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thesis.bib
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@article{Yashima2008,
author = {Yashima, Masatomo and Enoki, Makiko and Wakita, Takahiro and Ali, Roushown and Matsushita, Yoshitaka and Izumi, Fujio and Ishihara, Tatsumi},
doi = {10.1021/ja711478h},
file = {:mnt/work-data/literature/ja711478h.pdf:pdf},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
number = {9},
pages = {2762--2763},
title = {{Structural Disorder and Diffusional Pathway of Oxide Ions in a Doped \ce{Pr2NiO4} -Based Mixed Conductor}},
url = {http://pubs.acs.org/doi/abs/10.1021/ja711478h},
volume = {130},
year = {2008}
}
@article{Prestipino2012,
abstract = {We report a combined synchrotron X-ray and neutron diffraction study on as-grown La2CoO4.14 single- crystal from 10 to 470 K. Unprecedented structural features in terms of a (3 + 2)D incommensurate modulation have been detected and characterized in the Low Temperature Orthorhombic (LTO) phase already at room temperature despite the complex twinning that was unravelled. A new intermediate phase between the LTO and High Temperature Tetragonal (HTT) phases has been observed for the first time (in the range of 413−433 K). The transformation from LTO to this so-called HTLO (High Temperature Less Ortho- rhombic) phase is associated to a lowering of orthorhombicity and a loss of one modulation vector, yielding a (3 + 1)D incommensurate modulation. Conversely, above 433 K the HTT phase appears as nonmodulated but exhibits a strong dynamic disorder of CoO6 octahedra, which has been characterized in detail by reconstruction of nuclear densities via the Maximum Entropy Method (MEM).},
author = {Prestipino, Carmelo and Hernandez, Olivier and Schefer, Ju and Vaughan, Gavin and Paofai, Serge and Perez-mato, Juan Manuel and Hosoya, Shoichi and Paulus, Werner},
doi = {10.1021/Ic301165a},
file = {:mnt/work-data/literature/ic301165a.pdf:pdf},
isbn = {1520-510X (Electronic)$\backslash$r0020-1669 (Linking)},
issn = {0020-1669},
journal = {Inorganic Chemistry},
number = {18},
pages = {9789--9798},
pmid = {22950869},
title = {{Structural Modulation and Phase Transitions in La2CoO4.14 Investigated by Synchrotron X-ray and Neutron Single-Crystal Diffraction}},
volume = {51},
year = {2012}
}
@article{Villesuzanne2011,
abstract = {The structure of oxygen-intercalated $\backslash$ce{\{}La{\_}2CuO{\_}{\{}4.07{\}}{\}} has been investigated at 20 and 300{\~{}}K by neutron diffraction on an electrochemically oxidized single crystal. At 20{\~{}}K, reconstruction of the nuclear density by maximum entropy method shows strong displacements of the apical oxygen atoms towards [100] with respect to the {\$}F{\$}-centered unit cell, whilst displacements towards [110] and [100] were both found to be present at ambient temperature. Combining strucutal studies with first-principles lattice dynamical calculations, we interpret the displacements of the apical oxygen atoms to be at least partially of dynamic origin already at ambient temperature. Strong displacements of the apical oxygen atoms of stoichiometric and oxygen-doped $\backslash$ce{\{}La{\_}2CuO{\_}{\{}4+{\$}\backslashdelta{\$}{\}}{\}} and corresponding associated lattice instabilites, i.e. low-energy phonon modes, are considered as a general prerequisite of low-tempeature oxygen diffusion mechanisms. Lattice dynamical calculations on $\backslash$ce{\{}La{\_}2CuO{\_}{\{}4+{\$}\backslashdelta{\$}{\}}{\}} suggest that the oxygen species diffusing at low temperature are not the interstitial but, more prominently, the apical oxygen atoms. The presence of interstitial oxygen atoms is, however, important to amplify via specific low-energy phonon modes, a dynamic exchange mechanism between apical and vacant interstitial oxygen sites, thus allowing a dynamically triggerede, shallow potential oxygen diffusion pathway. The crucial role of lattice dynamics to enable low-temperature oxygen mobility in $\backslash$ce{\{}K{\_}2NiF{\_}4{\}}-type oxides is discussed on a microscopic scale and compared to similar low-temperature oxygen diffusion mechanisms, recently proposed for non-stoichiometric oxides with Brownmillerite-type structure.},
author = {Villesuzanne, Antoine and Paulus, Werner and Cousson, Alain and Hosoya, Shoichi and {Le Dr{\'{e}}au}, Lo{\"{i}}c and Hernandez, Olivier and Prestipino, Carmelo and {Ikbel Houchati}, Mohamed and Schefer, Juerg},
doi = {10.1007/s10008-010-1274-7},
file = {:mnt/work-data/literature/art{\%}3A10.1007{\%}2Fs10008-010-1274-7.pdf:pdf},
isbn = {1000801012},
issn = {14328488},
journal = {Journal of Solid State Electrochemistry},
keywords = {Density functional theory,Lattice dynamics,Neutron diffraction,Non-stoichiometry,Oxygen mobility,Ruddlesden-Popper series},
number = {2},
pages = {357--366},
title = {{On the role of lattice dynamics on low-temperature oxygen mobility in solid oxides: A neutron diffraction and first-principles investigation of La 2CuO 4+delta}},
volume = {15},
year = {2011}
}
@article{Zhou2010,
abstract = {The sintering of (La(0.8)Sr(0.2))(0.98)MnO(3) (LSM-20) solid oxide fuel cell cathodes (in the temperature range of 1050-1200 degrees C) on anode-supported cells utilizing a Ni-yttria-stabilized zirconia (YSZ) anode and a thin YSZ electrolyte ({\textless} 10 mu m thickness) revealed the need for a protective ceria interlayer to prevent a detrimental interaction between the YSZ and the LSM. The interaction, however, was not the typically assumed formation of insulating La- and Sr-zirconate, but rather the result of Ni diffusion from the anode through the YSZ electrolyte and into the LSM, resulting in coarsening and increased densification of the LSM microstructure. The protective Ce(0.8)Sm(0.2)O(1.9) layers at the cathode/electrolyte interface were effective in blocking the Ni diffusion. As an alternative to the use of a protective ceria interlayer, the presence of YSZ in the cathode material was able to suppress the coarsening of LSM, thereby significantly improving the electrochemical performance.},
author = {Zhou, X.-D. and Simner, S. P. and Templeton, J. W. and Nie, Z. and Stevenson, J. W. and Gorman, B. P.},
doi = {10.1149/1.3321829},
file = {:mnt/work-data/literature/J. Electrochem. Soc.-2010-Zhou-B1019-23.pdf:pdf},
issn = {00134651},
journal = {Journal of The Electrochemical Society},
number = {5},
pages = {B643},
title = {{Electrochemical Performance and Stability of the Cathode for Solid Oxide Fuel Cells}},
volume = {157},
year = {2010}
}
@article{Zhou2010a,
abstract = {The sintering of (La(0.8)Sr(0.2))(0.98)MnO(3) (LSM-20) solid oxide fuel cell cathodes (in the temperature range of 1050-1200 degrees C) on anode-supported cells utilizing a Ni-yttria-stabilized zirconia (YSZ) anode and a thin YSZ electrolyte ({\textless} 10 mu m thickness) revealed the need for a protective ceria interlayer to prevent a detrimental interaction between the YSZ and the LSM. The interaction, however, was not the typically assumed formation of insulating La- and Sr-zirconate, but rather the result of Ni diffusion from the anode through the YSZ electrolyte and into the LSM, resulting in coarsening and increased densification of the LSM microstructure. The protective Ce(0.8)Sm(0.2)O(1.9) layers at the cathode/electrolyte interface were effective in blocking the Ni diffusion. As an alternative to the use of a protective ceria interlayer, the presence of YSZ in the cathode material was able to suppress the coarsening of LSM, thereby significantly improving the electrochemical performance.},
author = {Zhou, X.-D. and Simner, S. P. and Templeton, J. W. and Nie, Z. and Stevenson, J. W. and Gorman, B. P.},
doi = {10.1149/1.3321829},
file = {:mnt/work-data/literature/J. Electrochem. Soc.-2010-Zhou-B220-7.pdf:pdf},
issn = {00134651},
journal = {Journal of The Electrochemical Society},
number = {5},
pages = {B643},
title = {{Electrochemical Performance and Stability of the Cathode for Solid Oxide Fuel Cells}},
volume = {157},
year = {2010}
}
@article{Dogdibegovic2016,
author = {Dogdibegovic, Emir and Wright, Christopher J. and Zhou, Xiao-Dong},
doi = {10.1111/jace.14291},
file = {:mnt/work-data/literature/Dogdibegovic{\_}et{\_}al-2016-Journal{\_}of{\_}the{\_}American{\_}Ceramic{\_}Society.pdf:pdf},
issn = {00027820},
journal = {Journal of the American Ceramic Society},
keywords = {au metal grid was,elec-,in this work,phase transformations,solid oxide fuel cell,the cathode current collector,the grid design provides,the oxide current col-,trochemical properties comparable to,used as,with the cathode},
pages = {1--5},
title = {{Stability and Activity of \ce{(Pr_{1-x}Nd_x)2NiO4} as Cathodes for Solid Oxide Fuel Cells: I. Quantification of Phase Evolution in \ce{Pr2NiO4}}},
url = {http://doi.wiley.com/10.1111/jace.14291},
volume = {5},
year = {2016}
}
@book{McQuarrie2000,
address = {Sausalito, CA},
author = {McQuarrie, Donald A.},
isbn = {978-1891389153},
publisher = {University Science Books},
title = {{Statistical Mechanics}},
year = {2000}
}
@article{Yevick2010,
abstract = {Small (1–5 nm) metal clusters may undergo significant surface relaxation under the influence of ligands, adsorbates, and substrate-induced stress. As a result, the nearest-neighbor distance between surface atoms can be reduced by up to 10{\%} relative to those in the cluster core, enhancing the disorder in the interatomic distances. Accordingly, the pair distribution function extracted from EXAFS data under the standard assumption that the distribution function of nearest-neighbor bonds is quasi-Gaussian yields systematic errors. Here we analyze the surface disorder effects with emphasis on their impact on the accuracy of the size and shape determination of nanocatalysts.},
author = {Yevick, Aaron and Frenkel, Anatoly I.},
doi = {10.1103/PhysRevB.81.115451},
file = {:mnt/work-data/literature/yevick-frenkel.pdf:pdf},
isbn = {1098-0121$\backslash$r1550-235X},
issn = {10980121},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {11},
pages = {1--7},
title = {{Effects of surface disorder on EXAFS modeling of metallic clusters}},
volume = {81},
year = {2010}
}
@article{Chen2013,
abstract = {Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide association studies (GWAS), progress has been frustratingly slow in explaining much of the heritability in common disease. Today's paradigm of testing independent hypotheses on each single nucleotide polymorphism (SNP) marker is unlikely to adequately reflect the complex biological processes in disease risk. Alternatively, modeling risk as an ensemble of SNPs that act in concert in a pathway, and/or interact non-additively on log risk for example, may be a more sensible way to approach gene mapping in modern studies. Implementing such analyzes genome-wide can quickly become intractable due to the fact that even modest size SNP panels on modern genotype arrays (500k markers) pose a combinatorial nightmare, require tens of billions of models to be tested for evidence of interaction. In this article, we provide an in-depth analysis of programs that have been developed to explicitly overcome these enormous computational barriers through the use of processors on graphics cards known as Graphics Processing Units (GPU). We include tutorials on GPU technology, which will convey why they are growing in appeal with today's numerical scientists. One obvious advantage is the impressive density of microprocessor cores that are available on only a single GPU. Whereas high end servers feature up to 24 Intel or AMD CPU cores, the latest GPU offerings from nVidia feature over 2600 cores. Each compute node may be outfitted with up to 4 GPU devices. Success on GPUs varies across problems. However, epistasis screens fare well due to the high degree of parallelism exposed in these problems. Papers that we review routinely report GPU speedups of over two orders of magnitude ({\textgreater}100x) over standard CPU implementations.},
author = {Chen, Gary K. and Guo, Yunfei},
doi = {10.3389/fgene.2013.00266},
file = {:mnt/work-data/literature/fgene-04-00266.pdf:pdf},
issn = {16648021},
journal = {Frontiers in Genetics},
keywords = {CUDA tutorial,Epistasis,GPU programming,Gene-gene interactions,High performance computing},
number = {DEC},
pages = {1--12},
pmid = {24348518},
title = {{Discovering epistasis in large scale genetic association studies by exploiting graphics cards}},
volume = {4},
year = {2013}
}
@article{Cervellino2006,
abstract = {Samples made of an isotropically oriented ensemble of atomic clusters or structures that are not large crystals (i.e. extended less than 10 periods in each direction) are at the frontier of today's material science and chemistry. Examples are nanoparticles, nanotubes, amorphous matter, polymers, and macromolecules in suspension. For such systems the computation of powder diffraction patterns (which may provide an efficient characterization) is to be performed the hard way, by summing contributions from each atom pair. This work deals with performing such computation in the most practical and efficient way. Three main points are developed: how to encode the enormous array of interatomic distances (which increase as the square or higher powers of the cluster diameter) to a much smaller array of equispaced values on a coarse grid (whose size increases linearly with the diameter); how to perform a fast computation of the diffraction pattern from this equispaced grid; how to optimize the grid step to obtain an arbitrarily small error on the computed diffraction pattern. Theory and examples are jointly developed and presented.},
author = {Cervellino, Antonio and Giannini, Cinzia and Guagliardi, Antonietta},
doi = {10.1002/jcc.20407},
file = {:mnt/work-data/literature/Cervellino{\_}et{\_}al-2006-Journal{\_}of{\_}Computational{\_}Chemistry.pdf:pdf},
issn = {01928651},
journal = {Journal of Computational Chemistry},
keywords = {Debye scattering function,Nanoparticles and clusters,Powder diffraction,Small-angle diffraction,Structure factor computation},
number = {9},
pages = {995--1008},
pmid = {16619200},
title = {{On the efficient evaluation of fourier patterns for nanoparticles and clusters}},
volume = {27},
year = {2006}
}
@article{Sanders2001,
abstract = {We present a simple method for adaptively binning the pixels in an image. The algorithm groups pixels into bins of size such that the fractional error on the photon count in a bin is less than or equal to a threshold value, and the size of the bin is as small as possible. The process is particularly useful for generating surface brightness and colour maps, with clearly defined error maps, from images with a large dynamic range of counts, for example X-ray images of galaxy clusters. We demonstrate the method in application to data from Chandra ACIS-S and ACIS-I observations of the Perseus cluster of galaxies. We use the algorithm to create intensity maps, and colour images which show the relative X-ray intensities in different bands. The colour maps can later be converted, through spectral models, into maps of physical parameters, such as temperature, column density, etc. The adaptive binning algorithm is applicable to a wide range of data, from observations or numerical simulations, and is not limited to two-dimensional data.},
archivePrefix = {arXiv},
arxivId = {astro-ph/0011500},
author = {Sanders, J. S. and Fabian, A. C.},
doi = {10.1046/j.1365-8711.2001.04410.x},
eprint = {0011500},
file = {:mnt/work-data/literature/MNRAS-2001-Sanders-178-86.pdf:pdf},
issn = {00358711},
journal = {Monthly Notices of the Royal Astronomical Society},
keywords = {Cooling flows,Galaxies: clusters: general,Intergalactic medium,Techniques: image processing,X-rays: Galaxies},
number = {1},
pages = {178--186},
primaryClass = {astro-ph},
title = {{Adaptive binning of X-ray galaxy cluster images}},
volume = {325},
year = {2001}
}
@article{Pauw2014,
abstract = {For obtaining reliable nanostructural details of large amounts of sample—and if it is applicable—small-angle scattering (SAS) is a prime technique to use. It promises to obtain bulk-scale, statistically sound information on the morphological details of the nanostructure, and has thus led to many a researcher investing their time in it over the last eight decades of development. Due to pressure from scientists requesting more details on increasingly complex nanostructures, as well as the ever improving instrumentation leaving less margin for ambiguity, small-angle scattering methodologies have been evolving at a high pace over the past few decades. As the quality of any results can only be as good as the data that go into these methodologies, the improvements in data collection and all imaginable data correction steps are reviewed here. This work is intended to provide a comprehensive overview of all data corrections, to aid the small-angle scatterer to decide which are relevant for their measurement and how these corrections are performed. Clear mathematical descriptions of the corrections are provided where feasible. Furthermore, as no quality data exist without a decent estimate of their precision, the error estimation and propagation through all these steps are provided alongside the corrections.With these data corrections, the collected small-angle scattering pattern can be made of the highest standard, allowing for authoritative nanostructural characterization through its analysis. A brief background of small-angle scattering, the instrumentation developments over the years, and pitfalls that may be encountered upon data interpretation are provided as well.},
author = {Pauw, B R},
doi = {10.1088/0953-8984/26/23/239501},
file = {:mnt/work-data/literature/8984{\_}25{\_}38{\_}383201.pdf:pdf},
issn = {0953-8984},
journal = {Journal of Physics: Condensed Matter},
number = {23},
pages = {239501},
title = {{Corrigendum: Everything SAXS: small-angle scattering pattern collection and correction (2013 J. Phys.: Condens. Matter 25 383201)}},
url = {http://stacks.iop.org/0953-8984/26/i=23/a=239501?key=crossref.93f58cc6c1a1ca73c9c964e9eb835abf},
volume = {26},
year = {2014}
}
@article{Yang2014,
abstract = {Optimal methods are explored for obtaining one-dimensional powder pattern intensities from two-dimensional planar detectors with good estimates of their standard deviations. Methods are described to estimate uncertainties when the same image is measured in multiple frames as well as from a single frame. The importance of considering the correlation of diffraction points during the integration and the resampling process of data analysis is shown. It is found that correlations between adjacent pixels in the image can lead to seriously overestimated uncertainties if such correlations are neglected in the integration process. Off-diagonal entries in the variance-covariance (VC) matrix are problematic as virtually all data processing and modeling programs cannot handle the full VC matrix. It is shown that the off-diagonal terms come mainly from the pixel-splitting algorithm used as the default integration algorithm in many popular two-dimensional integration programs, as well as from rebinning and resampling steps later in the processing. When the full VC matrix can be propagated during the data reduction, it is possible to get accurate refined parameters and their uncertainties at the cost of increasing computational complexity. However, as this is not normally possible, the best approximate methods for data processing in order to estimate uncertainties on refined parameters with the greatest accuracy from just the diagonal variance terms in the VC matrix is explored.},
archivePrefix = {arXiv},
arxivId = {1309.3614},
author = {Yang, X. and Juh{\'{a}}s, P. and Billinge, S. J L},
doi = {10.1107/S1600576714010516},
eprint = {1309.3614},
file = {:mnt/work-data/literature/S1600576714010516.pdf:pdf},
isbn = {1600-5767},
issn = {16005767},
journal = {Journal of Applied Crystallography},
keywords = {powder diffraction data,small-angle scattering data,statistical uncertainties,variance-covariance matrix},
number = {4},
pages = {1273--1283},
title = {{On the estimation of statistical uncertainties on powder diffraction and small-angle scattering data from two-dimensional X-ray detectors}},
volume = {47},
year = {2014}
}
@article{Kieffer2013,
abstract = {2D area detectors like CCD or pixel detectors have become popular in the last 15 years for diffraction experiments (e.g. for WAXS, SAXS, single crystal and powder diffraction (XRPD)). These detectors have a large sensitive area of millions of pixels with high spatial resolution. The software package pyFAI has been designed to reduce SAXS, WAXS and XRPD images taken with those detectors into 1D curves (azimuthal integration) usable by other software for in-depth analysis such as Rietveld refinement, or 2D images (a radial transformation named caking). As a library, the aim of pyFAI is to be integrated into other tools like PyMca or EDNA with a clean pythonic interface. However pyFAI features also command line tools for batch processing, converting data into q-space (q being the momentum transfer) or 2$\theta$-space ($\theta$ being the Bragg angle) and a calibration graphical interface for optimizing the geometry of the experiment using the Debye-Scherrer rings of a reference sample. PyFAI shares the geometry definition of SPD but can directly import geometries determined by the software FIT2D. PyFAI has been designed to work with any kind of detector and geometry (transmission or reflection) and relies on FabIO, a library able to read more than 20 image formats produced by detectors from 12 different manufacturers. During the transformation from cartesian space (x,y) to polar space (2$\theta$, $\chi$), both local and total intensities are conserved in order to obtain accurate quantitative results. Technical details on how this integration is implemented and how it has been ported to native code and parallelized on graphic cards are discussed in this paper.},
author = {Kieffer, J{\'{e}}r{\^{o}}me and Karkoulis, Dimitrios},
doi = {10.1088/1742-6596/425/20/202012},
file = {:mnt/work-data/literature/jpconf13{\_}425{\_}202012.pdf:pdf},
issn = {1742-6588},
journal = {Journal of Physics: Conference Series},
pages = {202012},
title = {{PyFAI, a versatile library for azimuthal regrouping}},
url = {http://iopscience.iop.org/1742-6596/425/20/202012},
volume = {425},
year = {2013}
}
@article{McGreevy,
author = {McGreevy, R L and Pusztai, L},
doi = {10.1080/08927028808080958},
file = {:mnt/work-data/literature/mcgreevy1988.pdf:pdf},
journal = {Molecular Simulation},
number = {6},
pages = {359--367},
title = {{Reverse Monte Carlo Simulation: A New Technique for the Determination of Disordered Structures}},
url = {http://dx.doi.org/10.1080/08927028808080958},
volume = {1},
year = {1988}
}
@article{Cliffe2013,
abstract = {We present a detailed study of the mechanism by which the INVERT method (Cliffe et al 2010 Phys. Rev. Lett. 104 125501) guides structure refinement of disordered materials. We present a number of different possible implementations of the central algorithm and explore the question of algorithm weighting. Our analysis includes quantification of the relative contributions of variance and fit-to-data terms during structure refinement, which leads us to study the roles of density fluctuations and configurational jamming in the RMC fitting process. We present a parametric study of the pair distribution function solution space for C60, a-Si and a-SiO2, which serves to highlight the difficulties faced in developing a transferable weighting scheme.},
archivePrefix = {arXiv},
arxivId = {1302.1514},
author = {Cliffe, Matthew J and Goodwin, Andrew L},
doi = {10.1088/0953-8984/25/45/454218},
eprint = {1302.1514},
file = {:mnt/work-data/literature/cm13{\_}45{\_}454218.pdf:pdf},
issn = {1361-648X},
journal = {Journal of physics. Condensed matter : an Institute of Physics journal},
number = {45},
pages = {454218},
pmid = {24140797},
title = {{Nanostructure determination from the pair distribution function: a parametric study of the INVERT approach.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24140797},
volume = {25},
year = {2013}
}
@article{Juhas2015,
abstract = {A strategy is described for regularizing ill posed structure and nanostructure scattering inverse problems ( i.e. structure solution) from complex material structures. This paper describes both the philosophy and strategy of the approach, and a software implementation, DiffPy Complex Modeling Infrastructure ( DiffPy-CMI ).},
author = {Juh{\'{a}}s, Pavol and Farrow, Christopher L. and Yang, Xiaohao and Knox, Kevin R. and Billinge, Simon J. L.},
doi = {10.1107/S2053273315014473},
file = {:mnt/work-data/literature/S2053273315014473.pdf:pdf},
issn = {2053-2733},
journal = {Acta Crystallographica Section A Foundations and Advances},
keywords = {a,analysis,complex modeling,iucr,nanostructure,org,python software framework,supporting information,supporting information at journals,this article has},
number = {6},
pages = {1--7},
title = {{Complex modeling: a strategy and software program for combining multiple information sources to solve ill posed structure and nanostructure inverse problems}},
url = {http://scripts.iucr.org/cgi-bin/paper?S2053273315014473},
volume = {71},
year = {2015}
}
@article{Bahn2002,
abstract = {The authors have created an object-oriented scripting interface to a mature density functional theory code. The interface gives users a high-level, flexible handle on the code without rewriting the underlying number-crunching code. The authors also discuss the design issues and advantages of homogeneous interfaces},
author = {Bahn, S.R. and Jacobsen, K.W.},
doi = {10.1109/5992.998641},
file = {:mnt/work-data/literature/00998641.pdf:pdf},
issn = {15219615},
journal = {Computing in Science {\&} Engineering},
keywords = {Chemistry,Computer interfaces,Density functional theory,Eigenvalues and eigenfunctions,Equations,Jacobian matrices,Object oriented programming,Physics computing,Quantum mechanics,Wave functions,density functional theory code,legacy code,object-oriented databases,object-oriented programming,scripting interface,user interface,user interfaces},
number = {3},
pages = {56--66},
shorttitle = {Computing in Science {\&} Engineering},
title = {{An object-oriented scripting interface to a legacy electronic structure code}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=998641},
volume = {4},
year = {2002}
}
@article{Blochl1994,
abstract = {An approach for electronic structure calculations is described that generalizes both the pseudopotential method and the linear augmented-plane-wave (LAPW) method in a natural way. The method allows high-quality first-principles molecular-dynamics calculations to be performed using the original fictitious Lagrangian approach of Car and Parrinello. Like the LAPW method it can be used to treat first-row and transition-metal elements with affordable effort and provides access to the full wave function. The augmentation procedure is generalized in that partial-wave expansions are not determined by the value and the derivative of the envelope function at some muffin-tin radius, but rather by the overlap with localized projector functions. The pseudopotential approach based on generalized separable pseudopotentials can be regained by a simple approximation.},
author = {Bl{\"{o}}chl, P. E.},
doi = {10.1103/PhysRevB.50.17953},
file = {:mnt/work-data/literature/PhysRevB.50.17953.pdf:pdf},
isbn = {0163-1829 (Print)$\backslash$n0163-1829 (Linking)},
issn = {01631829},
journal = {Physical Review B},
month = {dec},
number = {24},
pages = {17953--17979},
pmid = {9976227},
publisher = {American Physical Society},
title = {{Projector augmented-wave method}},
url = {http://journals.aps.org/prb/abstract/10.1103/PhysRevB.50.17953},
volume = {50},
year = {1994}
}
@article{Cui2013,
abstract = {Shape-selective monometallic nanocatalysts offer activity benefits based on structural sensitivity and high surface area. In bimetallic nanoalloys with well-defined shape, site-dependent metal surface segregation additionally affects the catalytic activity and stability. However, segregation on shaped alloy nanocatalysts and their atomic-scale evolution is largely unexplored. Exemplified by three octahedral PtxNi1-x alloy nanoparticle electrocatalysts with unique activity for the oxygen reduction reaction at fuel cell cathodes, we reveal an unexpected compositional segregation structure across the {\{}111{\}} facets using aberration-corrected scanning transmission electron microscopy and electron energy-loss spectroscopy. In contrast to theoretical predictions, the pristine PtxNi1-x nano-octahedra feature a Pt-rich frame along their edges and corners, whereas their Ni atoms are preferentially segregated in their {\{}111{\}} facet region. We follow their morphological and compositional evolution in electrochemical environments and correlate this with their exceptional catalytic activity. The octahedra preferentially leach in their facet centres and evolve into 'concave octahedra'. More generally, the segregation and leaching mechanisms revealed here highlight the complexity with which shape-selective nanoalloys form and evolve under reactive conditions.},
author = {Cui, Chunhua and Gan, Lin and Heggen, Marc and Rudi, Stefan and Strasser, Peter},
doi = {10.1038/nmat3668},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Cui et al. - 2013 - Compositional segregation in shaped Pt alloy nanoparticles and their structural behaviour during electrocatalysis.pdf:pdf;:mnt/work-data/literature/nmat3668.pdf:pdf},
isbn = {1476-1122},
issn = {1476-1122},
journal = {Nature materials},
number = {12},
pages = {765--771},
pmid = {23770725},
publisher = {Nature Publishing Group},
title = {{Compositional segregation in shaped Pt alloy nanoparticles and their structural behaviour during electrocatalysis.}},
url = {http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat3668.html},
volume = {12},
year = {2013}
}
@article{Proffen1997,
abstract = {The program DISCUS is a versatile tool for the analysis of diffuse scattering and for defect structure simulations. The model structure can be created from an asymmetric unit of a unit cell or a complete structure can be read from a file. A Fortran77 style interpreter that includes IF statements and various loops combined with predefined defect types like thermal displacements, waves and microdomains allows one to create all sorts of defect structures. The Fourier-transform segment of the program allows one to calculate neutron as well as X-ray intensities including isotropic temperature factors and anomalous scattering. The calculation of the inverse and difference Fourier transform as well as the Patterson function is also implemented. A model structure can be `fitted' to observed diffuse scattering data by reverse Monte Carlo (RMC) simulations. The RMC segment allows one to model displacive as well as occupational disorder. The program is completely written in Fortran77 and the source code is available via the World Wide Web.},
author = {Proffen, Th. and Neder, R. B.},
doi = {10.1107/S002188989600934X},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Proffen, Neder - 1997 - DISCUS a Program for Diffuse Scattering and Defect-Structure Simulation.pdf:pdf},
isbn = {0021-8898},
issn = {0021-8898},
journal = {Journal of Applied Crystallography},
pages = {171--175},
publisher = {International Union of Crystallography},
title = {{DISCUS: a Program for Diffuse Scattering and Defect-Structure Simulation}},
volume = {30},
year = {1997}
}
@article{Snurr1993,
abstract = {Adsorption isotherms and isosteric heats of adsorption for benzene andp-xylene in silicalite have been calculated from molecular simulations. The simulations were performed using newly developed grand canonical ensemble Monte Carlo (GCMC) techniques in which insertion attempts are biased toward the most favorable regions of the zeolite pore space. The new techniques result in a substantial improvement in the efficiency of the simulations compared to traditional GCMC. The adsorption thermodynamics and molecular-level structure were studied for benzene and p-xylene in silicalite with Pnma symmetry (ORTHO) and P2,2121 symmetry (PARA). The subtle differences between ORTHO and PARA silicalite result in qualitatively different sorption behavior. An explanation of the experimentally observed step in the adsorption isotherm is presented, based on the results of the simulations and the ORTHO to PARA framework transformation that is observed experimentally. Predictions of the adsorption isotherms, isosteric heats, and siting locations of the adsorbates are in good agreement with experiment.},
author = {Snurr, Randall Q. and Bell, Alexis T. and Theodorou, Doros N.},
doi = {10.1021/j100153a051},
file = {:mnt/work-data/literature/j100153a051.pdf:pdf},
isbn = {0022-3654},
issn = {0022-3654},
journal = {The Journal of Physical Chemistry},
language = {EN},
month = {dec},
number = {51},
pages = {13742--13752},
publisher = {American Chemical Society},
title = {{Prediction of adsorption of aromatic hydrocarbons in silicalite from grand canonical Monte Carlo simulations with biased insertions}},
url = {http://dx.doi.org/10.1021/j100153a051 http://pubs.acs.org.pallas2.tcl.sc.edu/doi/abs/10.1021/j100153a051},
volume = {97},
year = {1993}
}
@article{Hoffman2014,
abstract = {Hamiltonian Monte Carlo (HMC) is a Markov chain Monte Carlo (MCMC) algorithm that avoids the random walk behavior and sensitivity to correlated parameters that plague many MCMC methods by taking a series of steps informed by first-order gradient information. These features allow it to converge to high-dimensional target distributions much more quickly than simpler methods such as random walk Metropolis or Gibbs sampling. However, HMC's performance is highly sensitive to two user-specified parameters: a step size {\{}$\backslash$epsilon{\}} and a desired number of steps L. In particular, if L is too small then the algorithm exhibits undesirable random walk behavior, while if L is too large the algorithm wastes computation. We introduce the No-U-Turn Sampler (NUTS), an extension to HMC that eliminates the need to set a number of steps L. NUTS uses a recursive algorithm to build a set of likely candidate points that spans a wide swath of the target distribution, stopping automatically when it starts to double back and retrace its steps. Empirically, NUTS perform at least as efficiently as and sometimes more efficiently than a well tuned standard HMC method, without requiring user intervention or costly tuning runs. We also derive a method for adapting the step size parameter {\{}$\backslash$epsilon{\}} on the fly based on primal-dual averaging. NUTS can thus be used with no hand-tuning at all. NUTS is also suitable for applications such as BUGS-style automatic inference engines that require efficient "turnkey" sampling algorithms.},
archivePrefix = {arXiv},
arxivId = {1111.4246},
author = {Hoffman, Md Matthew D. and Gelman, Andrew},
eprint = {1111.4246},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hoffman, Gelman - 2014 - The No-U-Turn Sampler Adaptively Setting Path Lengths in Hamiltonian Monte Carlo.pdf:pdf;:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Homan, Gelman - 2014 - The No-U-turn sampler adaptively setting path lengths in Hamiltonian Monte Carlo.pdf:pdf},
issn = {15337928},
journal = {The Journal of Machine Learning Research},
keywords = {Bayesian inference,Hamiltonian Monte Carlo,Markov chain Monte Carlo,adaptive Monte Carlo,adaptive monte carlo,bayesian inference,dual averaging,hamiltonian monte carlo,markov chain monte carlo,monte carlo},
month = {jan},
number = {2008},
pages = {1593--1623},
publisher = {JMLR.org},
title = {{The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo}},
url = {http://dl.acm.org/citation.cfm?id=2627435.2638586},
volume = {15},
year = {2014}
}
@article{Yang2013a,
abstract = {The atomic pair distribution function (PDF) analysis of X-ray powder diffraction data has been used to study the structure of small and ultra-small CdSe nanoparticles. A method is described that uses a wurtzite and zinc-blende mixed phase model to account for stacking faults in CdSe particles. The mixed-phase model successfully describes the structure of nanoparticles larger than 2 nm yielding a stacking fault density of about 30{\%}. However, for ultrasmall nanoparticles smaller than 2 nm, the models cannot fit the experimental PDF showing that the structure is significantly modified from that of larger particles and the bulk. The observation of a significant change in the average structure at ultra-small size is likely to explain the unusual properties of the ultrasmall particles such as their white light emitting ability.},
author = {Yang, Xiaohao and Masadeh, Ahmad S and McBride, James R and Bo{\v{z}}in, Emil S and Rosenthal, Sandra J and Billinge, Simon J L},
doi = {10.1039/c3cp00111c},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Yang et al. - 2013 - Confirmation of disordered structure of ultrasmall CdSe nanoparticles from X-ray atomic pair distribution function.pdf:pdf},
issn = {1463-9084},
journal = {Physical chemistry chemical physics : PCCP},
month = {jun},
number = {22},
pages = {8480--6},
pmid = {23525376},
title = {{Confirmation of disordered structure of ultrasmall CdSe nanoparticles from X-ray atomic pair distribution function analysis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23525376},
volume = {15},
year = {2013}
}
@article{Gereben2012,
abstract = {An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness-of-fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard-Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor-based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future.},
author = {Gereben, Orsolya and Pusztai, L{\'{a}}szl{\'{o}}},
doi = {10.1002/jcc.23058},
file = {:mnt/work-data/literature/Gereben{\_}et{\_}al-2012-Journal{\_}of{\_}Computational{\_}Chemistry.pdf:pdf},
isbn = {1096-987X},
issn = {1096-987X},
journal = {Journal of Computational Chemistry},
keywords = {Algorithms,Molecular Dynamics Simulation,Molecular Structure,Monte Carlo Method,Sulfides,Sulfides: chemistry},
number = {29},
pages = {2285--91},
pmid = {22782785},
title = {{RMC{\_}POT: a computer code for reverse Monte Carlo modeling the structure of disordered systems containing molecules of arbitrary complexity.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22782785},
volume = {33},
year = {2012}
}
@article{Rose-Petruck1999,
abstract = {Fundamental processes on the molecular level, such as vibrations and rotations in single molecules, liquids or crystal lattices and the breaking and formation of chemical bonds, occur on timescales of femtoseconds to picoseconds. The electronic changes associated with such processes can be monitored in a time-resolved manner by ultrafast optical spectroscopic techniques1, but the accompanying structural rearrangements have proved more difficult to observe. Time-resolved X-ray diffraction has the potential to probe fast, atomic-scale motions2, 3, 4, 5. This is made possible by the generation of ultrashort X-ray pulses6, 7, 8, 9, 10, and several X-ray studies of fast dynamics have been reported6, 7, 8,11, 12, 13, 14, 15. Here we report the direct observation of coherent acoustic phonon propagation in crystalline gallium arsenide using a non-thermal, ultrafast-laser-driven plasma — a high-brightness, laboratory-scale source of subpicosecond X-ray pulses16, 17, 18, 19. We are able to follow a 100-ps coherent acoustic pulse, generated through optical excitation of the crystal surface, as it propagates through the X-ray penetration depth. The time-resolved diffraction data are in excellent agreement with theoretical predictions for coherent phonon excitation20 in solids, demonstrating that it is possible to obtain quantitative information on atomic motions in bulk media during picosecond-scale lattice dynamics.},
author = {Rose-Petruck, Christoph and Jimenez, Ralph and Guo, Ting and Cavalleri, Andrea and Siders, Craig W. and Rksi, Ferenc and Squier, Jeff A. and Walker, Barry C. and Wilson, Kent R. and Barty, Christopher P. J.},
doi = {10.1038/18631},
file = {:mnt/work-data/literature/398310a0.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = {mar},
number = {6725},
pages = {310--312},
shorttitle = {Nature},
title = {{Picosecond–milli{\aa}ngstr{\"{o}}m lattice dynamics measured by ultrafast X-ray diffraction}},
url = {http://dx.doi.org/10.1038/18631},
volume = {398},
year = {1999}
}
@article{Farrow2007,
abstract = {PDFfit2 is a program as well as a library for real-space refinement of crystal structures. It is capable of fitting a theoretical three-dimensional (3D) structure to atomic pair distribution function data and is ideal for nanoscale investigations. The fit system accounts for lattice constants, atomic positions and anisotropic atomic displacement parameters, correlated atomic motion, and experimental factors that may affect the data. The atomic positions and thermal coefficients can be constrained to follow the symmetry requirements of an arbitrary space group. The PDFfit2 engine is written in C++ and is accessible via Python, allowing it to inter-operate with other Python programs. PDFgui is a graphical interface built on the PDFfit2 engine. PDFgui organizes fits and simplifies many data analysis tasks, such as configuring and plotting multiple fits. PDFfit2 and PDFgui are freely available via the Internet.},
author = {Farrow, C L and Juhas, P and Liu, J W and Bryndin, D and Bo{\v{z}}in, E S and Bloch, J and Proffen, Th and Billinge, S J L},
doi = {10.1088/0953-8984/19/33/335219},
file = {:mnt/work-data/literature/farrow-jpcm07-pdfgui.pdf:pdf;:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Farrow et al. - 2007 - PDFfit2 and PDFgui computer programs for studying nanostructure in crystals.pdf:pdf},
isbn = {0953-8984 (Print)$\backslash$n0953-8984 (Linking)},
issn = {0953-8984},
journal = {Journal of Physics. Condensed Matter : an Institute of Physics journal},
month = {aug},
number = {33},
pages = {335219},
pmid = {21694142},
title = {{PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21694142},
volume = {19},
year = {2007}
}
@article{Redmond2012,
author = {Redmond, Erin L. and Setzler, Brian P. and Juhas, Pavol and Billinge, Simon J. L. and Fuller, Thomas F.},
doi = {10.1149/2.004206esl},
file = {:mnt/work-data/literature/Electrochem. Solid-State Lett.-2012-Redmond-B72-4.pdf:pdf},
issn = {10990062},
journal = {Electrochemical and Solid-State Letters},
language = {en},
month = {jan},
number = {5},
pages = {B72},
publisher = {The Electrochemical Society},
title = {{In-Situ Monitoring of Particle Growth at PEMFC Cathode under Accelerated Cycling Conditions}},
url = {http://esl.ecsdl.org/content/15/5/B72.full},
volume = {15},
year = {2012}
}
@article{Weller2000,
abstract = {▪ Abstract Areal density progress in magnetic recording is largely determined by the ability to fabricate low-noise, granular thin lm media with sufficient stability against thermal agitation to warrant long-term data storage. A key requirement is a medium microstructure with small, magnetically isolated grains to establish optimal macro- and micro-magnetic properties. A lower bound for the minimal average grain diameter, compatible with thermal stability, is imposed by the write field capability of the recording head. It is 10–12 nm assuming maximal writeable coercivities of 400 kA/m (5000 Oe). These are already achieved in today's state-of-the-art CoCr-based thin lm alloy media, leaving little room for further improvements and density gains based on continued grain size reduction. A threefold reduction in grain diameter, however, translating into a tenfold increase in areal density is theoretically possible if write field constraints can be overcome, allowing utilization of magnetically harder alloys. T...},
author = {Weller, Dieter and Doerner, Mary F.},
doi = {10.1146/annurev.matsci.30.1.611},
file = {:mnt/work-data/literature/annurev{\%}2Ematsci{\%}2E30{\%}2E1{\%}2E611.pdf:pdf},
issn = {0084-6600},
journal = {Annual Review of Materials Science},
keywords = {CoCr-based media,by the ability to,cocr-based media,fabricate low-noise,grain size scaling,granular thin lm media,high anisotropy media,is largely determined,progress in magnetic recording,s abstract areal density,thermal limits,with suf cient stability,write coercivity},
language = {en},
month = {aug},
number = {1},
pages = {611--644},
publisher = {Annual Reviews 4139 El Camino Way, P.O. Box 10139, Palo Alto, CA 94303-0139, USA},
title = {{EXTREMELY HIGH-DENSITY LONGITUDINAL MAGNETIC RECORDINGMEDIA}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.matsci.30.1.611},
volume = {30},
year = {2000}
}
@article{Tuaev2013,
abstract = {When exposed to corrosive anodic electrochemical environments, Pt alloy nanoparticles (NPs) undergo selective dissolution of the less noble component, resulting in catalytically active bimetallic Pt-rich core-shell structures. Structural evolution of PtNi6 and PtNi3 NP catalysts during their electrochemical activation and catalysis was studied by in situ anomalous small-angle X-ray scattering to obtain insight in element-specific particle size evolution and time-resolved insight in the intraparticle structure evolution. Ex situ high-energy X-ray diffraction coupled with pair distribution function analysis was employed to obtain detailed information on the atomic-scale ordering, particle phases, structural coherence lengths, and particle segregation. Our studies reveal a spontaneous electrochemically induced formation of PtNi particles of ordered Au3Cu-type alloy structures from disordered alloy phases (solid solutions) concomitant with surface Ni dissolution, which is coupled to spontaneous residual Ni metal segregation during the activation of PtNi6. Pt-enriched core-shell structures were not formed using the studied Ni-rich nanoparticle precursors. In contrast, disordered PtNi3 alloy nanoparticles lose Ni more rapidly, forming Pt-enriched core-shell structures with superior catalytic activity. Our X-ray scattering results are confirmed by STEM/EELS results on similar nanoparticles.},
author = {Tuaev, Xenia and Rudi, Stefan and Petkov, Valeri and Hoell, Armin and Strasser, Peter},
doi = {10.1021/nn402406k},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Tuaev et al. - 2013 - In Situ Study of Atomic Structure Transformations of Pt-Ni Nanoparticle Catalysts during Electrochemical Potential.pdf:pdf},
issn = {1936-086X},
journal = {ACS Nano},
keywords = {asaxs,at the,efforts have been directed,fuel cell catalysis,great research,in situ characterization,optimization of electrocatalysts for,pair distribution function,ptni alloys,ver the past decade},
month = {jul},
number = {7},
pages = {5666--74},
pmid = {23805992},
title = {{In Situ Study of Atomic Structure Transformations of Pt-Ni Nanoparticle Catalysts during Electrochemical Potential Cycling.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23805992},
volume = {7},
year = {2013}
}
@article{Shan2014,
abstract = {Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of {\~{}}50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.},
author = {Shan, Shiyao and Petkov, Valeri and Yang, Lefu and Luo, Jin and Joseph, Pharrah and Mayzel, Dina and Prasai, Binay and Wang, Lingyan and Engelhard, Mark and Zhong, Chuan-Jian},
doi = {10.1021/ja5026744},
file = {:mnt/work-data/literature/ja5026744.pdf:pdf},
issn = {1520-5126},
journal = {Journal of the American Chemical Society},
language = {EN},
month = {may},
number = {19},
pages = {7140--51},
pmid = {24794852},
publisher = {American Chemical Society},
title = {{Atomic-structural synergy for catalytic CO oxidation over palladium-nickel nanoalloys.}},
url = {http://pubs.acs.org.pallas2.tcl.sc.edu/doi/abs/10.1021/ja5026744},
volume = {136},
year = {2014}
}
@article{Tibshirani2011,
abstract = {Ribosomes translate genetic information encoded by messenger RNA into proteins. Many aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are much larger and intricate than their bacterial counterparts. We report the crystal structure of the 80S ribosome from the yeast Saccharomyces cerevisiae--including nearly all ribosomal RNA bases and protein side chains as well as an additional protein, Stm1--at a resolution of 3.0 angstroms. This atomic model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core, and describes all eukaryote-specific bridges between the two ribosomal subunits. It forms the structural framework for the design and analysis of experiments that explore the eukaryotic translation apparatus and the evolutionary forces that shaped it.},
author = {Ben-Shem, Adam and {Garreau de Loubresse}, Nicolas and Melnikov, Sergey and Jenner, Lasse and Yusupova, Gulnara and Yusupov, Marat},
doi = {10.1126/science.1212642},
file = {:mnt/work-data/literature/Science-2011-Ben-Shem-1524-9.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Cryoelectron Microscopy,Crystallography,DNA-Binding Proteins,DNA-Binding Proteins: ultrastructure,Fungal,Fungal: ultrastructure,Models,Molecular,RNA,Ribosomal,Ribosomal: ultrastructure,Ribosomes,Ribosomes: ultrastructure,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: ultrastructure,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: ultrastructure,X-Ray},
month = {dec},
number = {6062},
pages = {1524--1529},
pmid = {22096102},
title = {{The structure of the eukaryotic ribosome at 3.0 {\AA} resolution.}},
url = {http://www.sciencemag.org/content/334/6062/1524.short},
volume = {334},
year = {2011}
}
@article{Manthiram2014,
abstract = {Although the vast majority of hydrocarbon fuels and products are presently derived from petroleum, there is much interest in the development of routes for synthesizing these same products by hydrogenating CO2. The simplest hydrocarbon target is methane, which can utilize existing infrastructure for natural gas storage, distribution, and consumption. Electrochemical methods for methanizing CO2 currently suffer from a combination of low activities and poor selectivities. We demonstrate that copper nanoparticles supported on glassy carbon (n-Cu/C) achieve up to 4 times greater methanation current densities compared to high-purity copper foil electrodes. The n-Cu/C electrocatalyst also exhibits an average Faradaic efficiency for methanation of 80{\%} during extended electrolysis, the highest Faradaic efficiency for room-temperature methanation reported to date. We find that the level of copper catalyst loading on the glassy carbon support has an enormous impact on the morphology of the copper under catalytic conditions and the resulting Faradaic efficiency for methane. The improved activity and Faradaic efficiency for methanation involves a mechanism that is distinct from what is generally thought to occur on copper foils. Electrochemical data indicate that the early steps of methanation on n-Cu/C involve a pre-equilibrium one-electron transfer to CO2 to form an adsorbed radical, followed by a rate-limiting non-electrochemical step in which the adsorbed CO2 radical reacts with a second CO2 molecule from solution. These nanoscale copper electrocatalysts represent a first step toward the preparation of practical methanation catalysts that can be incorporated into membrane-electrode assemblies in electrolyzers.},
author = {Manthiram, Karthish and Beberwyck, Brandon J and Alivisatos, A Paul},
doi = {10.1021/ja5065284},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Manthiram, Beberwyck, Alivisatos - 2014 - Enhanced electrochemical methanation of carbon dioxide with a dispersible nanoscale copper cat.pdf:pdf;:mnt/work-data/literature/ja5065284.pdf:pdf},
isbn = {0002-7863},
issn = {1520-5126},
journal = {Journal of the American Chemical Society},
month = {sep},
number = {38},
pages = {13319--25},
pmid = {25137433},
title = {{Enhanced electrochemical methanation of carbon dioxide with a dispersible nanoscale copper catalyst.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25137433},
volume = {136},
year = {2014}
}
@article{Farrow2009,
abstract = {The relationship between the equations used in the atomic pair distribution function (PDF) method and those commonly used in small-angle-scattering (SAS) analyses is explicitly shown. The origin of the sloping baseline, -4pirrho0, in PDFs of bulk materials is identified as originating from the SAS intensity that is neglected in PDF measurements. The nonlinear baseline in nanoparticles has the same origin, and contains information about the shape and size of the nanoparticles.},
author = {Farrow, Christopher L and Billinge, Simon J L},
doi = {10.1107/S0108767309009714},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Farrow, Billinge - 2009 - Relationship between the atomic pair distribution function and small-angle scattering implications for modelin.pdf:pdf},
issn = {1600-5724},
journal = {Acta Crystallographica Section A Foundations of Crystallography},
keywords = {ATOMIC PAIR DISTRIBUTION FUNCTION,MODELING,NANOPARTICLES,SMALL-ANGLE SCATTERING},
language = {en},
month = {may},
number = {Pt 3},
pages = {232--9},
pmid = {19349667},
publisher = {International Union of Crystallography},
title = {{Relationship between the atomic pair distribution function and small-angle scattering: implications for modeling of nanoparticles.}},
url = {http://scripts.iucr.org/cgi-bin/paper?cn5017},
volume = {65},
year = {2009}
}
@article{Page2011,
abstract = {High-energy X-ray and spallation neutron total scattering data provide information about each pair of atoms in a nanoparticle sample, allowing for quantitative whole-particle structural modeling based on pair distribution function analysis. The realization of this capability has been hindered by a lack of versatile tools for describing complex finite structures. Here, the implementation of whole-particle refinement for complete nanoparticle systems is described within two programs, DISCUS and DIFFEV, and the diverse capabilities they present are demonstrated. The build-up of internal atomic structure (including defects, chemical ordering and other types of disorder), and nanoparticle size, shape and architecture (including core-shell structures, surface relaxation and ligand capping), are demonstrated using the program DISCUS. The structure refinement of a complete nanoparticle system (4 nm Au particles with organic capping ligands at the surface), based on neutron pair distribution function data, is demonstrated using DIFFEV, a program using a differential evolutionary algorithm to generate parameter values. These methods are a valuable addition to other probes appropriate for nanomaterials, adaptable to a diverse and complex set of materials systems, and extendable to additional data-set types.},
author = {Page, Katharine and Hood, Taylor C. and Proffen, Thomas and Neder, Reinhard B.},
doi = {10.1107/S0021889811001968},
file = {:mnt/work-data/literature/S0021889811001968.pdf:pdf},
isbn = {0021-8898},
issn = {00218898},
journal = {Journal of Applied Crystallography},
keywords = {nanoparticles,pair distribution functions,total scattering data,whole-particle modeling},
language = {en},
month = {feb},
number = {2},
pages = {327--336},
publisher = {International Union of Crystallography},
title = {{Building and refining complete nanoparticle structures with total scattering data}},
url = {http://scripts.iucr.org/cgi-bin/paper?wf5081},
volume = {44},
year = {2011}
}
@article{Metropolis1953,
abstract = {A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two‐dimensional rigid‐sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four‐term virial coefficient expansion.},
archivePrefix = {arXiv},
arxivId = {5744249209},
author = {Metropolis, Nicholas and Rosenbluth, Arianna W. and Rosenbluth, Marshall N. and Teller, Augusta H. and Teller, Edward},
doi = {doi:10.1063/1.1699114},
eprint = {5744249209},
file = {:mnt/work-data/literature/1.1699114.pdf:pdf},
isbn = {doi:10.1063/1.1699114},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {6},
pages = {1087--1092},
pmid = {2797},
title = {{Equation of State Calculations by Fast Computing Machines}},
url = {http://jcp.aip.org/resource/1/jcpsa6/v21/i6/p1087{\_}s1?bypassSSO=1 http://dx.doi.org/10.1063/1.4790150},
volume = {21},
year = {1953}
}
@misc{Bastien-Theano-2012,
abstract = {Theano is a linear algebra compiler that optimizes a user's symbolically-specified
mathematical computations to produce efficient low-level implementations. In
this paper, we present new features and efficiency improvements to Theano, and
benchmarks demonstrating Theano's performance relative to Torch7, a recently
introduced machine learning library, and to RNNLM, a C++ library targeted at
recurrent neural networks.},
author = {Bastien, Fr{\'{e}}d{\'{e}}ric and Lamblin, Pascal and Pascanu, Razvan and Bergstra, James and Goodfellow, Ian J and Bergeron, Arnaud and Bouchard, Nicolas and Bengio, Yoshua},
howpublished = {Deep Learning and Unsupervised Feature Learning NIPS 2012 Workshop},
title = {{Theano: new features and speed improvements}},
year = {2012}
}
@article{DaSilva2010,
abstract = {Cuboctahedron ?CUB? and icosahedron ?ICO? model structures are widely used in the study of transition- metal ?TM? nanoparticles ?NPs?, however, it might not provide a reliable description for small TM NPs such as the Pt55 and Au55 systems in gas phase. In this work, we combined density-functional theory calculations with atomic configurations generated by the basin hopping Monte Carlo algorithm within the empirical Sutton- Chen embedded atom potential. We identified alternative lower energy configurations compared with the ICO and CUB model structures, e.g., our lowest energy structures are 5.22 eV ?Pt55? and 2.01 eV ?Au55? lower than ICO. The energy gain is obtained by the Pt and Au diffusion from the ICO core region to the NP surface, which is driven by surface compression ?only 12 atoms? on the ICO core region. Therefore, in the lowest energy configurations, the core size reduces from 13 atoms ?ICO, CUB? to about 9 atoms while the NP surface increases from 42 atoms ?ICO, CUB? to about 46 atoms. The present mechanism can provide an improved atom-level understanding of small TM NPs reconstructions.},
author = {{Da Silva}, Juarez L F and Kim, Hyoung Gyu and Piotrowski, Maur{\'{i}}cio J. and Prieto, Maur{\'{i}}cio J. and Tremiliosi-Filho, Germano},
doi = {10.1103/PhysRevB.82.205424},
file = {:mnt/work-data/literature/PhysRevB.82.205424.pdf:pdf},
issn = {10980121},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {20},
pages = {1--6},
title = {{Reconstruction of core and surface nanoparticles: The example of Pt55 and Au55}},
volume = {82},
year = {2010}
}
@article{Ferrando2008,
author = {Ferrando, Riccardo and Jellinek, Julius and Johnston, Roy L},
doi = {10.1021/cr040090g},
file = {:mnt/work-data/literature/cr040090g.pdf:pdf},
journal = {Chemical Reviews},
number = {3},
pages = {846--904},
title = {{Nanoalloys: From Theory to Applications of Alloy Clusters and Nanoparticles}},
volume = {108},
year = {2008}
}
@article{Cliffe2010,
abstract = {We show that the information gained in spectroscopic experiments regarding the number and distribution of atomic environments can be used as a valuable constraint in the refinement of the atomic-scale structures of nanostructured or amorphous materials from pair distribution function (PDF) data. We illustrate the effectiveness of this approach for three paradigmatic disordered systems: molecular C60, a-Si, and a-SiO2. Much improved atomistic models are attained in each case without any a priori assumptions regarding coordination number or local geometry. We propose that this approach may form the basis for a generalized methodology for structure "solution" from PDF data applicable to network, nanostructured and molecular systems alike.},
archivePrefix = {arXiv},
arxivId = {arXiv:0912.1971v2},
author = {Cliffe, Matthew J. and Dove, Martin T. and Drabold, D. A. and Goodwin, Andrew L.},
doi = {10.1103/PhysRevLett.104.125501},
eprint = {arXiv:0912.1971v2},
file = {:mnt/work-data/literature/PhysRevLett.104.125501.pdf:pdf},
issn = {00319007},
journal = {Physical Review Letters},
number = {12},
pages = {1--4},
pmid = {20366543},
title = {{Structure determination of disordered materials from diffraction data}},
volume = {104},
year = {2010}
}
@article{Kresse1994,
abstract = {We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal- amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence cal- culation of the exact Hellmann-Feynman forces after each molecular-dynamics step using precon- ditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nose dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.},
author = {Kresse,G. and Hafner,0J.},
doi = {10.1103/PhysRevB.49.14251},
file = {:mnt/work-data/literature/PhysRevB.49.14251.pdf:pdf},
isbn = {0163-1829 (Print)$\backslash$n0163-1829 (Linking)},
issn = {0163-1829},
journal = {Physical Review B},
month = {may},
number = {20},
pages = {14251--14269},
pmid = {10010505},
publisher = {American Physical Society (APS)},
title = {{Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium}},
url = {http://dx.doi.org/10.1103/PhysRevB.49.14251},
volume = {49},
year = {1994}
}
@article{Jadzinsky2007,
abstract = {Structural information on nanometer-sized gold particles has been limited, due in part to the problem of preparing homogeneous material. Here we report the crystallization and x-ray structure determination of a p-mercaptobenzoic acid (p-MBA)-protected gold nanoparticle, which comprises 102 gold atoms and 44 p-MBAs. The central gold atoms are packed in a Marks decahedron, surrounded by additional layers of gold atoms in unanticipated geometries. The p-MBAs interact not only with the gold but also with one another, forming a rigid surface layer. The particles are chiral, with the two enantiomers alternating in the crystal lattice. The discrete nature of the particle may be explained by the closing of a 58-electron shell.},
author = {Jadzinsky, Pablo D and Calero, Guillermo and Ackerson, Christopher J and Bushnell, David A and Kornberg, Roger D},
doi = {10.1126/science.1148624},
file = {:mnt/work-data/literature/Science-2007-Jadzinsky-430-3 (1).pdf:pdf},
isbn = {1095-9203},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
keywords = {Benzoates,Benzoates: chemistry,Chemical,Chemistry,Crystallization,Crystallography,Gold,Gold: chemistry,Macromolecular Substances,Macromolecular Substances: chemistry,Metal Nanoparticles,Metal Nanoparticles: chemistry,Models,Molecular Structure,Physical,Physicochemical Phenomena,Stereoisomerism,Sulfhydryl Compounds,Sulfhydryl Compounds: chemistry,X-Ray},
month = {oct},
number = {5849},
pages = {430--433},
pmid = {17947577},
title = {{Structure of a thiol monolayer-protected gold nanoparticle at 1.1 A resolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17947577},
volume = {318},
year = {2007}
}
@article{Zhang2008,
abstract = {Amorphous titania (TiO2) is an important precursor for synthesis of single-phase nanocrystalline anatase. We synthesized amorphous titania by hydrolysis of titanium ethoxide at the ice point. Transmission electron microscopy examination and nitrogen gas adsorption indicated that the particle size of the synthesized titania is ∼2 nm. Synchrotron wide-angle x-ray scattering (WAXS) was used to probe the atomic correlations in this amorphous sample. Atomic pair-distribution function (PDF) derived from Fourier transform of the WAXS data was used for reverse Monte Carlo (RMC) simulations of the atomic structure of the amorphous TiO2 nanoparticles. Molecular-dynamics simulations were used to generate input structures for the RMC. X-ray-absorption spectroscopy (XAS) simulations were used to screen candidate structures obtained from the RMC by comparing with experimental XAS data. The structure model that best describes both the WAXS and XAS data shows that amorphous TiO2 particles consist of a highly distorted shell and a small strained anataselike crystalline core. The average coordination number of Ti is 5.3 and most Ti-O bonds are populated around 1.940 {\AA}. Relative to bulk TiO2, the reduction in the coordination number is primarily due to the truncation of the Ti-O octahedra at the amorphous nanoparticle surface and the shortening of the Ti-O bond length to the bond contraction in the distorted shell. The pre-existence of the anataselike core may be critical to the formation of single-phase nanocrystalline anatase in crystallization of amorphous TiO2 upon heating.},
author = {Zhang, Hengzhong and Chen, Bin and Banfield, Jillian F. and Waychunas, Glenn A.},
doi = {10.1103/PhysRevB.78.214106},
file = {:mnt/work-data/literature/eScholarship UC item 64j177cw.pdf:pdf},
issn = {1098-0121},
journal = {Physical Review B},
month = {dec},
number = {21},
pages = {214106},
title = {{Atomic structure of nanometer-sized amorphous TiO2}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.78.214106},
volume = {78},
year = {2008}
}
@article{Tucker2007,
abstract = {A new approach to the reverse Monte Carlo analysis of total scattering data from polycrystalline materials is presented. The essential new feature is the incorporation of an explicit analysis of the Bragg peaks using a profile refinement, taking account of the instrument resolution function. Other new features including fitting data from magnetic materials, modelling lattice site disorder and new restraint and constraint options. The new method is demonstrated by a brief review of studies carried out during its development. The new program RMCProfile represents a significant advance in the analysis of polycrystalline total scattering data, especially where the local structure is to be explored within the true constraints of the long-range average structure.},
author = {Tucker, Matthew G and Keen, David A and Dove, Martin T and Goodwin, Andrew L and Hui, Qun},
doi = {10.1088/0953-8984/19/33/335218},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Tucker et al. - 2007 - RMCProfile reverse Monte Carlo for polycrystalline materials.pdf:pdf},
issn = {0953-8984},
journal = {Journal of Physics. Condensed Matter : an Institute of Physics journal},
month = {aug},
number = {33},
pages = {335218},
pmid = {21694141},
title = {{RMCProfile: reverse Monte Carlo for polycrystalline materials.}},
url = {http://stacks.iop.org/0953-8984/19/i=33/a=335218},
volume = {19},
year = {2007}
}
@article{Kresse1993,
abstract = {We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using sub-space lignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations for metals based on the use of a fictitious Newtonian dynamics for the electronic degree of freedom. This method gives perfect control of the adiabaticity and allows us to perform simulations over several picoseconds.},
author = {Kresse, G. and Hafner, J.},
doi = {10.1103/PhysRevB.47.558},
file = {:mnt/work-data/literature/PhysRevB.47.558.pdf:pdf},
isbn = {0163-1829 (Print)$\backslash$n0163-1829 (Linking)},
issn = {0163-1829},
journal = {Physical Review B},
month = {jan},
number = {1},
pages = {558--561},
pmid = {9984901},
publisher = {American Physical Society (APS)},
title = {{Ab initio molecular dynamics for liquid metals}},
url = {http://dx.doi.org/10.1103/PhysRevB.47.558},
volume = {47},
year = {1993}
}
@article{Li2008,
abstract = {We present first principles, density functional theory (DFT) calculations of the structural and electronic properties of thiolate-protected gold nanoparticles [Au(102)(MBA)(44) ] that have been recently crystallized and measured by X-ray diffraction. Our calculations yield structural properties in very good agreement with experiment and reveal the impact of thiolate adsorption on both the surface geometry and the electronic structure of the gold core; in particular, within DFT we observe the emergence of an energy gap of about 0.5 eV, upon MBA adsorption. Using a localized orbital analysis, we characterize the electron distribution in the nanoparticle and provide insight into the bonding of thiolates on curved gold surfaces.},
author = {Li, Yan and Galli, Giulia and Gygi, Fran{\c{c}}ois},
doi = {10.1021/nn800340f},
file = {:mnt/work-data/literature/nn800340f.pdf:pdf},
isbn = {1936-086X (Electronic)$\backslash$r1936-0851 (Linking)},
issn = {19360851},
journal = {ACS Nano},
keywords = {Change transfer,DFT,Electronic structure,Gold cluster,Thiolates},
number = {9},
pages = {1896--1902},
pmid = {19206430},
title = {{Electronic structure of thiolate-covered gold nanoparticles: Au102(MBA)44}},
url = {http://dx.doi.org/10.1021/nn800340f},
volume = {2},
year = {2008}
}
@article{Bozin2015,
abstract = {A long-standing puzzle regarding the disparity of local and long-range CuO6 octahedral tilt correlations in the underdoped regime of La2−xBaxCuO4 is addressed by utilizing complementary neutron powder diffraction and inelastic neutron scattering (INS) approaches.This system is of interest because of the strong depression of the bulk superconducting transition at x = 1/8 in association with charge and spin stripe order. The latter unidirectional order is tied to Cu-O bond-length anisotropy present in the so-called low-temperature tetragonal (LTT) phase. On warming, the lattice exhibits two sequential structural transitions, involving changes in the CuO6 tilt pattern, first to the low-temperature orthorhombic (LTO) and then the high-temperature tetragonal (HTT) phase. Despite the changes in static order, inspection of the instantaneous local atomic structure suggests that the LTT-type tilts persist through the transitions. Analysis of the INS spectra for the x = 1/8 composition reveals the dynamic nature of the LTT-like tilt fluctuations within the LTO and HTT phases. Within the low-temperature phase, the Cu-O bond-length splitting inferred from lattice symmetry and fitted atomic position parameters reaches a maximum of 0.3{\%} at x = 1/8, suggesting that electron-phonon coupling may contribute to optimizing the structure to stabilize stripe order. This splitting is much too small to be resolved in the pair distribution function, and in fact we do not resolve any enhancement of the instantaneous bond-length distribution in association with stripe order. This study exemplifies the importance of a systematic approach using complementary techniques when investigating systems exhibiting a large degree of complexity and subtle structural responses.},
author = {Bozin, Emil S. and Zhong, Ruidan and Knox, Kevin R. and Gu, Genda and Hill, John P. and Tranquada, John M. and Billinge, Simon J. L.},
doi = {10.1103/PhysRevB.91.054521},
file = {:mnt/work-data/literature/PhysRevB.91.054521.pdf:pdf},
issn = {1098-0121},
journal = {Physical Review B},
number = {5},
pages = {1--13},
title = {{Reconciliation of local and long-range tilt correlations in underdoped La2−xBa}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.91.054521},
volume = {91},
year = {2015}
}
@article{Medintz2005,
abstract = {One of the fastest moving and most exciting interfaces of nanotechnology is the use of quantum dots (QDs) in biology. The unique optical properties of QDs make them appealing as in vivo and in vitro fluorophores in a variety of biological investigations, in which traditional fluorescent labels based on organic molecules fall short of providing long-term stability and simultaneous detection of multiple signals. The ability to make QDs water soluble and target them to specific biomolecules has led to promising applications in cellular labelling, deep-tissue imaging, assay labelling and as efficient fluorescence resonance energy transfer donors. Despite recent progress, much work still needs to be done to achieve reproducible and robust surface functionalization and develop flexible bioconjugation techniques. In this review, we look at current methods for preparing QD bioconjugates as well as presenting an overview of applications. The potential of QDs in biology has just begun to be realized and new avenues will arise as our ability to manipulate these materials improves.},
author = {Medintz, Igor L and Uyeda, H Tetsuo and Goldman, Ellen R and Mattoussi, Hedi},
doi = {10.1038/nmat1390},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Medintz et al. - 2005 - Quantum dot bioconjugates for imaging, labelling and sensing.pdf:pdf},
issn = {1476-1122},
journal = {Nature Materials},
keywords = {Analytical,Analytical: methods,Biosensing Techniques,Biosensing Techniques: methods,Chemistry Techniques,Fluorescence,Fluorescence: methods,Microscopy,Molecular Probe Techniques,Quantum Dots,Spectrometry,Staining and Labeling,Staining and Labeling: methods},
month = {jun},
number = {6},
pages = {435--46},
pmid = {15928695},
title = {{Quantum dot bioconjugates for imaging, labelling and sensing.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15928695},
volume = {4},
year = {2005}
}
@article{Marks1994,
abstract = {Data on the experimental structure of small particles is reviewed, the emphasis being an attempt to correlate experimental information with theoretical models. First, a general discussion of some of the controlling factors is presented, primarily equilibrium shapes of small particles, the effect of surface stresses, kinetics, and the role of chemisorption and the substrate. Experimental techniques for obtaining information about small particles are then described, primarily electron microscopy approaches. Experimental data on the static structure of small particles is then reviewed, both single crystals and the many, complicated twinned structures in face-centred cubic materials. An overview is then given of some of the more recent results on dynamic phenomena in small particles. Finally, a general model merging thermodynamic and kinetic factors is presented to attempt to rationalize the available data, followed by a brief discussion.},
author = {Marks, L D},
doi = {10.1088/0034-4885/57/6/002},
file = {:mnt/work-data/literature/0034-4885{\_}57{\_}6{\_}002.pdf:pdf},
isbn = {0034-4885},
issn = {0034-4885},
journal = {Reports on Progress in Physics},
language = {en},
month = {jun},
number = {6},
pages = {603--649},
publisher = {IOP Publishing},
title = {{Experimental studies of small particle structures}},
url = {http://iopscience.iop.org/0034-4885/57/6/002},
volume = {57},
year = {1994}
}
@article{Jeong2002,
abstract = {The mean-square relative displacements (MSRD) of atomic pair motions in crystals are studied as a function of pair distance and temperature using the atomic pair distribution function (PDF). The effects of the lattice vibrations on the PDF peak widths are modelled using both a multi-parameter Born von-Karman (BvK) force model and a single-parameter Debye model. These results are compared to experimentally determined PDFs. We find that the near-neighbor atomic motions are strongly correlated, and that the extent of this correlation depends both on the interatomic interactions and crystal structure. These results suggest that proper account of the lattice vibrational effects on the PDF peak width is important in extracting information on static disorder in a disordered system such as an alloy. Good agreement is obtained between the BvK model calculations of PDF peak widths and the experimentally determined peak widths. The Debye model successfully explains the average, though not detailed, natures of the MSRD of atomic pair motion with just one parameter. Also the temperature dependence of the Debye model largely agrees with the BvK model predictions. Therefore, the Debye model provides a simple description of the effects of lattice vibrations on the PDF peak widths.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0209603},
author = {Jeong, I. -K. and Heffner, R. H. and Graf, M. J. and Billinge, S. J. L.},
doi = {10.1103/PhysRevB.67.104301},
eprint = {0209603},
file = {:mnt/work-data/literature/PhysRevB.67.104301.pdf:pdf},
issn = {0163-1829},
keywords = {ADPs},
mendeley-tags = {ADPs},
pages = {9},
pmid = {16403598},
primaryClass = {cond-mat},
title = {{Lattice dynamics and correlated atomic motion from the atomic pair distribution function}},
url = {http://arxiv.org/abs/cond-mat/0209603},
year = {2002}
}
@article{Guo2013,
abstract = {Advances in chemical syntheses have led to the formation of various kinds of nanoparticles (NPs) with more rational control of size, shape, composition, structure and catalysis. This review highlights recent efforts in the development of Pt and non-Pt based NPs into advanced nanocatalysts for efficient oxygen reduction reaction (ORR) under fuel-cell reaction conditions. It first outlines the shape controlled synthesis of Pt NPs and their shape-dependent ORR. Then it summarizes the studies of alloy and core-shell NPs with controlled electronic (alloying) and strain (geometric) effects for tuning ORR catalysis. It further provides a brief overview of ORR catalytic enhancement with Pt-based NPs supported on graphene and coated with an ionic liquid. The review finally introduces some non-Pt NPs as a new generation of catalysts for ORR. The reported new syntheses with NP parameter-tuning capability should pave the way for future development of highly efficient catalysts for applications in fuel cells, metal-air batteries, and even in other important chemical reactions.},
author = {Guo, Shaojun and Zhang, Sen and Sun, Shouheng},
doi = {10.1002/anie.201207186},
file = {:mnt/work-data/literature/Guo{\_}et{\_}al-2013-Angewandte{\_}Chemie{\_}International{\_}Edition.pdf:pdf},
isbn = {1521-3773 (Electronic)$\backslash$n1433-7851 (Linking)},
issn = {14337851},
journal = {Angewandte Chemie - International Edition},
keywords = {alloys,core-shell nanoparticles,fuel cells,oxygen reduction reaction,platinum},
number = {33},
pages = {8526--8544},
pmid = {23775769},
title = {{Tuning nanoparticle catalysis for the oxygen reduction reaction}},
url = {http://onlinelibrary.wiley.com/doi/10.1002/anie.201207186/abstract},
volume = {52},
year = {2013}
}
@article{Farrow2011,
abstract = {We have systematically studied the optimal real-space sampling of atomic pair distribution (PDF) data by comparing refinement results from oversampled and resampled data. Based on nickel and a complex perovskite system, we show that not only is the optimal sampling bounded by the Nyquist interval described by the Nyquist-Shannon (NS) sampling theorem as expected, but near this sampling interval, the data points in the PDF are minimally correlated, which results in more reliable uncertainty estimates in the modelling. Surprisingly, we find that PDF refinements quickly become unstable for data on coarser grids. Although the Nyquist-Shannon sampling theorem is well known, it has not been applied to PDF refinements, despite the growing popularity of the PDF method and its adoption in a growing number of communities. Here we give explicit expressions for the application of NS sampling theorem to the PDF case, and establish through modeling that it is working in practice, which lays the groundwork for this to become more widely adopted. This has implications for the speed and complexity of possible refinements that can be carried out many times faster than currently with no loss of information, and it establishes a theoretically sound limit on the amount of information contained in the PDF that will prevent over-parametrization during modeling.},
archivePrefix = {arXiv},
arxivId = {1104.0874},
author = {Farrow, Christopher L. and Shaw, Margaret and Kim, Hyunjeong and Juh{\'{a}}s, Pavol and Billinge, Simon J L},
doi = {10.1103/PhysRevB.84.134105},
eprint = {1104.0874},
file = {:mnt/work-data/literature/farroprb12.pdf:pdf},
issn = {10980121},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {13},
pages = {1--7},
title = {{Nyquist-Shannon sampling theorem applied to refinements of the atomic pair distribution function}},
volume = {84},
year = {2011}
}
@article{Peterson2014,
author = {Peterson, Andrew A.},
doi = {10.1007/s11244-013-0161-8},
file = {:mnt/work-data/literature/art{\%}3A10.1007{\%}2Fs11244-013-0161-8.pdf:pdf},
issn = {10225528},
journal = {Topics in Catalysis},
keywords = {Adsorption,Constrained minima hopping,Constrained optimization,Electronic structure theory,Global optimization},
number = {1-4},
pages = {40--53},
title = {{Global optimization of adsorbate-surface structures while preserving molecular identity}},
volume = {57},
year = {2014}
}
@article{Evrard2005,
abstract = {The basic reverse Monte Carlo algorithm, as applied primarily for the study of disordered systems, is introduced, using an example of a new reverse Monte Carlo computer code. RMC++ is a new implementation of the RMC algorithm in C++. Its main purpose is to provide the community with a fast, flexible and documented code for RMC simulations, compatible with the rmca distribution. The source code, the documentation and the executable files are made available through the Internet. The flexibility of the code is exemplified by the implementation of a 'molecular move' step in the Metropolis algorithm. This feature, as well as a performance comparison, is illustrated with simulations performed for molecular liquids such as CCl4 and C2Cl4.},
author = {Evrard, Guillaume and Pusztai, L{\'{a}}szl{\'{o}}},
doi = {10.1088/0953-8984/17/5/001},
file = {:mnt/work-data/literature/0953-8984{\_}17{\_}5{\_}001.pdf:pdf},
issn = {0953-8984},
journal = {Journal of Physics: Condensed Matter},
number = {5},
pages = {S1--S13},
title = {{Reverse Monte Carlo modelling of the structure of disordered materials with RMC++ : a new implementation of the algorithm in C++}},
url = {http://iopscience.iop.org/0953-8984/17/5/001/},
volume = {17},
year = {2005}
}
@article{Kassiba2002,
abstract = {Visible photoluminescence (PL) broad bands are observed in the Raman spectra of SiC nanoparticles (np-SiC) with diameters ranging from 10 to 25 nm. The phenomenon is studied versus the particle size, chemical composition, annealing, and oxidation treatments. In the case of quasistoichiometric np-SiC, excitation by 514-nm radiation gives rise to broad red PL emissions mainly enhanced by the amorphous fraction of the particles and by the surface chemical disorder induced by oxidation. The PL spectra are quantitatively analyzed using numerical methods based on cluster approaches. PL bands are calculated as a function of the cluster geometry and defects (carbon and silicon vacancies), as well as the oxygen location within np-SiC sites. The relevance of this numerical analysis is discussed to account for the main features of the PL broad structure. The PL signature in SiC nanopowders can be used to monitor the physical organization of the np-SiC and to point out their amorphous structure fraction, surface states, and the defect contents.},
author = {Kassiba, A. and Makowska-Janusik, M. and Boucl{\'{e}}, J. and Bardeau, J. and Bulou, A. and Herlin-Boime, N.},
doi = {10.1103/PhysRevB.66.155317},
file = {:mnt/work-data/literature/PhysRevB.66.155317.pdf:pdf},
isbn = {1098-0121},
issn = {0163-1829},
journal = {Physical Review B},
number = {15},
pages = {1--7},
title = {{Photoluminescence features on the Raman spectra of quasistoichiometric SiC nanoparticles: Experimental and numerical simulations}},
volume = {66},
year = {2002}
}
@article{Nield1995,
abstract = {The scattering from crystals has two components, Bragg and diffuse. In the case of disordered crystalline materials, or those at high temperature, the latter contribution is considerable and contains a great deal of information about any static or thermal disorder in the system. However, interpretation of this diffuse scattering is in general difficult. A new and widely applicable technique for modelling single-crystal diffuse scattering has been developed, which is most useful for the study of disordered crystalline materials. The algorithm, based on the reverse Monte Carlo method, is described in detail, and the information that can be obtained using it is discussed with reference to a study on ice Ih.},
author = {Nield, V. M. and Keen, D. A. and McGreevy, R. L.},
doi = {10.1107/S0108767395004399},
issn = {0108-7673},
journal = {Acta Crystallographica Section A Foundations of Crystallography},
language = {en},
month = {sep},
number = {5},
pages = {763--771},
publisher = {International Union of Crystallography},
title = {{The interpretation of single-crystal diffuse scattering using reverse Monte Carlo modelling}},
url = {http://scripts.iucr.org/cgi-bin/paper?ha0137},
volume = {51},
year = {1995}
}
@article{Yusupov2001,
abstract = {We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.},
author = {Yusupov, M M and Yusupova, G Z and Baucom, A and Lieberman, K and Earnest, T N and Cate, J H and Noller, H F},
doi = {10.1126/science.1060089},
file = {:mnt/work-data/literature/Science-2001-Yusupov-883-96.pdf:pdf},
isbn = {0036-8075 (Print)$\backslash$n0036-8075 (Linking)},
issn = {00368075},
journal = {Science (New York, N.Y.)},
number = {5518},
pages = {883--896},
pmid = {11283358},
title = {{Crystal structure of the ribosome at 5.5 A resolution.}},
volume = {292},
year = {2001}
}
@article{PERD1996,
abstract = {Generalized gradient approximations (GGA's) for the exchange-correlation energy improve upon the local spin density (LSD) description of atoms, molecules, and solids. We present a simple derivation of a simple GGA, in which all parameters (other than those in LSD) are fundamental constants. Only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked. Improvements over PW91 include an accurate description of the linear response of the uniform electron gas, correct behavior under uniform scaling, and a smoother potential.},
author = {Perdew, John P. and Burke, Kieron and Ernzerhof, Matthias},
doi = {10.1103/PhysRevLett.77.3865},
file = {:mnt/work-data/literature/PhysRevLett.77.3865.pdf:pdf},
isbn = {9780596529321},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {oct},
number = {18},
pages = {3865--3868},
pmid = {10062328},
publisher = {American Physical Society (APS)},
title = {{Generalized Gradient Approximation Made Simple}},
url = {http://dx.doi.org/10.1103/PhysRevLett.77.3865},
volume = {77},
year = {1996}
}
@article{SHENG2011,
abstract = {Highly optimized embedded-atom-method (EAM) potentials have been developed for 14 face-centered-cubic (fcc) elements across the periodic table. The potentials were developed by fitting the potential-energy surface (PES) of each element derived from high-precision first-principles calculations. The as-derived potential-energy surfaces were shifted and scaled to match experimental reference data. In constructing the PES, a variety of properties of the elements were considered, including lattice dynamics,mechanical properties, thermal behavior, energetics of competing crystal structures, defects, deformation paths, liquid structures, and so forth. For each element, the constructed EAM potentials were tested against the experiment data pertaining to thermal expansion, melting, and liquid dynamics via molecular dynamics computer simulation. The as-developed potentials demonstrate high fidelity and robustness. Owing to their improved accuracy and wide applicability, the potentials are suitable for high-quality atomistic computer simulation of practical applications.},
author = {Sheng, H. W. and Kramer, M. J. and Cadien, A. and Fujita, T. and Chen, M. W.},
doi = {10.1103/PhysRevB.83.134118},
file = {:mnt/work-data/literature/PhysRevB.83.134118.pdf:pdf},
issn = {10980121},
journal = {Physical Review B - Condensed Matter and Materials Physics},
month = {apr},
number = {13},
pages = {134118},
publisher = {American Physical Society},
title = {{Highly optimized embedded-atom-method potentials for fourteen FCC metals}},
url = {http://link.aps.org/doi/10.1103/PhysRevB.83.134118},
volume = {83},
year = {2011}
}
@article{Billinge2007a,
abstract = {Emerging complex functional materials often have atomic order limited to the nanoscale. Examples include nanoparticles, species encapsulated in mesoporous hosts, and bulk crystals with intrinsic nanoscale order. The powerful methods that we have for solving the atomic structure of bulk crystals fail for such materials. Currently, no broadly applicable, quantitative, and robust methods exist to replace crystallography at the nanoscale. We provide an overview of various classes of nanostructured materials and review the methods that are currently used to study their structure. We suggest that successful solutions to these nanostructure problems will involve interactions among researchers from materials science, physics, chemistry, computer science, and applied mathematics, working within a "complex modeling" paradigm that combines theory and experiment in a self-consistent computational framework.},
author = {Billinge, Simon J L and Levin, Igor},
doi = {10.1126/science.1135080},
file = {:home/christopher/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Billinge, Levin - 2007 - The problem with determining atomic structure at the nanoscale.pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
month = {apr},
number = {5824},
pages = {561--565},
pmid = {17463280},
title = {{The problem with determining atomic structure at the nanoscale.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17463280},
volume = {316},
year = {2007}
}
@article{Frenkel2007,
abstract = {We discuss methods of Extended X-ray Ab- sorption Fine-Structure (EXAFS) analysis that provide three-dimensional structural characterization of metal na- noparticles, both mono- and bi-metallic. For the bimetallic alloys, we use short range order measurements to discri- minate between random and non-random inter-particle dis- tributions of atoms. We also discuss the application of EXAFS to heterogeneous nanoparticle systems.},
author = {Frenkel, Anatoly},
doi = {10.1524/zkri.2007.222.11.605},
file = {:mnt/work-data/literature/zkri.2007.222.11.605.pdf:pdf},
issn = {0044-2968},
journal = {Zeitschrift f{\"{u}}r Kristallographie},
number = {11},
pages = {605--611},
title = {{Solving the 3D structure of metal nanoparticles}},
url = {http://www.degruyter.com/view/j/zkri.2007.222.issue-11/zkri.2007.222.11.605/zkri.2007.222.11.605.xml},
volume = {222},
year = {2007}
}
@article{Arnold2013,
abstract = {The exceptional upconverting properties of lanthanide-doped nanoparticles make them attractive systems with applications ranging from photovoltaics to biological labeling, imaging, and therapeutics. While they draw considerable interest, structural data, which are necessary to understand the upconversion process, remain scarce. In this work, we demonstrate the use of 23Na, 19F, and 89Y solid-state NMR together with DFT calculations to characterize the structure of cubic NaYF4 nanoparticles with and without Er3+ doping. By measuring 23Na MAS NMR spectra at various magnetic fields and 3QMAS spectra at ultrahigh field, we show that the spectra are characteristic of a solid solution in which cation sites are statistically occupied by Na+ or Y3+ ions. The 23Na NMR spectra are broadened as a result of isotropic chemical shift distribution, whereas the extracted quadrupolar products appear to be small (≤1.8 MHz), which is in good agreement with DFT calculations using CASTEP. The chemical shift distribution in 19F NMR spectra is well-predicted by CASTEP calculations and shown to strongly depend on coordination by Y3+. Finally, the 89Y NMR spectra consist of a single broad pattern, which also results from a chemical shift distribution that can be correlated to the coordination environment of the Y3+ cations. Our results show that the structure is a slightly distorted cubic phase and lanthanide doping has only a minor effect on the lattice parameters. The approach appears to be promising for gaining additional insight into the atomic level structure details to better understand properties that govern the upconversion process and its efficiency.},
author = {Arnold, Alexandre A. and Terskikh, Victor and Li, Qian Ying and Naccache, Rafik and Marcotte, Isabelle and Capobianco, John A.},
doi = {10.1021/jp405813a},
file = {:mnt/work-data/literature/jp405813a.pdf:pdf},
isbn = {1932-7447},
issn = {19327447},
journal = {Journal of Physical Chemistry C},
number = {48},
pages = {25733--25741},
title = {{Structure of NaYF4 upconverting nanoparticles: A multinuclear solid-state NMR and DFT computational study}},
url = {http://pubs.acs.org/doi/abs/10.1021/jp405813a},
volume = {117},
year = {2013}
}
@article{Gilbert2004,
abstract = {Nanoparticles may contain unusual forms of structural disorder that can substantially modify materials properties and thus cannot solely be considered as small pieces of bulk material. We have developed a method to quantify intermediate-range order in 3.4-nanometer-diameter zinc sulfide nanoparticles and show that structural coherence is lost over distances beyond 2 nanometers. The zinc-sulfur Einstein vibration frequency in the nanoparticles is substantially higher than that in the bulk zinc sulfide, implying structural stiffening. This cannot be explained by the observed 1{\%} radial compression and must be primarily due to inhomogeneous internal strain caused by competing relaxations from an irregular surface. The methods developed here are generally applicable to the characterization of nanoscale solids, many of which may exhibit complex disorder and strain.},
author = {Gilbert, Benjamin and Huang, Feng and Zhang, Hengzhong and Waychunas, Glenn A. and Banfield, Jillian F},
doi = {10.1126/science.1098454},
file = {:mnt/work-data/literature/Science-2004-Gilbert-651-4.pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
number = {5684},
pages = {651--654},
pmid = {15232073},
title = {{Nanoparticles: strained and stiff.}},
url = {http://www.sciencemag.org/content/305/5684/651},
volume = {305},
year = {2004}
}
@book{Pecharsky2009,
author = {Pecharsky, Vitalij and Zavalij, Peter},
publisher = {Springer Science},
title = {{Fundamentals of Powder Diffraction and Structural Characterization of Materials}},
year = {2009}
}
@article{Petkov2013,