If a single number [int] is given, all of the ions will be hydrated by the same number of waters. To specify number of waters per ion-type the entry should be a citionary, then the total number of water molecules will be mapped to the specifications given for each of the interlayer occupancies I in the CSV entry. Example: A given number of waters will be added for each cation, which quantity is specified in the clay stoichiometry CSV file. ION_WATERS: Ca: 12 Na: 12 K: 10 UC_WATERS - number of water molecules per unit cell [int] The specified number of water molecules multiplied by the number of unit cells is added into each of the interlayer spaces. SPACING_WATERS - hydrated interleyer spacing, in A [float] (Default 10.0 A) Target interlayer spacing filled with water, final value may vary due to the water rearrangement when in contact with clay surface and packing around ions. Simulation Box Specifications BOX_HEIGHT - simulation box height in A [float] Size of the final simulation box in z-direction in A, note the clay layers are positioned in xy-plane. BULK_SOLV - bulk solvent presence [bool] (Default: True ) If True the box space will be filled with water, otherwise False will keep the box empty. This is useful if further plan is to add other species, such as oil, into the system. BULK_IONS - type of ions and their concentration in mol/L [int, Dict[str: int]] Ions to be added into the bulk solvated space. Note : GROMACS will not be happy if the system is not neutral! Example: This will create a simulation box of 120 A height, filled with 0.1 M NaCl solution. # full simulation box height in A BOX_HEIGHT: 120.0 # Bulk solvent added or not (Default: True) BULK_SOLV: True BULK_IONS: Na: 0.1 Cl: 0.1 GROMACS version specification Sometimes more than one version of GROMACS may be installed, this allows user to specify the one to use. GMX - bash alias for your favourite GROMACS version [str] Example: To use your MPI-compiled version: GMX: gmx_mpi ClayCode.siminp System Specifications YAML file ClayCode.simpinp reads the parameters specified in this file and generates simulation inputs for GROMACS. Coming soon...","title":"YAML"},{"location":"YAML/#claycodebuilder-system-specifications-yaml-file","text":"ClayCode.builder reads the parameters specified in this file.","title":"ClayCode.builder System Specifications YAML file"},{"location":"YAML/#required-parameters","text":"The first section contains general parameters that are required for the model construction. OUTPATH - output directory path [str] Directory in which output folder is created. SYSNAME - clay system name [str] Th name for clay type, must to match a column header in the CSV file, the created output folder will also have this name. Avoid spaces and unusual symbols. CLAY_COMP - filename.csv [str] Name of CSV file where the target stoichiometry for the system specified under SYSNAME . CLAY_TYPE - unit cell type [str] Clay unit cell type, available in data/UCS directory. Such as: Dioctahedral 2:1 - D21 Trioctahedral 2:1 - T21 Dioctahedral 1:1 - D11 Trioctahedral 1:1 - T11 layered double hydroxide 3:1 - L31 layered double hydroxide 2:1 - L21 Sepiolite - SEP Note : Only D21, D11 and L31 are supplied with current release. Example: # output directory path OUTPATH: /path/to/output/directory # name of system SYSNAME: NAu-1-fe # name of CSV file with target stoichiometry CLAY_COMP: /path/to/clay_comp.csv # clay type CLAY_TYPE: D21 # Dioctahedral 2:1 - D21","title":"Required Parameters"},{"location":"YAML/#optional-parameters","text":"This is an optional parameter section, if the directives are not given by the user, ClayCode.builder will use default values.","title":"Optional Parameters"},{"location":"YAML/#clay-sheet-size","text":"X_CELLS - Unit cell number [int] (Default: 7) Number of unit cells in x-direction. Note : Future version will have the option to specify target x-dimensions X_DIM Y_CELLS - Unit cell number [int] (Default: 5) Number of unit cells in y-direction. Note : Future version will have the option to specify target y-dimensions Y_DIM N_SHEETS - Unit cell number [int] (Default: 3) Number of sheets of 1 unit cell thickness to be stacked in z-direction. Example: # number of unit cells in x direction (Default 7) X_CELLS: 7 # number of unit cells in y direction (Default 5) Y_CELLS: 5 # number of unit cells in z direction (Default 3) N_SHEETS: 3","title":"Clay Sheet Size"},{"location":"YAML/#clay-composition","text":"ClayCode.builder calculates the number and type of unit cells necessary to match the desired composition, as given in CSV file. If, instead, the user would like to specify this manually, the following parameters can be used: UC_INDEX_LIST - unit cell list [list] required unit cells, as specified in data/UCS directory, to use for building the system UC_RATIOS_LIST - probabilities [list] probability list for the above unit cells, total probability must be 1.00 Example: The following script will use the dioctohedral 2:1 unit cells, which are both neutral smectite unit cells, with the latter having 1 octohedral Al substitution for the Fe3. This will produce a neutral smectite with the following stoichiometry: \\mathrm{Si_8 \\left[Al_{3.8}Fe_{0.2}\\right]} . # required UCs to builder system as list UC_INDEX_LIST: [D221 D228] # probability list of unit cells in system UC_RATIOS_LIST: [0.8 0.2]","title":"Clay Composition"},{"location":"YAML/#interlayer-solvent-and-ions","text":"IL_SOLV - interlayer solvent presence [bool] (Default: True ) If True interlayer space should be solvated, otherwise False will produce non-hydrated clay. There are three options to handle interlayer water and interlayer ions, only one should be specified : ION_WATERS - number of waters per ion [int, Dict[str: int]] Number of water molecules that should be added per ion. If a single number [int] is given, all of the ions will be hydrated by the same number of waters. To specify number of waters per ion-type the entry should be a citionary, then the total number of water molecules will be mapped to the specifications given for each of the interlayer occupancies I in the CSV entry. Example: A given number of waters will be added for each cation, which quantity is specified in the clay stoichiometry CSV file. ION_WATERS: Ca: 12 Na: 12 K: 10 UC_WATERS - number of water molecules per unit cell [int] The specified number of water molecules multiplied by the number of unit cells is added into each of the interlayer spaces. SPACING_WATERS - hydrated interleyer spacing, in A [float] (Default 10.0 A) Target interlayer spacing filled with water, final value may vary due to the water rearrangement when in contact with clay surface and packing around ions.","title":"Interlayer Solvent and Ions"},{"location":"YAML/#simulation-box-specifications","text":"BOX_HEIGHT - simulation box height in A [float] Size of the final simulation box in z-direction in A, note the clay layers are positioned in xy-plane. BULK_SOLV - bulk solvent presence [bool] (Default: True ) If True the box space will be filled with water, otherwise False will keep the box empty. This is useful if further plan is to add other species, such as oil, into the system. BULK_IONS - type of ions and their concentration in mol/L [int, Dict[str: int]] Ions to be added into the bulk solvated space. Note : GROMACS will not be happy if the system is not neutral! Example: This will create a simulation box of 120 A height, filled with 0.1 M NaCl solution. # full simulation box height in A BOX_HEIGHT: 120.0 # Bulk solvent added or not (Default: True) BULK_SOLV: True BULK_IONS: Na: 0.1 Cl: 0.1","title":"Simulation Box Specifications"},{"location":"YAML/#gromacs-version-specification","text":"Sometimes more than one version of GROMACS may be installed, this allows user to specify the one to use. GMX - bash alias for your favourite GROMACS version [str] Example: To use your MPI-compiled version: GMX: gmx_mpi","title":"GROMACS version specification"},{"location":"YAML/#claycodesiminp-system-specifications-yaml-file","text":"ClayCode.simpinp reads the parameters specified in this file and generates simulation inputs for GROMACS. Coming soon...","title":"ClayCode.siminp System Specifications YAML file"},{"location":"builder/","text":"ClayCode.builder Builds clay models based on average target occupancies for a specified unit cell type. ClayCode.builder will match a combination of differently substituted unit cells to fit the average target occupancies specified by the user. Usage Arguments for builder are: -f : System specifications YAML file (include .csv file path) -comp : Clay composition in CSV format (can also be given in system specifications YAML, see Pyrophyllite Tutorial ) --manual_setup : (run builder in interactive mode) Example: ClayCode builder -f path/to/input_Clay.yaml","title":"ClayCode.builder"},{"location":"builder/#claycodebuilder","text":"Builds clay models based on average target occupancies for a specified unit cell type. ClayCode.builder will match a combination of differently substituted unit cells to fit the average target occupancies specified by the user.","title":"ClayCode.builder"},{"location":"builder/#usage","text":"Arguments for builder are: -f : System specifications YAML file (include .csv file path) -comp : Clay composition in CSV format (can also be given in system specifications YAML, see Pyrophyllite Tutorial ) --manual_setup : (run builder in interactive mode)","title":"Usage"},{"location":"builder/#example","text":"ClayCode builder -f path/to/input_Clay.yaml","title":"Example:"},{"location":"developers/","text":"developers guide coming soon ... Code structure: Modules: ClayCode.builder ClayCode.siminp ClayCode.config ClayCode.data ClayCode.tests Environemnt set up files: setup.py ... The code structure is as follows: ClayCode \u2502 \u251c\u2500\u2500 builder \u2502 \u251c\u2500\u2500 config \u2502 \u2514\u2500\u2500 tests \u2502 \u2514\u2500\u2500 data \u251c\u2500\u2500 config \u251c\u2500\u2500 core \u251c\u2500\u2500 data \u2502 \u251c\u2500\u2500 FF \u2502 \u2502 \u251c\u2500\u2500 ClayFF_Fe.ff \u2502 \u251c\u2500\u2500 MDP \u2502 \u251c\u2500\u2500 UCS \u2502 \u2502 \u251c\u2500\u2500 D11 \u2502 \u2502 \u251c\u2500\u2500 D21 \u2502 \u2502 \u2514\u2500\u2500 LDH31 \u2502 \u2514\u2500\u2500 user \u2514\u2500\u2500 siminp","title":"Developers Guide"},{"location":"developers/#code-structure","text":"Modules: ClayCode.builder ClayCode.siminp ClayCode.config ClayCode.data ClayCode.tests Environemnt set up files: setup.py ... The code structure is as follows: ClayCode \u2502 \u251c\u2500\u2500 builder \u2502 \u251c\u2500\u2500 config \u2502 \u2514\u2500\u2500 tests \u2502 \u2514\u2500\u2500 data \u251c\u2500\u2500 config \u251c\u2500\u2500 core \u251c\u2500\u2500 data \u2502 \u251c\u2500\u2500 FF \u2502 \u2502 \u251c\u2500\u2500 ClayFF_Fe.ff \u2502 \u251c\u2500\u2500 MDP \u2502 \u251c\u2500\u2500 UCS \u2502 \u2502 \u251c\u2500\u2500 D11 \u2502 \u2502 \u251c\u2500\u2500 D21 \u2502 \u2502 \u2514\u2500\u2500 LDH31 \u2502 \u2514\u2500\u2500 user \u2514\u2500\u2500 siminp","title":"Code structure:"},{"location":"imt/","text":"imt.md Illite IMt-1 and IMt-2 ORIGIN: Silver Hill, Montana, USA CHEMICAL COMPOSITION (%): SiO2: 49.3 Al2O3: 24.25, TiO2: 0.55, Fe2O3:7.32, FeO: 0.55, MnO: 0.03, MgO: 2.56, CaO: 0.43, Na2O: 0, K2O: 7.83, P2O5: 0.08, LOI: 8.02 STRUCTURE: (Mg.09 Ca.06 K1.37)[Al2.69 Fe(III).76 Fe(II).06 Mntr Mg.43 Ti.06][Si6.77 Al1.23]O20(OH)4, Octahedral charge:-.44, Tetrahedral charge:-1.23, Interlayer charge:-1.68, Unbalanced charge:0.00 The supplied exp_clay.csv file and contains clay structures corresponding to the Source Clays listed under \"Physical and Chemical Data of Source Clays\" clays.org . NO interlayer water ClayCode builder -f path/to/input_Clay.yaml","title":"Illite"},{"location":"kao/","text":"Kaolinite NOTE treatment of the Ti in the structure and what is the origin of the Ti, why to ignore Kaolin KGa-1(KGa-1b), (low-defect) ORIGIN: Tuscaloosa formation? (Cretaceous?) (stratigraphy uncertain) County of Washington, State of Georgia, USA LOCATION: 32\u00b058\u2032 N-82\u00b053\u2032 W approximately, topographic map Tabernacle, Georgia N 3252.5-W 8252.5/7.5, Collected from face of Coss-Hodges pit, October 3,1972. CHEMICAL COMPOSITION (%): SiO2: 44.2, Al2O3: 39.7, TiO2: 1.39, Fe2O3: 0.13,FeO: 0.08, MnO: 0.002, MgO: 0.03, CaO: n.d., Na2O: 0.013, K2O: 0.05, F:0.013,P2O5: 0.034, Loss on heating: -550\u00b0C: 12.6; 550-1000\u00b0C: 1.18. CATION EXCHANGE CAPACITY (CEC): 2.0 meq/100g SURFACE AREA: N2 area: 10.05 +/- 0.02 m2 /g THERMAL ANALYSIS: DTA: endotherm at 630oC, exotherm at 1015oC, TG: dehydroxylation weight loss 13.11% (theory 14%) indicating less than 7% impurities. INFRARED SPECTROSCOPY: Typical spectrum for well crystallized kaolinite,however not as well crystallized as a typical China clay from Cornwall,as judged from the intensity of the 3669 cm-1 band. Splitting of the 1100cm- 1 band is due to the presence of coarse crystals. STRUCTURE:(Mg.02 Ca.01 Na.01 K.01)[Al3.86 Fe(III).02 Mntr Ti.11][Si3.83Al.17] O10(OH)8, Octahedral charge:.11, Tetrahedral charge:-.17,Interlayer charge:-.06, Unbalanced charge:0.00 The supplied exp_clay.csv file and contains clay structures corresponding to the Source Clays listed under \"Physical and Chemical Data of Source Clays\" clays.org . Removing invalid atom types: sheet - at-type: occupancy O - Mn : 0.00, O - Ti : 0.11 Could not guess Ti charge. Enter Ti charge value: (or exit with 'e') 4 Assuming Ti charge of 4. Getting sheet occupancies: Found 'O' sheet occupancies of 3.8800/4.0000 (-0.1200) Found 'T' sheet occupancies of 4.0000/4.0000 (+0.0000) Adjusting values to match expected occupancies: old occupancies -> new occupancies per unit cell: sheet - atom type : occupancies (difference) 'O' - 'ao' : 3.8600 -> 3.9800 (+0.1200) Splitting total iron content (0.0200) to match charge. Will use the following target composition: 'T' - 'at' : 0.1700 'T' - 'st' : 3.8300 'O' - 'ao' : 3.9800 'O' - 'feo' : 0.0200 Writing new target clay composition to 'KGa-1_exp_df.csv' ClayCode builder -f path/to/input_Clay.yaml","title":"Kaolinite"},{"location":"ldh/","text":"ldh example 3:1 Al-Mg LDH ClayCode builder -f path/to/input_Clay.yaml","title":"LDH"},{"location":"mmt/","text":"Montmorillonite Clay composition Wyoming montmorillonite is widely studied and used smectite. It is available for purchase from Source Clays of The Clay Minerals Society , and is identified as SWy-1, SWy-2 or SWy-3, depending on the batch. This is a well-characterised clay with the structure listed under \"Physical and Chemical Data of Source Clays\" at the clays.org , as: Swy-1: \\mathrm {Ca_{0.12} Na_{0.32} K_{0.05} ~\\left[ Si_{7.98} Al_{0.02}\\right]^{-0.02} \\left[ Al_{3.01} Fe^{III}_{0.41} Mn_{0.01} Mg_{0.54} Ti_{0.02}\\right]^{-0.52} } , with unbalanced charge of 0.05. Ti is often identified during clay analysis, but is attributed to the TiO inclusions, therefore, we will omit it in the input. Meanwhile, ClayFF force field does not have parameters for Mn, which is shown at the level of detection and so we will also omit this entry. The provided clay_comp.csv file contains an entry SWy-1 which corresponds to this Wyoming montmorillonite clay. Construction of the model Let's examine the Swy1.yaml , which is provided in the Tutorial directory. This file contains all of the information necessary to build the clay model. Please consult YAML for the parameter description Required parameters # ============================================================================= # General specifications for clay model construction # ============================================================================= # ============================================================================= # Required Parameters # ============================================================================= OUTPATH: . # name of system to call according to CLAY_COMP (exp_clay.csv) # compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'LDH31' 'IMt-1' 'KGa-1' SYSNAME: SWy-1 # specify whether new clay model should be constructed: # new - a new clay model is constructed # load - sheet coordinates or unit cell sequences are loaded from existent .gro or .npy files # load: [X, Y] # with X - 'np' or 'gro', Y - '.npy' or '.gro' filename # False - no clay model is constructed BUILD: new # name of .csv file with target stoichiometry CLAY_COMP: exp_clay.csv # clay type available options in 'clay_units' directory: # Dioctahedral 2:1 - D21 # Trioctahedral 2:1 - T21 # Dioctahedral 1:1 - D11 # Trioctahedral 1:1 - T11 # layered double hydroxide 3:1 - L31 # layered double hydroxide 2:1 - L21 # Sepiolite - SEP CLAY_TYPE: D21 # ============================================================================= # Optional: Clay Sheet and Interlayer Specifications # ============================================================================= # number of unit cells in x direction (Default 7) X_CELLS: 7 # number of unit cells in y direction (Default 5) Y_CELLS: 5 # number of unit cells in z direction (Default 3) N_SHEETS: 3 # ---------------------------------------------------------------------------- # Optional: Unit Cell Composition and Ratios input # if not given, these will be calculated from data in the CLAY_COMP .csv file # (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: []) # ----------------------------------------------------------------------------- # required UCs to builder system as list # UC_INDEX_LIST: [1] # probability list of unit cells in system # p(tot): 1.00 # UC_RATIOS_LIST: [1] # ----------------------------------------------------------------------------- # interlayer solvent present or not (Default True) IL_SOLV: True # ----------------------------------------------------------------------------- # Optional: Interlayer Ion Specification Options (comment the other options!) # (Default UC_WATERS: 20) # ----------------------------------------------------------------------------- # 1. Number of water molecules that should be added per ion (ION_WATERS) # a. as ion species dictionary for hydration number # ION_WATERS: {'Ca': 12, # 'Na': 12 # } # b. as ion species int for hydration number # ION_WATERS : 12 # 3. OR per unit cell #UC_WATERS: 25 # 4. OR for a target d-spacing value in A SPACING_WATERS: 20 # ============================================================================= # Optional: Simulation Box Specifications # ============================================================================= # full simulation box height in A (Default 150.0) BOX_HEIGHT: 150.0 # ============================================================================= # Optional: Solvation and Bulk Ions Specifications # ============================================================================= # Bulk solvent added or not (Default: True) BULK_SOLV: True # Ion species and concentration in mol/L name to add in bulk solvent # (Default: BULK_IONS: # Na: 0.1) BULK_IONS: Na: 0.1 Cl: 0.05 # ============================================================================= # Optional: Simulation Runs Specifications # ============================================================================= # Generate scripts and '.mdp' files for simulation runs. # Available options: # EM - energy minimisation # EQ - equilibration # D-SPACE - d-spacing equilibration # P - production # SIMINP: [EM, D-SPACE] # select where EM and EQ should be run (Default: False) # MDRUNS_REMOTE: False # ----------------------------------------------------------------------------- # d-spacing equilibration options # ----------------------------------------------------------------------------- # Target d-spacing in A # D_SPACE: 19.5 # Water molecules to be removed at a time during d-spacing equilibration runs # REMOVE_STEPS: 1000 # Absolute number of water molecules per interlayer space # SHEET_WAT: 2 # Number of water molecules per unit cell # UC_WAT: 0.1 # Percentage of water molecules from interlayer # PERCENT_WAT: 5 # ----------------------------------------------------------------------------- # bash alias for used GROMACS version # ----------------------------------------------------------------------------- GMX: gmx run as ClayCode builder -f path/to/input_Clay.yaml","title":"Montmorillonite"},{"location":"mmt/#montmorillonite","text":"","title":"Montmorillonite"},{"location":"mmt/#clay-composition","text":"Wyoming montmorillonite is widely studied and used smectite. It is available for purchase from Source Clays of The Clay Minerals Society , and is identified as SWy-1, SWy-2 or SWy-3, depending on the batch. This is a well-characterised clay with the structure listed under \"Physical and Chemical Data of Source Clays\" at the clays.org , as: Swy-1: \\mathrm {Ca_{0.12} Na_{0.32} K_{0.05} ~\\left[ Si_{7.98} Al_{0.02}\\right]^{-0.02} \\left[ Al_{3.01} Fe^{III}_{0.41} Mn_{0.01} Mg_{0.54} Ti_{0.02}\\right]^{-0.52} } , with unbalanced charge of 0.05. Ti is often identified during clay analysis, but is attributed to the TiO inclusions, therefore, we will omit it in the input. Meanwhile, ClayFF force field does not have parameters for Mn, which is shown at the level of detection and so we will also omit this entry. The provided clay_comp.csv file contains an entry SWy-1 which corresponds to this Wyoming montmorillonite clay.","title":"Clay composition"},{"location":"mmt/#construction-of-the-model","text":"Let's examine the Swy1.yaml , which is provided in the Tutorial directory. This file contains all of the information necessary to build the clay model. Please consult YAML for the parameter description","title":"Construction of the model"},{"location":"mmt/#required-parameters","text":"# ============================================================================= # General specifications for clay model construction # ============================================================================= # ============================================================================= # Required Parameters # ============================================================================= OUTPATH: . # name of system to call according to CLAY_COMP (exp_clay.csv) # compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'LDH31' 'IMt-1' 'KGa-1' SYSNAME: SWy-1 # specify whether new clay model should be constructed: # new - a new clay model is constructed # load - sheet coordinates or unit cell sequences are loaded from existent .gro or .npy files # load: [X, Y] # with X - 'np' or 'gro', Y - '.npy' or '.gro' filename # False - no clay model is constructed BUILD: new # name of .csv file with target stoichiometry CLAY_COMP: exp_clay.csv # clay type available options in 'clay_units' directory: # Dioctahedral 2:1 - D21 # Trioctahedral 2:1 - T21 # Dioctahedral 1:1 - D11 # Trioctahedral 1:1 - T11 # layered double hydroxide 3:1 - L31 # layered double hydroxide 2:1 - L21 # Sepiolite - SEP CLAY_TYPE: D21 # ============================================================================= # Optional: Clay Sheet and Interlayer Specifications # ============================================================================= # number of unit cells in x direction (Default 7) X_CELLS: 7 # number of unit cells in y direction (Default 5) Y_CELLS: 5 # number of unit cells in z direction (Default 3) N_SHEETS: 3 # ---------------------------------------------------------------------------- # Optional: Unit Cell Composition and Ratios input # if not given, these will be calculated from data in the CLAY_COMP .csv file # (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: []) # ----------------------------------------------------------------------------- # required UCs to builder system as list # UC_INDEX_LIST: [1] # probability list of unit cells in system # p(tot): 1.00 # UC_RATIOS_LIST: [1] # ----------------------------------------------------------------------------- # interlayer solvent present or not (Default True) IL_SOLV: True # ----------------------------------------------------------------------------- # Optional: Interlayer Ion Specification Options (comment the other options!) # (Default UC_WATERS: 20) # ----------------------------------------------------------------------------- # 1. Number of water molecules that should be added per ion (ION_WATERS) # a. as ion species dictionary for hydration number # ION_WATERS: {'Ca': 12, # 'Na': 12 # } # b. as ion species int for hydration number # ION_WATERS : 12 # 3. OR per unit cell #UC_WATERS: 25 # 4. OR for a target d-spacing value in A SPACING_WATERS: 20 # ============================================================================= # Optional: Simulation Box Specifications # ============================================================================= # full simulation box height in A (Default 150.0) BOX_HEIGHT: 150.0 # ============================================================================= # Optional: Solvation and Bulk Ions Specifications # ============================================================================= # Bulk solvent added or not (Default: True) BULK_SOLV: True # Ion species and concentration in mol/L name to add in bulk solvent # (Default: BULK_IONS: # Na: 0.1) BULK_IONS: Na: 0.1 Cl: 0.05 # ============================================================================= # Optional: Simulation Runs Specifications # ============================================================================= # Generate scripts and '.mdp' files for simulation runs. # Available options: # EM - energy minimisation # EQ - equilibration # D-SPACE - d-spacing equilibration # P - production # SIMINP: [EM, D-SPACE] # select where EM and EQ should be run (Default: False) # MDRUNS_REMOTE: False # ----------------------------------------------------------------------------- # d-spacing equilibration options # ----------------------------------------------------------------------------- # Target d-spacing in A # D_SPACE: 19.5 # Water molecules to be removed at a time during d-spacing equilibration runs # REMOVE_STEPS: 1000 # Absolute number of water molecules per interlayer space # SHEET_WAT: 2 # Number of water molecules per unit cell # UC_WAT: 0.1 # Percentage of water molecules from interlayer # PERCENT_WAT: 5 # ----------------------------------------------------------------------------- # bash alias for used GROMACS version # ----------------------------------------------------------------------------- GMX: gmx run as ClayCode builder -f path/to/input_Clay.yaml","title":"Required parameters"},{"location":"nont/","text":"Nontronites In this Tutorial we look at the two South Australian nontronite clays, part of the Source Clays of The Clay Minerals Society . These are commonly known as NAu-1 or the Uley green nontronite and NAu-2 or Uley brown nontronite. Their structures are listed under \"Physical and Chemical Data of Source Clays\" at the clays.org , as: NAu-1: \\mathrm{M^{+1} \\left[Si_{7}Al_{1}\\right] \\left[Al_{0.58}Fe_{3.38}Mg_{0.05}\\right]} NAu-2: \\mathrm{M^{+0.97} \\left[Si_{7.57}Al_{0.01}\\right] \\left[Al_{0.52}Fe_{3.32}Mg_{0.7}\\right]} , where \\mathrm{M^{charge}} indicates interlayer counter-balancing cationic charge. Assigning iron distribution and valence Iron can be present as either Fe(II) or Fe(III) and found in both, the tetrahedral and the octahedral sheets, as well as a charge compensating cation in the interlayer space space. Furthermore, in many samples, such as NAu-2, ferrihydrydes are adsorbed to clay surfaces. 1 While methods such as near-infrared (NIR), extended X-ray adsorption fine structures (EXAFS), Moessbauer spectroscopy, X-ray diffraction (XRD) and thermogravimetric analysis (TGA) have been used to determine the charge distributions of Fe in the sample, 2 3 4 the exact composition of these nontronites remains matter of debate. Conventionally, when Al and Fe(III), are present in a structure, because of their larger ionic radius, Fe(III) is assigned complitely to the octahedral sheet. Only once all octahedral spaces are occupied by Fe(III), the structure is assumed to also have Fe(III) in tetrahedral positions. However, this assignment is not necessarily correct and due to the detection limits of commonly used spectroscopic or chemical analysis techniques tetrahedral Fe(III) contents below 5% often remain undetected. 3 To this end, after a review of the literature, we use the structures identified by Gates et al 2 . We note that the octahedral occupancy fro NAu-2 is 3.93 instead of full 4. ClayCode will address this when generating the structure. Furthermore, we assign \\mathrm{Ca^{2+}} as counterbalancing ion to all the systems. Resulting structures are, therefore, as follows: NAu-1: \\mathrm{0.525 ~Ca^{2+} \\left[Si_{6.98}Al_{0.95}Fe_{0.07}\\right]^{-1.02} \\left[Al_{0.36}Fe_{3.61}Mg_{0.04}\\right]^{-0.03}} NAu-2: \\mathrm{0.36 ~Ca^{2+} \\left[Si_{7.55}Al_{0.16}Fe_{0.29}\\right]^{-0.45} \\left[Al_{0.34}Fe_{3.54}Mg_{0.05}\\right]^{-0.27}} Tutorial directory provides the clay_comp.csv file which contains the above clay structures. See CSV for details on this file. sheet element NAu-1-fe NAu-2-fe T Si 6.98 7.55 T Al 0.95 0.16 T Fe 0.07 0.29 O Fe 3.61 3.54 O Al 0.36 0.34 O Mg 0.04 0.05 I Ca 0.525 0.36 I Na 0 0 I Mg 0 0 I K 0 0 I Cl 0 0 C T -1.02 -0.45 C O -0.03 -0.27 C tot -1.05 -0.72 System specification We now create the system specification YAML file, which will contain the information necessary to build the clay structures of or interest. The files NAu-1.yaml and NAu-2.yaml are provided. The first section contains general parameters that are required for the model construction. If the directives in the optional section are not given by the user, ClayCode will use default values. # ============================================================================= # General specifications for clay model construction # ============================================================================= # ============================================================================= # Required Parameters # ============================================================================= OUTPATH: /path/to/output/directory # name of system SYSNAME: NAu-1-fe # name of CSV file with target stoichiometry CLAY_COMP: /path/to/clay_comp.csv # clay type available options in 'clay_units' directory: # Dioctahedral 2:1 - D21 # Trioctahedral 2:1 - T21 # Dioctahedral 1:1 - D11 # Trioctahedral 1:1 - T11 # layered double hydroxide 3:1 - L31 # layered double hydroxide 2:1 - L21 # Sepiolite - SEP CLAY_TYPE: D21 # ============================================================================= # Optional: Clay Sheet and Interlayer Specifications # ============================================================================= # number of unit cells in x direction (Default 7) X_CELLS: 7 # number of unit cells in y direction (Default 5) Y_CELLS: 5 # number of unit cells in z direction (Default 3) N_SHEETS: 3 # ---------------------------------------------------------------------------- # Optional: Unit Cell Composition and Ratios input # if not given, these will be calculated from data in the CLAY_COMP CSV file # (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: []) # ----------------------------------------------------------------------------- # required UCs to builder system as list # UC_INDEX_LIST: [1] # probability list of unit cells in system # p(tot) = 1.00 # UC_RATIOS_LIST: [1] # ----------------------------------------------------------------------------- # interlayer solvent present or not (Default True) IL_SOLV: True # ----------------------------------------------------------------------------- # Optional: Interlayer Ion Specification Options (comment the other options!) # (Default UC_WATERS: 20) # ----------------------------------------------------------------------------- # 1. Number of water molecules that should be added per ion (ION_WATERS) # a. as ion species dictionary for hydration number # ION_WATERS = {'Ca': 12, # 'Na': 12 # } # b. as ion species int for hydration number # ION_WATERS = 12 # 3. OR per unit cell UC_WATERS: 20 # 4. OR for a target d-spacing value in A # SPACING_WATERS = 10.0 # ============================================================================= # Optional: Simulation Box Specifications # ============================================================================= # full simulation box height in A (Default 150.0) BOX_HEIGHT: 150.0 # ============================================================================= # Optional: Solvation and Bulk Ions Specifications # ============================================================================= # Bulk solvent added or not (Default: True) BULK_SOLV: True # Ion species and concentration in mol/L name to add in bulk solvent # (Default: BULK_IONS: # Na: 0.1 # Cl: 0.1) BULK_IONS: Na: 0.1 Cl: 0.1 # ----------------------------------------------------------------------------- # bash alias for used GROMACS version # ----------------------------------------------------------------------------- GMX: gmx_mpi ClayCode builder -f path/to/input_Clay.yaml Ray L. Frost, J. Theo Kloprogge, and Zhe Ding. The Garfield and Uley nontronites - An infrared spectroscopic comparison. Spectrochimica Acta - Part A Molecular and Biomolecular Spectroscopy , 58(9):1881\u20131894, 7 2002. doi:10.1016/S1386-1425(01)00638-2 . \u21a9 W. P. Gates, P. G. Slade, A. Manceau, and B. Lanson. Site Occupancies by Iron in Nontronites. Clays and Clay Minerals , 50(2):223\u2013239, 4 2002. doi:10.1346/000986002760832829 . \u21a9 \u21a9 Fabien Baron, Sabine Petit, Martin Pentr\u00e1k, Alain Decarreau, and Joseph W. Stucki. Revisiting the nontronite M\u00f6ssbauer spectra. American Mineralogist , 102(7):1501\u20131515, 7 2017. doi:10.2138/am-2017-1501x . \u21a9 \u21a9 A. Decarreau and S. Petit. Fe 3+ /Al 3+ partitioning between tetrahedral and octahedral sites in dioctahedral smectites. Clay Minerals , 49(5):657\u2013665, 12 2014. doi:10.1180/claymin.2014.049.5.03 . \u21a9","title":"Nontronite"},{"location":"nont/#nontronites","text":"In this Tutorial we look at the two South Australian nontronite clays, part of the Source Clays of The Clay Minerals Society . These are commonly known as NAu-1 or the Uley green nontronite and NAu-2 or Uley brown nontronite. Their structures are listed under \"Physical and Chemical Data of Source Clays\" at the clays.org , as: NAu-1: \\mathrm{M^{+1} \\left[Si_{7}Al_{1}\\right] \\left[Al_{0.58}Fe_{3.38}Mg_{0.05}\\right]} NAu-2: \\mathrm{M^{+0.97} \\left[Si_{7.57}Al_{0.01}\\right] \\left[Al_{0.52}Fe_{3.32}Mg_{0.7}\\right]} , where \\mathrm{M^{charge}} indicates interlayer counter-balancing cationic charge.","title":"Nontronites"},{"location":"nont/#assigning-iron-distribution-and-valence","text":"Iron can be present as either Fe(II) or Fe(III) and found in both, the tetrahedral and the octahedral sheets, as well as a charge compensating cation in the interlayer space space. Furthermore, in many samples, such as NAu-2, ferrihydrydes are adsorbed to clay surfaces. 1 While methods such as near-infrared (NIR), extended X-ray adsorption fine structures (EXAFS), Moessbauer spectroscopy, X-ray diffraction (XRD) and thermogravimetric analysis (TGA) have been used to determine the charge distributions of Fe in the sample, 2 3 4 the exact composition of these nontronites remains matter of debate. Conventionally, when Al and Fe(III), are present in a structure, because of their larger ionic radius, Fe(III) is assigned complitely to the octahedral sheet. Only once all octahedral spaces are occupied by Fe(III), the structure is assumed to also have Fe(III) in tetrahedral positions. However, this assignment is not necessarily correct and due to the detection limits of commonly used spectroscopic or chemical analysis techniques tetrahedral Fe(III) contents below 5% often remain undetected. 3 To this end, after a review of the literature, we use the structures identified by Gates et al 2 . We note that the octahedral occupancy fro NAu-2 is 3.93 instead of full 4. ClayCode will address this when generating the structure. Furthermore, we assign \\mathrm{Ca^{2+}} as counterbalancing ion to all the systems. Resulting structures are, therefore, as follows: NAu-1: \\mathrm{0.525 ~Ca^{2+} \\left[Si_{6.98}Al_{0.95}Fe_{0.07}\\right]^{-1.02} \\left[Al_{0.36}Fe_{3.61}Mg_{0.04}\\right]^{-0.03}} NAu-2: \\mathrm{0.36 ~Ca^{2+} \\left[Si_{7.55}Al_{0.16}Fe_{0.29}\\right]^{-0.45} \\left[Al_{0.34}Fe_{3.54}Mg_{0.05}\\right]^{-0.27}} Tutorial directory provides the clay_comp.csv file which contains the above clay structures. See CSV for details on this file. sheet element NAu-1-fe NAu-2-fe T Si 6.98 7.55 T Al 0.95 0.16 T Fe 0.07 0.29 O Fe 3.61 3.54 O Al 0.36 0.34 O Mg 0.04 0.05 I Ca 0.525 0.36 I Na 0 0 I Mg 0 0 I K 0 0 I Cl 0 0 C T -1.02 -0.45 C O -0.03 -0.27 C tot -1.05 -0.72","title":"Assigning iron distribution and valence"},{"location":"nont/#system-specification","text":"We now create the system specification YAML file, which will contain the information necessary to build the clay structures of or interest. The files NAu-1.yaml and NAu-2.yaml are provided. The first section contains general parameters that are required for the model construction. If the directives in the optional section are not given by the user, ClayCode will use default values. # ============================================================================= # General specifications for clay model construction # ============================================================================= # ============================================================================= # Required Parameters # ============================================================================= OUTPATH: /path/to/output/directory # name of system SYSNAME: NAu-1-fe # name of CSV file with target stoichiometry CLAY_COMP: /path/to/clay_comp.csv # clay type available options in 'clay_units' directory: # Dioctahedral 2:1 - D21 # Trioctahedral 2:1 - T21 # Dioctahedral 1:1 - D11 # Trioctahedral 1:1 - T11 # layered double hydroxide 3:1 - L31 # layered double hydroxide 2:1 - L21 # Sepiolite - SEP CLAY_TYPE: D21 # ============================================================================= # Optional: Clay Sheet and Interlayer Specifications # ============================================================================= # number of unit cells in x direction (Default 7) X_CELLS: 7 # number of unit cells in y direction (Default 5) Y_CELLS: 5 # number of unit cells in z direction (Default 3) N_SHEETS: 3 # ---------------------------------------------------------------------------- # Optional: Unit Cell Composition and Ratios input # if not given, these will be calculated from data in the CLAY_COMP CSV file # (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: []) # ----------------------------------------------------------------------------- # required UCs to builder system as list # UC_INDEX_LIST: [1] # probability list of unit cells in system # p(tot) = 1.00 # UC_RATIOS_LIST: [1] # ----------------------------------------------------------------------------- # interlayer solvent present or not (Default True) IL_SOLV: True # ----------------------------------------------------------------------------- # Optional: Interlayer Ion Specification Options (comment the other options!) # (Default UC_WATERS: 20) # ----------------------------------------------------------------------------- # 1. Number of water molecules that should be added per ion (ION_WATERS) # a. as ion species dictionary for hydration number # ION_WATERS = {'Ca': 12, # 'Na': 12 # } # b. as ion species int for hydration number # ION_WATERS = 12 # 3. OR per unit cell UC_WATERS: 20 # 4. OR for a target d-spacing value in A # SPACING_WATERS = 10.0 # ============================================================================= # Optional: Simulation Box Specifications # ============================================================================= # full simulation box height in A (Default 150.0) BOX_HEIGHT: 150.0 # ============================================================================= # Optional: Solvation and Bulk Ions Specifications # ============================================================================= # Bulk solvent added or not (Default: True) BULK_SOLV: True # Ion species and concentration in mol/L name to add in bulk solvent # (Default: BULK_IONS: # Na: 0.1 # Cl: 0.1) BULK_IONS: Na: 0.1 Cl: 0.1 # ----------------------------------------------------------------------------- # bash alias for used GROMACS version # ----------------------------------------------------------------------------- GMX: gmx_mpi ClayCode builder -f path/to/input_Clay.yaml Ray L. Frost, J. Theo Kloprogge, and Zhe Ding. The Garfield and Uley nontronites - An infrared spectroscopic comparison. Spectrochimica Acta - Part A Molecular and Biomolecular Spectroscopy , 58(9):1881\u20131894, 7 2002. doi:10.1016/S1386-1425(01)00638-2 . \u21a9 W. P. Gates, P. G. Slade, A. Manceau, and B. Lanson. Site Occupancies by Iron in Nontronites. Clays and Clay Minerals , 50(2):223\u2013239, 4 2002. doi:10.1346/000986002760832829 . \u21a9 \u21a9 Fabien Baron, Sabine Petit, Martin Pentr\u00e1k, Alain Decarreau, and Joseph W. Stucki. Revisiting the nontronite M\u00f6ssbauer spectra. American Mineralogist , 102(7):1501\u20131515, 7 2017. doi:10.2138/am-2017-1501x . \u21a9 \u21a9 A. Decarreau and S. Petit. Fe 3+ /Al 3+ partitioning between tetrahedral and octahedral sites in dioctahedral smectites. Clay Minerals , 49(5):657\u2013665, 12 2014. doi:10.1180/claymin.2014.049.5.03 . \u21a9","title":"System specification"},{"location":"output/","text":"The OUTPUT directory: The
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ClayCode.siminp coming soon ...
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/sitemap.xml b/sitemap.xml
new file mode 100644
index 00000000..5972ae9f
--- /dev/null
+++ b/sitemap.xml
@@ -0,0 +1,88 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Instalation
+This package requires python version >=3.9 and pipx, and it also uses some of the functionality of GROMACS.
+-
+
- Install Python 3.9: Follow the Python Setup and Usage guide +
- Install pipx: Follow the Installation guide +
- Install Gromacs: Follow the Current Gromacs installation guide +
- Install ClayCode: +
gh repo clone Erastova-group/ClayCode
+ cd ClayCode
+ bash install.sh
+Running ClayCode
+ClayCode builder -f path/to/input_Clay.yaml
+For further details see:
+
+User Guide
+Tutorials
+
+
+
+
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/swa/index.html b/swa/index.html
new file mode 100644
index 00000000..eaa9d85b
--- /dev/null
+++ b/swa/index.html
@@ -0,0 +1,188 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ swa.md
+Ferruginous Smectite SWa-1
+STRUCTURE: (Mg.18 Ca.36 K.01)[Al.61 Fe(III) 3.08 Mntr Mg.24 Ti.07][Si7.09 Al.91]O20(OH)4, Octahedral charge:-.18, Tetrahedral charge:-.91, Interlayer charge:-1.09, Unbalanced charge:0.00,
+The supplied exp_clay.csv file and contains clay structures corresponding to the Source Clays listed under "Physical and Chemical Data of Source Clays" clays.org.
Run with:
+ClayCode builder -f Tutorial/SWa1.yaml --comp Tutorial/clay_comp.csv
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/tutorials/index.html b/tutorials/index.html
new file mode 100644
index 00000000..25265214
--- /dev/null
+++ b/tutorials/index.html
@@ -0,0 +1,221 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Tutorials
+In this section we show how to set up the following clay systems:
+-
+
- Wyoming Montmorillonite, +
- Illite, +
- Pyrophyllite, +
- Brown and green Uley nontronites, +
- Ferruginous Smectite, +
- Kaolinite, +
- Layered double hydroxide. +
All the necessary input files (the .CSV and corresponding .YAML files) can be found in the Tutorial directory.
The supplied exp_clay.csv file and contains clay structures corresponding to the Source Clays listed under "Physical and Chemical Data of Source Clays" clays.org.
-
+
-
+
1:1 (TO) dioctohedral smectite:
+-
+
- Kaolin KGa-1; +
+ -
+
2:1 (TOT) dioctohedral smectite:
+-
+
- Na-Montmorillonite (Wyoming) SWy-1, +
- Illite IMt-1, +
- Ferruginous Smectite SWa-1, +
- Nontronite NAu-1-fe, +
- Nontronite NAu-2-fe, +
- Nontronite NG-1; +
+ -
+
example Al-Mg 3:1 layered double hydroxide:
+-
+
- LDH31. +
+
Note, that Pyrophyllite composition is not given in the .CSV file, and it s fully described in the .YAML.
+ +
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/userguide/index.html b/userguide/index.html
new file mode 100644
index 00000000..3200d8f7
--- /dev/null
+++ b/userguide/index.html
@@ -0,0 +1,387 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ +
+ User Guide
+Dependencies
+ClayCode is compatible with UNIX operating systems.
+It relies on the following python libraries: NumPy (1.21.2), Pandas (1.3.4) and MDAnalysis (2.0.0).
+Furthermore, solvent molecules and ions are added as GROMACS subprocesses. Therefore, in order to execute builder, a local GROMACS installation is required.
+Data files
+The data files store information necessary to construct the clay structures for MD simulation.
+The files are stored within ClayCode/data/ directory:
ClayCode
+│
+...
+│
+└── data
+ ├── FF
+ │ └── ClayFF_Fe.ff
+ │ └── Ions.ff
+ ├── MDP
+ ├── UCS
+ │ ├── D11
+ │ ├── D21
+ │ └── LDH31
+ └── user
+
+
+where:
+-
+
data/FFcontains force fields files, as dictated by GROMACS format, currently included: + - ClayFF force field12 (with added Fe parameters based on personal communication with Andrey Kalinichev) in a directoryClayFF_Fe.ff, and + - Ions by Pengfei Li 34 inIons.ff, default is IOD-type, HFE and CN also included.
+data/UCScontains unit cell structures in .GRO format and their corresponding .ITP, topology assigned to ClayFF force field. The files are grouped per type, whereD21us dioctohedral 2:1 clay,D11is dioctohedral 1:1 andLDH31is a layered double hydroxide. To include new UCs, see Adding Unit Cells.
+data/MDPcontains GROMACS version-specific .MDP files for energy minimisation and equilibration.
+data/userreserved for user files.
+
Clay Composition
+The file in .CSV format containing the reduced unit cell structure, including partial atomic occupancies, charge balancing ions and layer charges for each clay listed.
+See full details in the Input files: CSV
+It is also possible to supply clay composition within the .YAML input only. See Pyrophyllite as an example
+Input Parameters
+System specification for the set-up are done given in .YAML format. See full details in Input files: YAML
+Parameters
+
Output
+See Output files
++ +
Adding Unit Cells
+Use of ClayCode should not be dictated only by the Unite Cells provided with this release. To add a new unit cell, one needs to:
+1 - Obtain a crystal structure.
+We recommend downloading .cif from the American Mineralogist Crystal Structure Database.
2 - Convert it to full occupancy expanded structure .gro (or .pdb).
+We recommend using one of the the following OpenBabel, Avogadro5 (not Avogadro2) or Mercury by CCDC (licence needed). We prefer Avogadro.
3 - Manually rename the atoms in the .gro to have unique names.
4 - Create an include topology file (.itp), please reffer to GROMACS manual.
+Assign each unique atom name in the .gro to an atom type, as given in the ClayFF.ff/atomtypes.atp:
hw 1.008 ; water hydrogen
+ho 1.008 ; hydroxyl hydrogen
+ow 16.00 ; water hydrogen
+oh 16.00 ; hydroxyl oxygen
+ob 16.00 ; bridging oxygen
+obos 16.00 ; bridging oxygen with octahedral substitution
+obts 16.00 ; bridging oxygen with tetrahedral substitution
+obss 16.00 ; bridging oxygen with double substitution
+ohs 16.00 ; hydroxyl oxygen with substitution
+st 28.09 ; tetrahedral silicon
+ao 26.98 ; octahedral aluminum
+at 26.98 ; tetrahedral aluminum
+mgo 24.31 ; octahedral magnesium
+mgh 24.31 ; hydroxide magnesium
+cao 40.08 ; octahedral calcium
+cah 40.08 ; hydroxide calcium
+feo 55.85 ; octahedral iron (III)
+fe2 55.85 ; octahedral iron (II)
+lio 6.941 ; octahedral lithium
+Example UC.gro and UC.itp
+A unit cell for Dioctohedral 1:1 (Kaolinite-type) with stocheometery D101.gro:
Dioctahedral 1:1 unit cell 1
+ 34
+ 1D101 AO1 1 0.061 0.433 0.332
+ 1D101 AO2 2 0.321 0.283 0.332
+ 1D101 AO3 3 0.320 0.880 0.332
+ 1D101 AO4 4 0.064 0.730 0.332
+ 1D101 ST1 5 0.237 0.749 0.065
+ 1D101 ST2 6 0.500 0.594 0.067
+ 1D101 ST3 7 0.493 0.301 0.065
+ 1D101 ST4 8 0.244 0.147 0.067
+ 1D101 OB1 9 0.225 0.751 0.226
+ 1D101 OB2 10 0.255 0.135 0.227
+ 1D101 OB3 11 0.258 0.000 0.000
+ 1D101 OB4 12 0.359 0.651 0.021
+ 1D101 OB5 13 0.360 0.236 0.001
+ 1D101 OB6 14 0.480 0.304 0.226
+ 1D101 OB7 15 0.510 0.582 0.227
+ 1D101 OB8 16 0.002 0.447 0.000
+ 1D101 OB9 17 0.100 0.204 0.021
+ 1D101 OB10 18 0.104 0.683 0.001
+ 1D101 OH1 19 0.223 0.413 0.232
+ 1D101 OH2 20 0.123 0.581 0.433
+ 1D101 OH3 21 0.164 0.855 0.431
+ 1D101 OH4 22 0.162 0.306 0.434
+ 1D101 OH5 23 0.480 0.860 0.232
+ 1D101 OH6 24 0.379 0.134 0.433
+ 1D101 OH7 25 0.420 0.408 0.431
+ 1D101 OH8 26 0.420 0.753 0.434
+ 1D101 HO1 27 0.530 0.940 0.233
+ 1D101 HO2 28 0.410 0.129 0.527
+ 1D101 HO3 29 0.400 0.434 0.522
+ 1D101 HO4 30 0.137 0.264 0.519
+ 1D101 HO5 31 0.272 0.497 0.233
+ 1D101 HO6 32 0.150 0.576 0.527
+ 1D101 HO7 33 0.136 0.880 0.522
+ 1D101 HO8 34 0.400 0.712 0.519
+ 0.51540 0.89420 0.63910
+and corresponding D101.itp:
[ moleculetype ]
+; name nrexcl
+ D101 1
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 KAO rtp KAO q 0.0
+ 1 ao 1 D101 AO1 1 1.575 26.98 ;
+ 2 ao 1 D101 AO2 2 1.575 26.98 ;
+ 3 ao 1 D101 AO3 3 1.575 26.98 ;
+ 4 ao 1 D101 AO4 4 1.575 26.98 ;
+ 5 st 1 D101 ST1 5 2.1 28.09 ;
+ 6 st 1 D101 ST2 6 2.1 28.09 ;
+ 7 st 1 D101 ST3 7 2.1 28.09 ;
+ 8 st 1 D101 ST4 8 2.1 28.09 ;
+ 9 ob 1 D101 OB1 9 -1.05 16 ;
+ 10 ob 1 D101 OB2 10 -1.05 16 ;
+ 11 ob 1 D101 OB3 11 -1.05 16 ;
+ 12 ob 1 D101 OB4 12 -1.05 16 ;
+ 13 ob 1 D101 OB5 13 -1.05 16 ;
+ 14 ob 1 D101 OB6 14 -1.05 16 ;
+ 15 ob 1 D101 OB7 15 -1.05 16 ;
+ 16 ob 1 D101 OB8 16 -1.05 16 ;
+ 17 ob 1 D101 OB9 17 -1.05 16 ;
+ 18 ob 1 D101 OB10 18 -1.05 16 ;
+ 19 oh 1 D101 OH1 19 -0.95 16 ;
+ 20 oh 1 D101 OH2 20 -0.95 16 ;
+ 21 oh 1 D101 OH3 21 -0.95 16 ;
+ 22 oh 1 D101 OH4 22 -0.95 16 ;
+ 23 oh 1 D101 OH5 23 -0.95 16 ;
+ 24 oh 1 D101 OH6 24 -0.95 16 ;
+ 25 oh 1 D101 OH7 25 -0.95 16 ;
+ 26 oh 1 D101 OH8 26 -0.95 16 ;
+ 27 ho 1 D101 HO1 27 0.425 1.008 ;
+ 28 ho 1 D101 HO2 28 0.425 1.008 ;
+ 29 ho 1 D101 HO3 29 0.425 1.008 ;
+ 30 ho 1 D101 HO4 30 0.425 1.008 ;
+ 31 ho 1 D101 HO5 31 0.425 1.008 ;
+ 32 ho 1 D101 HO6 32 0.425 1.008 ;
+ 33 ho 1 D101 HO7 33 0.425 1.008 ;
+ 34 ho 1 D101 HO8 34 0.425 1.008 ;
+
+[ bonds ]
+; i j funct length force.c.
+19 31 1 0.1 463532.808
+20 32 1 0.1 463532.808
+21 33 1 0.1 463532.808
+22 30 1 0.1 463532.808
+23 27 1 0.1 463532.808
+24 28 1 0.1 463532.808
+25 29 1 0.1 463532.808
+26 34 1 0.1 463532.808
+
+
+
+
+ +
-
+
-
+
Randall T. Cygan, Jian Jie Liang, and Andrey G. Kalinichev. Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. Journal of Physical Chemistry B, 108(4):1255–1266, 1 2004. doi:10.1021/JP0363287. ↩
+
+ -
+
Randall T. Cygan, Jeffery A. Greathouse, and Andrey G. Kalinichev. Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces. Journal of Physical Chemistry C, 125(32):17573–17589, 8 2021. doi:10.1021/ACS.JPCC.1C04600. ↩
+
+ -
+
Pengfei Li. Advances in metal ion modeling. Michigan State University, 2016. ↩
+
+ -
+
Madelyn Smith, Zhen Li, Luke Landry, Kenneth M Merz Jr, and Pengfei Li. Consequences of overfitting the van der waals radii of ions. Journal of Chemical Theory and Computation, 19(7):2064–2074, 2023. doi:10.1021/acs.jctc.2c01255. ↩
+
+ -
+
Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, and Geoffrey R Hutchison. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of cheminformatics, 4(1):1–17, 2012. doi:10.1186/1758-2946-4-17. ↩
+
+
+
+
+
+ ClayCode
+
+
+
+ « Previous
+
+
+ Next »
+
+
+
+
+
+
+
+
+
+
+
+
+