1-20 of 128
Coarse-grained simulations
Close
Save search
Follow your search
Access your saved searches in your account
Close Modal
Sort by
Journal Articles

Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution

Available to Purchase
Sweta Pradhan, Mithun Biswas
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 225101 (2025)
https://doi.org/10.1063/5.0260968
Published: June 2025
View articletitled, Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution
Open the PDF for Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution in another window
Journal Articles

Modeling the impact of drug-nanocarriers in lipid membranes

Available to Purchase
Germán Pérez-Sánchez, João A. P. Coutinho, Manuel Melle-Franco
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 214901 (2025)
https://doi.org/10.1063/5.0259927
Published: June 2025
View articletitled, Modeling the impact of drug-nanocarriers in lipid membranes
Open the PDF for Modeling the impact of drug-nanocarriers in lipid membranes in another window
Journal Articles

Application of Nosé–Hoover dynamics for coarse-graining molecular systems: An evaluation of reproducibility in Lennard-Jones systems

Available to Purchase
Toru Yamada, Yohei Morinishi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 134107 (2025)
https://doi.org/10.1063/5.0254868
Published: April 2025
View articletitled, Application of Nosé–Hoover dynamics for coarse-graining molecular systems: An evaluation of reproducibility in Lennard-Jones systems
Open the PDF for Application of Nosé–Hoover dynamics for coarse-graining molecular systems: An evaluation of reproducibility in Lennard-Jones systems in another window
Journal Articles

Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems

Available to Purchase
Jaehyeok Jin, Gregory A. Voth
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 124114 (2025)
https://doi.org/10.1063/5.0254388
Published: March 2025
View articletitled, Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems
Open the PDF for Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems in another window
Journal Articles

Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis

Available to Purchase
Abhik Ghosh Moulick, Rutika Patel, Augustine Onyema, Sharon M. Loverde
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 065101 (2025)
https://doi.org/10.1063/5.0246977
Published: February 2025
View articletitled, Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis
Open the PDF for Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis in another window
Journal Articles

Compaction and clustering of a heterogeneous polymer by biomolecular crowding

Available to Purchase
Amir Sadeghi, Changbong Hyeon, Youngkyun Jung, Bae-Yeun Ha
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 184904 (2024)
https://doi.org/10.1063/5.0226892
Published: November 2024
View articletitled, Compaction and clustering of a heterogeneous polymer by biomolecular crowding
Open the PDF for Compaction and clustering of a heterogeneous polymer by biomolecular crowding in another window
Journal Articles

Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation

Available to Purchase
Marco Oestereich, Jürgen Gauss, Gregor Diezemann
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 154903 (2024)
https://doi.org/10.1063/5.0228198
Published: October 2024
View articletitled, Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation
Open the PDF for Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation in another window
Journal Articles

Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins

FeaturedOpen Access
Guoqing Zhang, Xiakun Chu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 095102 (2024)
https://doi.org/10.1063/5.0220861
Published: September 2024
View articletitled, Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins
Open the PDF for Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins in another window
Journal Articles

Modeling temperature-dependent transport properties in dissipative particle dynamics: A top-down coarse-graining toward realistic dynamics at the mesoscale

Available to Purchase
N. Lauriello, M. Lísal, G. Boccardo, D. Marchisio, A. Buffo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 034112 (2024)
https://doi.org/10.1063/5.0207530
Published: July 2024
View articletitled, Modeling temperature-dependent transport properties in dissipative particle dynamics: A top-down coarse-graining toward realistic dynamics at the mesoscale
Open the PDF for Modeling temperature-dependent transport properties in dissipative particle dynamics: A top-down coarse-graining toward realistic dynamics at the mesoscale in another window
Journal Articles

Intermediate scattering function for polymer molecules: An approach based on relaxation mode analysis

Available to Purchase
Naoyuki Karasawa, Ayori Mitsutake, Hiroshi Takano
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 024902 (2024)
https://doi.org/10.1063/5.0211504
Published: July 2024
View articletitled, Intermediate scattering function for polymer molecules: An approach based on relaxation mode analysis
Open the PDF for Intermediate scattering function for polymer molecules: An approach based on relaxation mode analysis in another window
Journal Articles

Modeling microgel swelling: Influence of chain finite extensibility

Available to Purchase
Mariano E. Brito, Christian Holm
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 204901 (2024)
https://doi.org/10.1063/5.0205608
Published: May 2024
View articletitled, Modeling microgel swelling: Influence of chain finite extensibility
Open the PDF for Modeling microgel swelling: Influence of chain finite extensibility in another window
Journal Articles

Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations

Available to Purchase
Diego Becerra, Alexander R. Klotz, Lisa M. Hall
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 114906 (2024)
https://doi.org/10.1063/5.0191295
Published: March 2024
View articletitled, Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations
Open the PDF for Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations in another window
Includes: Supplementary data
Journal Articles

Effect of ion distribution on stress relaxation in polyelectrolyte complex gels

Available to Purchase
Alexey A. Gavrilov, Elena Yu. Kramarenko
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 114901 (2024)
https://doi.org/10.1063/5.0198332
Published: March 2024
View articletitled, Effect of ion distribution on stress relaxation in polyelectrolyte complex gels
Open the PDF for Effect of ion distribution on stress relaxation in polyelectrolyte complex gels in another window
Includes: Supplementary data
Journal Articles

Tracer dynamics in polymer networks: Generalized Langevin description

FeaturedOpen Access
Sebastian Milster, Fabian Koch, Christoph Widder, Tanja Schilling, Joachim Dzubiella
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 094901 (2024)
https://doi.org/10.1063/5.0189166
Published: March 2024
View articletitled, Tracer dynamics in polymer networks: Generalized Langevin description
Open the PDF for Tracer dynamics in polymer networks: Generalized Langevin description in another window
Journal Articles

Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins

Available to Purchase
Jiachen Wei, Yue Xue, Yawei Liu, Hao Tian, Yingfeng Shao, Yi Qin Gao
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 054904 (2024)
https://doi.org/10.1063/5.0189692
Published: February 2024
View articletitled, Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins
Open the PDF for Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins in another window
Includes: Supplementary data
Journal Articles

Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model

Available to Purchase
Zhongyan Zhang (张中岩), Wenbo Zhao (赵文博), Zhiyuan Cheng (程志远), Guojie Zhang (张国杰), Hong Liu (刘鸿)
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 054906 (2024)
https://doi.org/10.1063/5.0190580
Published: February 2024
View articletitled, Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model
Open the PDF for Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model in another window
Journal Articles

Effect of amphiphilic polymers on phase separating binary mixtures: A DPD simulation study

Available to Purchase
Avinash Chauhan, Dorothy Gogoi, Sanjay Puri, Awaneesh Singh
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 204901 (2023)
https://doi.org/10.1063/5.0173817
Published: November 2023
View articletitled, Effect of amphiphilic polymers on phase separating binary mixtures: A DPD simulation study
Open the PDF for Effect of amphiphilic polymers on phase separating binary mixtures: A DPD simulation study in another window
Journal Articles

Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures

Available to Purchase
Shivam Gupta, Jatin Soni, Awneesh Kumar, Taraknath Mandal
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 165102 (2023)
https://doi.org/10.1063/5.0167144
Published: October 2023
View articletitled, Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures
Open the PDF for Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures in another window
Includes: Supplementary data
Journal Articles

Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents

Available to Purchase
Cameron J. Shock, Mark J. Stevens, Amalie L. Frischknecht, Issei Nakamura
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 134507 (2023)
https://doi.org/10.1063/5.0165481
Published: October 2023
View articletitled, Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents
Open the PDF for Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents in another window
Journal Articles

Dynamic coarse-graining of linear and non-linear systems: Mori–Zwanzig formalism and beyond

Available to Purchase
Bernd Jung, Gerhard Jung
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 084110 (2023)
https://doi.org/10.1063/5.0165541
Published: August 2023
View articletitled, Dynamic coarse-graining of linear and non-linear systems: Mori–Zwanzig formalism and beyond
Open the PDF for Dynamic coarse-graining of linear and non-linear systems: Mori–Zwanzig formalism and beyond in another window