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Journal Articles

Analysis of mapping atomic models to coarse-grained resolution

Katherine M. Kidder, W. G. Noid
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 134113 (2024)
https://doi.org/10.1063/5.0220989
Published: October 2024
View article titled, Analysis of mapping atomic models to coarse-grained resolution
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Journal Articles

In silico study of DNA mononucleotide self-assembly

Mattia Trapella, Tommaso Bellini, Cristiano De Michele
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 134905 (2024)
https://doi.org/10.1063/5.0226019
Published: October 2024
View article titled, <em>In silico</em> study of DNA mononucleotide self-assembly
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Journal Articles

Domain growth kinetics in active binary mixtures

Sayantan Mondal, Prasenjit Das
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 134902 (2024)
https://doi.org/10.1063/5.0217795
Published: October 2024
View article titled, Domain growth kinetics in active binary mixtures
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Journal Articles

Enhancing (quasi-)long-range order in a two-dimensional driven crystal

R. Maire, A. Plati
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 054902 (2024)
https://doi.org/10.1063/5.0217958
Published: August 2024
View article titled, Enhancing (quasi-)long-range order in a two-dimensional driven crystal
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Journal Articles

Understanding dynamics in coarse-grained models. IV. Connection of fine-grained and coarse-grained dynamics with the Stokes–Einstein and Stokes–Einstein–Debye relations

Jaehyeok Jin, Gregory A. Voth
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 034114 (2024)
https://doi.org/10.1063/5.0212973
Published: July 2024
View article titled, Understanding dynamics in coarse-grained models. IV. Connection of fine-grained and coarse-grained dynamics with the Stokes–Einstein and Stokes–Einstein–Debye relations
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Journal Articles

pyMBE: The Python-based molecule builder for ESPResSo

David Beyer, Paola B. Torres, Sebastian P. Pineda, Claudio F. Narambuena, Jean-Noël Grad, Peter Košovan, Pablo M. Blanco
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 022502 (2024)
https://doi.org/10.1063/5.0216389
Published: July 2024
View article titled, pyMBE: The Python-based molecule builder for ESPResSo
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Journal Articles

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

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 article titled, Intermediate scattering function for polymer molecules: An approach based on relaxation mode analysis
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Journal Articles

Stability and deformation of biomolecular condensates under the action of shear flow

Luis E. Coronas, Thong Van, Antonio Iorio, Lisa J. Lapidus, Michael Feig, Fabio Sterpone
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 215101 (2024)
https://doi.org/10.1063/5.0209119
Published: June 2024
View article titled, Stability and deformation of biomolecular condensates under the action of shear flow
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Journal Articles

ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems

F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 205102 (2024)
https://doi.org/10.1063/5.0202829
Published: May 2024
View article titled, ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems
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Journal Articles

A Gauss–Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations

Viktor Klippenstein, Niklas Wolf, Nico F. A. van der Vegt
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 204115 (2024)
https://doi.org/10.1063/5.0203832
Published: May 2024
View article titled, A Gauss–Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations
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Journal Articles

Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA+

Editor’s Pick
Wout Laeremans, Midas Segers, Aderik Voorspoels, Enrico Carlon, Jef Hooyberghs
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 144105 (2024)
https://doi.org/10.1063/5.0197053
Published: April 2024
View article titled, Insights into elastic properties of coarse-grained DNA models: <em>q</em>-stiffness of cgDNA vs cgDNA+
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Journal Articles

Molecular modeling of the carbohydrate corona formation on a polyvinyl chloride nanoparticle and its impact on the adhesion to lipid bilayers

Daniel G. Angelescu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 144901 (2024)
https://doi.org/10.1063/5.0198254
Published: April 2024
View article titled, Molecular modeling of the carbohydrate corona formation on a polyvinyl chloride nanoparticle and its impact on the adhesion to lipid bilayers
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Includes: Supplementary data
Journal Articles

Interfacial exchange dynamics of biomolecular condensates are highly sensitive to client interactions

Ushnish Rana, Ned S. Wingreen, Clifford P. Brangwynne, Athanassios Z. Panagiotopoulos
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 145102 (2024)
https://doi.org/10.1063/5.0188461
Published: April 2024
View article titled, Interfacial exchange dynamics of biomolecular condensates are highly sensitive to client interactions
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Includes: Supplementary data
Journal Articles

Stochastic kinetic theory applied to coarse-grained polymer model

Shangren Zhu, Patrick T. Underhill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 114903 (2024)
https://doi.org/10.1063/5.0186783
Published: March 2024
View article titled, Stochastic kinetic theory applied to coarse-grained polymer model
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Journal Articles

Diffusive dynamics of a model protein chain in solution

Margarita Colberg, Jeremy Schofield
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 075101 (2024)
https://doi.org/10.1063/5.0182607
Published: February 2024
View article titled, Diffusive dynamics of a model protein chain in solution
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Journal Articles

Asymmetric membrane “sticky tape” enables simultaneous relaxation of area and curvature in simulation

Samuel L. Foley, Markus Deserno
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 064111 (2024)
https://doi.org/10.1063/5.0189771
Published: February 2024
View article titled, Asymmetric membrane “sticky tape” enables simultaneous relaxation of area and curvature in simulation
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Includes: Supplementary data
Journal Articles

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

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 article titled, Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins
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Includes: Supplementary data
Journal Articles

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

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 article titled, Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model
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Journal Articles

Surveying the energy landscape of coarse-grained mappings

Editor’s Pick
Katherine M. Kidder, M. Scott Shell, W. G. Noid
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 054105 (2024)
https://doi.org/10.1063/5.0182524
Published: February 2024
View article titled, Surveying the energy landscape of coarse-grained mappings
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Includes: Supplementary data
Journal Articles

Molecularly informed field theory for estimating critical micelle concentrations of intrinsically disordered protein surfactants

My. V. T. Nguyen, Kate Dolph, Kris T. Delaney, Kevin Shen, Nicholas Sherck, Stephan Köhler, Rohini Gupta, Matthew B. Francis, M. Scott Shell, Glenn H. Fredrickson
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 244904 (2023)
https://doi.org/10.1063/5.0178910
Published: December 2023
View article titled, Molecularly informed field theory for estimating critical micelle concentrations of intrinsically disordered protein surfactants
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Includes: Supplementary data