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Journal Articles

Scaling properties of RNA as a randomly branching polymer

Domen Vaupotič, Angelo Rosa, Luca Tubiana, Anže Božič
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 234901 (2023)
https://doi.org/10.1063/5.0152604
Published: June 2023
View article titled, Scaling properties of RNA as a randomly branching polymer
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Includes: Supplementary data
Journal Articles

An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators

Simone Bonfrate, Nicolas Ferré, Miquel Huix-Rotllant
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 021101 (2023)
https://doi.org/10.1063/5.0133646
Published: January 2023
View article titled, An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators
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Includes: Supplementary data
Journal Articles

Explicit models of motions to analyze NMR relaxation data in proteins

Nicolas Bolik-Coulon, Fabien Ferrage
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 125102 (2022)
https://doi.org/10.1063/5.0095910
Published: September 2022
View article titled, Explicit models of motions to analyze NMR relaxation data in proteins
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Includes: Supplementary data
Journal Articles

Empty liquid state and re-entrant phase behavior of the patchy colloids confined in porous media

Editor’s Pick
T. V. Hvozd, Yu. V. Kalyuzhnyi, V. Vlachy, P. T. Cummings
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 161102 (2022)
https://doi.org/10.1063/5.0088716
Published: April 2022
View article titled, Empty liquid state and re-entrant phase behavior of the patchy colloids confined in porous media
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Includes: Supplementary data
Journal Articles

Ultra-coarse-graining modeling of liquid water

Min Li, WenCai Lu, John ZengHui Zhang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 224506 (2021)
https://doi.org/10.1063/5.0055453
Published: June 2021
View article titled, Ultra-coarse-graining modeling of liquid water
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Includes: Supplementary data
Journal Articles

Dynamics of rare gas solids irradiated by electron beams

J. Candanedo, C. Caleman, N. Tîmneanu, O. Beckstein, J. C. H. Spence
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 144303 (2020)
https://doi.org/10.1063/1.5134801
Published: April 2020
View article titled, Dynamics of rare gas solids irradiated by electron beams
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Includes: Supplementary data
Journal Articles

TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules

Lizhe Zhu, Fu Kit Sheong, Siqin Cao, Song Liu, Ilona C. Unarta, Xuhui Huang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 124105 (2019)
https://doi.org/10.1063/1.5082633
Published: March 2019
View article titled, TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules
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Includes: Supplementary data
Journal Articles

An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling

Wei Wang, Tong Liang, Fu Kit Sheong, Xiaodan Fan, Xuhui Huang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 072337 (2018)
https://doi.org/10.1063/1.5027001
Published: August 2018
View article titled, An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling
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Includes: Supplementary data
Journal Articles

Representations in neural network based empirical potentials

Ekin D. Cubuk, Brad D. Malone, Berk Onat, Amos Waterland, Efthimios Kaxiras
Journal: The Journal of Chemical Physics
J. Chem. Phys. 147, 024104 (2017)
https://doi.org/10.1063/1.4990503
Published: July 2017
View article titled, Representations in neural network based empirical potentials
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Includes: Supplementary data
Journal Articles

Non-exponential kinetics of unfolding under a constant force

Samuel Bell, Eugene M. Terentjev
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 185102 (2016)
https://doi.org/10.1063/1.4966922
Published: November 2016
View article titled, Non-exponential kinetics of unfolding under a constant force
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Journal Articles

Dynamics of semiflexible scale-free polymer networks

Mircea Galiceanu, Adriane S. Reis, Maxim Dolgushev
Journal: The Journal of Chemical Physics
J. Chem. Phys. 141, 144902 (2014)
https://doi.org/10.1063/1.4897563
Published: October 2014
View article titled, Dynamics of semiflexible scale-free polymer networks
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Journal Articles

Accelerated weight histogram method for exploring free energy landscapes

V. Lindahl, J. Lidmar, B. Hess
Journal: The Journal of Chemical Physics
J. Chem. Phys. 141, 044110 (2014)
https://doi.org/10.1063/1.4890371
Published: July 2014
View article titled, Accelerated weight histogram method for exploring free energy landscapes
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Journal Articles

Gaussian semiflexible rings under angular and dihedral restrictions

Maxim Dolgushev, Thomas Guérin, Alexander Blumen, Olivier Bénichou, Raphaël Voituriez
Journal: The Journal of Chemical Physics
J. Chem. Phys. 141, 014901 (2014)
https://doi.org/10.1063/1.4885445
Published: July 2014
View article titled, Gaussian semiflexible rings under angular and dihedral restrictions
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Includes: Supplementary data
Journal Articles

Analyzing milestoning networks for molecular kinetics: Definitions, algorithms, and examples

Shruthi Viswanath, Steven M. Kreuzer, Alfredo E. Cardenas, Ron Elber
Journal: The Journal of Chemical Physics
J. Chem. Phys. 139, 174105 (2013)
https://doi.org/10.1063/1.4827495
Published: November 2013
View article titled, Analyzing milestoning networks for molecular kinetics: Definitions, algorithms, and examples
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Journal Articles

Mathematical methods for restricted domain ternary liquid mixture free energy determination using light scattering

Chris W. Wahle, David S. Ross, George M. Thurston
Journal: The Journal of Chemical Physics
J. Chem. Phys. 139, 124114 (2013)
https://doi.org/10.1063/1.4822004
Published: September 2013
View article titled, Mathematical methods for restricted domain ternary liquid mixture free energy determination using light scattering
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Journal Articles

A boundary correction algorithm for metadynamics in multiple dimensions

Michael McGovern, Juan de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 139, 084102 (2013)
https://doi.org/10.1063/1.4818153
Published: August 2013
View article titled, A boundary correction algorithm for metadynamics in multiple dimensions
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Includes: Supplementary data
Journal Articles

Multiscale modeling with smoothed dissipative particle dynamics

Pandurang M. Kulkarni, Chia-Chun Fu, M. Scott Shell, L. Gary Leal
Journal: The Journal of Chemical Physics
J. Chem. Phys. 138, 234105 (2013)
https://doi.org/10.1063/1.4810754
Published: June 2013
View article titled, Multiscale modeling with smoothed dissipative particle dynamics
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Journal Articles

Dynamics of discrete semiflexible chains under dihedral constraints: Analytic results

Maxim Dolgushev, Alexander Blumen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 138, 204902 (2013)
https://doi.org/10.1063/1.4807058
Published: May 2013
View article titled, Dynamics of discrete semiflexible chains under dihedral constraints: Analytic results
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Includes: Supplementary data
Journal Articles

Comparison of Brownian dynamics algorithms with hydrodynamic interaction

Ricardo Rodríguez Schmidt, José G. Hernández Cifre, José García de la Torre
Journal: The Journal of Chemical Physics
J. Chem. Phys. 135, 084116 (2011)
https://doi.org/10.1063/1.3626868
Published: August 2011
View article titled, Comparison of Brownian dynamics algorithms with hydrodynamic interaction
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Journal Articles

Langevin dynamics for the transport of flexible biological macromolecules in confined geometries

Michael H. Peters
Journal: The Journal of Chemical Physics
J. Chem. Phys. 134, 025105 (2011)
https://doi.org/10.1063/1.3525381
Published: January 2011
View article titled, Langevin dynamics for the transport of flexible biological macromolecules in confined geometries
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