diff --git a/docs/source/main.bib b/docs/source/main.bib index 3d015eb1..c2e3a46b 100644 --- a/docs/source/main.bib +++ b/docs/source/main.bib @@ -2,93 +2,93 @@ @book{treloar1949physics title={The Physics of Rubber Elasticity}, author={Treloar, Leslie Ronald George}, year={1949}, - location = {Cambridge, UK}, + location={Cambridge, UK}, publisher={Clarendon Press}, - url = {https://global.oup.com/academic/product/the-physics-of-rubber-elasticity-9780198570271} + url={https://global.oup.com/academic/product/the-physics-of-rubber-elasticity-9780198570271} } @book{rubinstein2003polymer, title={Polymer Physics}, author={Rubinstein, Michael and Colby, Ralph H}, year={2003}, - location = {New York}, + location={New York}, publisher={Oxford University Press}, - url = {https://global.oup.com/academic/product/polymer-physics-9780198520597} + url={https://global.oup.com/academic/product/polymer-physics-9780198520597} } @book{mcq, title={Statistical Mechanics}, author={McQuarrie, Donald A.}, year={2000}, - location = {Mill Valley, CA}, + location={Mill Valley, CA}, publisher={University Science Books}, - url = {https://uscibooks.aip.org/books/statistical-mechanics/} + url={https://uscibooks.aip.org/books/statistical-mechanics/} } @book{zwanzig2001nonequilibrium, title={Nonequilibrium Statistical Mechanics}, author={Zwanzig, Robert}, year={2001}, - location = {New York}, + location={New York}, publisher={Oxford University Press}, - url = {https://global.oup.com/academic/product/nonequilibrium-statistical-mechanics-9780195140187} + url={https://global.oup.com/academic/product/nonequilibrium-statistical-mechanics-9780195140187} } @book{bender2013advanced, title={Advanced Mathematical Methods for Scientists and Engineers I: Asymptotic Methods and Perturbation Theory}, author={Bender, Carl M and Orszag, Steven A}, year={2013}, - location = {New York}, + location={New York}, publisher={Springer Science \& Business Media}, - doi = {10.1007/978-1-4757-3069-2} + doi={10.1007/978-1-4757-3069-2} } @book{bleistein1975asymptotic, title={Asymptotic Expansions of Integrals}, author={Bleistein, Norman and Handelsman, Richard A}, year={1975}, - location = {New York}, + location={New York}, publisher={Ardent Media}, url={https://store.doverpublications.com/0486650820.html} } @article{buche2022freely, - title = {Freely jointed chain models with extensible links}, - author = {Buche, Michael R. and Silberstein, Meredith N. and Grutzik, Scott J.}, - journal = {Physical Review E}, - shortjournal = {Phys. Rev. E}, - volume = {106}, - pages = {024502}, - number = {024502}, - numpages = {10}, - year = {2022}, - publisher = {American Physical Society}, - doi = {10.1103/PhysRevE.106.024502}, + title={Freely jointed chain models with extensible links}, + author={Buche, Michael R. and Silberstein, Meredith N. and Grutzik, Scott J.}, + journal={Physical Review E}, + shortjournal={Phys. Rev. E}, + volume={106}, + pages={024502}, + number={024502}, + numpages={10}, + year={2022}, + publisher={American Physical Society}, + doi={10.1103/PhysRevE.106.024502}, } @article{buche2020statistical, - title = {Statistical mechanical constitutive theory of polymer networks: The inextricable links between distribution, behavior, and ensemble}, - author = {Buche, Michael R. and Silberstein, Meredith N.}, - journal = {Physical Review E}, - shortjournal = {Phys. Rev. E}, - volume = {102}, - pages = {012501}, - number = {012501}, - numpages = {14}, - year = {2020}, - publisher = {American Physical Society}, - doi = {10.1103/PhysRevE.102.012501}, + title={Statistical mechanical constitutive theory of polymer networks: The inextricable links between distribution, behavior, and ensemble}, + author={Buche, Michael R. and Silberstein, Meredith N.}, + journal={Physical Review E}, + shortjournal={Phys. Rev. E}, + volume={102}, + pages={012501}, + number={012501}, + numpages={14}, + year={2020}, + publisher={American Physical Society}, + doi={10.1103/PhysRevE.102.012501}, } @article{buche2021chain, - title = {Chain breaking in the statistical mechanical constitutive theory of polymer networks}, - journal = {Journal of the Mechanics and Physics of Solids}, - volume = {156}, - pages = {104593}, - year = {2021}, - issn = {0022-5096}, - doi = {10.1016/j.jmps.2021.104593}, - author = {Michael R. Buche and Meredith N. Silberstein}, + title={Chain breaking in the statistical mechanical constitutive theory of polymer networks}, + journal={Journal of the Mechanics and Physics of Solids}, + volume={156}, + pages={104593}, + year={2021}, + issn={0022-5096}, + doi={10.1016/j.jmps.2021.104593}, + author={Michael R. Buche and Meredith N. Silberstein}, } @phdthesis{buche2021fundamental, @@ -115,27 +115,38 @@ @article{fiasconaro2019analytical title={Analytical results of the extensible freely jointed chain model}, author={Fiasconaro, Alessandro and Falo, Fernando}, journal={Physica A: Statistical Mechanics and its Applications}, - shortjournal = {Physica A}, + shortjournal={Physica A}, volume={532}, pages={121929}, year={2019}, publisher={Elsevier}, - doi = {10.1016/j.physa.2019.121929} + doi={10.1016/j.physa.2019.121929} } @article{radiom2017influence, - title = {Influence of ligand-receptor interactions on force-extension behavior within the freely jointed chain model}, - author = {Radiom, Milad and Borkovec, Michal}, - journal = {Physical Review E}, - shortjournal = {Phys. Rev. E}, - volume = {96}, - issue = {6}, - pages = {062501}, - numpages = {7}, - year = {2017}, - month = {Dec}, - publisher = {American Physical Society}, - doi = {10.1103/PhysRevE.96.062501} + title={Influence of ligand-receptor interactions on force-extension behavior within the freely jointed chain model}, + author={Radiom, Milad and Borkovec, Michal}, + journal={Physical Review E}, + shortjournal={Phys. Rev. E}, + volume={96}, + issue={6}, + pages={062501}, + numpages={7}, + year={2017}, + month={Dec}, + publisher={American Physical Society}, + doi={10.1103/PhysRevE.96.062501} +} + +@article{becker2010radial, + title={The radial distribution function of worm-like chains}, + author={Becker, NB and Rosa, A and Everaers, R}, + journal={The European Physical Journal E}, + volume={32}, + pages={53--69}, + year={2010}, + publisher={Springer}, + doi={10.1140/epje/i2010-10596-0} } @article{morse1929diatomic, @@ -148,7 +159,7 @@ @article{morse1929diatomic pages={57}, year={1929}, publisher={APS}, - doi = {10.1103/PhysRev.34.57} + doi={10.1103/PhysRev.34.57} } @article{jones1924determinationii, diff --git a/docs/source/physics/single_chain/wlc.rst b/docs/source/physics/single_chain/wlc.rst index c88a8e0b..25ab4543 100644 --- a/docs/source/physics/single_chain/wlc.rst +++ b/docs/source/physics/single_chain/wlc.rst @@ -6,7 +6,7 @@ WLC model Thermodynamics -.. autoclass:: polymers.physics.single_chain.fjc::WLC(number_of_links, link_length, hinge_mass, persistance_length) +.. autoclass:: polymers.physics.single_chain.wlc::WLC(number_of_links, link_length, hinge_mass, persistance_length) .. autoattribute:: number_of_links .. autoattribute:: link_length diff --git a/docs/source/physics/single_chain/wlc/thermodynamics.rst b/docs/source/physics/single_chain/wlc/thermodynamics.rst index e320d1c3..d72ff076 100644 --- a/docs/source/physics/single_chain/wlc/thermodynamics.rst +++ b/docs/source/physics/single_chain/wlc/thermodynamics.rst @@ -5,7 +5,7 @@ WLC model thermodynamics :maxdepth: 1 Isometric - Isometric + Isotensional .. autoclass:: polymers.physics.single_chain.wlc.thermodynamics::WLC(number_of_links, link_length, hinge_mass, persistance_length) diff --git a/docs/source/physics/single_chain/wlc/thermodynamics/isotensional.rst b/docs/source/physics/single_chain/wlc/thermodynamics/isotensional.rst index c38a6710..49b4f114 100644 --- a/docs/source/physics/single_chain/wlc/thermodynamics/isotensional.rst +++ b/docs/source/physics/single_chain/wlc/thermodynamics/isotensional.rst @@ -25,10 +25,3 @@ WLC model thermodynamics (isotensional) .. automethod:: nondimensional_gibbs_free_energy_per_link(nondimensional_force, temperature) .. automethod:: nondimensional_relative_gibbs_free_energy(nondimensional_force) .. automethod:: nondimensional_relative_gibbs_free_energy_per_link(nondimensional_force) - -.. raw:: - html - -
- -.. footbibliography:: diff --git a/src/physics/single_chain/wlc/thermodynamics/isometric/mod.jl b/src/physics/single_chain/wlc/thermodynamics/isometric/mod.jl index c720376d..fbdeef0b 100644 --- a/src/physics/single_chain/wlc/thermodynamics/isometric/mod.jl +++ b/src/physics/single_chain/wlc/thermodynamics/isometric/mod.jl @@ -601,9 +601,11 @@ The equilibrium probability density of end-to-end lengths ``g_\\mathrm{eq}`` as parameterized by the number of links ``N_b``, link length ``\\ell_b``, and persistance length ``\\ell_p``, ```math -g_\\mathrm{eq}(\\xi) = 4\\pi\\xi^2 P_\\mathrm{eq}(\\xi). +g_\\mathrm{eq}(\\xi) = 4\\pi\\xi^2 P_\\mathrm{eq}(\\xi), ``` +which is calculated using the accurate analytic approximation provided by [Becker, Rosa, and Everaers](https://doi.org/10.1140/epje/i2010-10596-0). + $(TYPEDSIGNATURES) """ function equilibrium_radial_distribution( diff --git a/src/physics/single_chain/wlc/thermodynamics/isometric/py.rs b/src/physics/single_chain/wlc/thermodynamics/isometric/py.rs index 27823e29..db37fc6c 100644 --- a/src/physics/single_chain/wlc/thermodynamics/isometric/py.rs +++ b/src/physics/single_chain/wlc/thermodynamics/isometric/py.rs @@ -240,10 +240,12 @@ impl WLC { nondimensional_end_to_end_length_per_link.as_array().mapv(|nondimensional_end_to_end_length_per_link: f64| super::nondimensional_equilibrium_distribution(&self.nondimensional_persistance_length, &self.normalization_nondimensional_equilibrium_distribution, &nondimensional_end_to_end_length_per_link)).into_pyarray(py) } - /// The equilibrium probability density of end-to-end lengths as a function of the end-to-end length, given by :footcite:t:`treloar1949physics` as + /// The equilibrium probability density of end-to-end lengths as a function of the end-to-end length, /// /// .. math:: - /// g_\mathrm{eq}(\xi) = 4\pi\xi^2 P_\mathrm{eq}(\xi). + /// g_\mathrm{eq}(\xi) = 4\pi\xi^2 P_\mathrm{eq}(\xi), + /// + /// which is calculated using the accurate analytic approximation provided by :footcite:t:`becker2010radial`. /// /// Args: /// end_to_end_length (numpy.ndarray): The end-to-end length :math:`\xi`.