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Journal Articles

Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity

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Adip Jhaveri, Smriti Chhibber, Nandan Kulkarni, Margaret E. Johnson
Journal: The Journal of Chemical Physics
J. Chem. Phys. 163, 034116 (2025)
https://doi.org/10.1063/5.0275282
Published: July 2025
View article titled, Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity
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Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations

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Ryo Okabe, Natsuumi Ito, Yuya Matsubara, Nozomi Morishita Watanabe, Hiroshi Umakoshi, Kento Kasahara, Nobuyuki Matubayasi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 163, 034708 (2025)
https://doi.org/10.1063/5.0279530
Published: July 2025
View article titled, Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
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AutoSIM: Redesigning and automating umbrella sampling for biomolecular conformational transitions

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Mitradip Das, Ravindra Venkatramani
Journal: The Journal of Chemical Physics
J. Chem. Phys. 163, 014111 (2025)
https://doi.org/10.1063/5.0268626
Published: July 2025
View article titled, AutoSIM: Redesigning and automating umbrella sampling for biomolecular conformational transitions
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Nuclear quantum effects at the liquid/vapor interface from neural-network based path integral molecular dynamics simulations

Editor’s PickOpen Access
Elias Eingang, Christoph Dellago, Marcello Sega
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 244709 (2025)
https://doi.org/10.1063/5.0268072
Published: June 2025
View article titled, Nuclear quantum effects at the liquid/vapor interface from neural-network based path integral molecular dynamics simulations
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Towards a robust approach to infer causality from molecular dynamics simulations

FeaturedScilightOpen Access
Vittorio Del Tatto, Debarshi Banerjee, Ali Hassanali, Alessandro Laio
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 244105 (2025)
https://doi.org/10.1063/5.0267926
Published: June 2025
View article titled, Towards a robust approach to infer causality from molecular dynamics simulations
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Journal Articles

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

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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 article titled, Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution
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Additive strategy for nucleation pathway control based on the understanding of molecular size effect on crystallization

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Yuya Iida, Shotaro Hiraide, Satoshi Watanabe
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 214503 (2025)
https://doi.org/10.1063/5.0266286
Published: June 2025
View article titled, Additive strategy for nucleation pathway control based on the understanding of molecular size effect on crystallization
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Journal Articles

You reap what you sow: On the impact of nuclei morphology on seeded molecular dynamics simulations

Open Access
Katarina E. Blow, Gabriele C. Sosso, David Quigley
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 184503 (2025)
https://doi.org/10.1063/5.0261353
Published: May 2025
View article titled, You reap what you sow: On the impact of nuclei morphology on seeded molecular dynamics simulations
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Journal Articles

Nanoscale surface effects on heterogeneous vapor bubble nucleation

Open Access
P. Sullivan, D. Dockar, R. Pillai
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 184501 (2025)
https://doi.org/10.1063/5.0259208
Published: May 2025
View article titled, Nanoscale surface effects on heterogeneous vapor bubble nucleation
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Considerations in the use of machine learning force fields for free energy calculations

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Orlando A. Mendible-Barreto, Jonathan K. Whitmer, Yamil J. Colón
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 174119 (2025)
https://doi.org/10.1063/5.0252043
Published: May 2025
View article titled, Considerations in the use of machine learning force fields for free energy calculations
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An iterative and automatic collective variable optimization scheme via unsupervised feature selection with CUR matrix decomposition

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Yunsong Fu, Ye Mei, Chungen Liu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 174101 (2025)
https://doi.org/10.1063/5.0259470
Published: May 2025
View article titled, An iterative and automatic collective variable optimization scheme via unsupervised feature selection with CUR matrix decomposition
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Journal Articles

Erratum: “Evolution equations for open systems and collective variables: Which equation would you like to solve by molecular dynamics simulation?” [J. Chem. Phys. 161, 191501 (2024)]

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Tanja Schilling
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 169902 (2025)
https://doi.org/10.1063/5.0273476
Published: April 2025
View article titled, Erratum: “Evolution equations for open systems and collective variables: Which equation would you like to solve by molecular dynamics simulation?” [J. Chem. Phys. 161, 191501 (2024)]
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Journal Articles

Data efficient learning of molecular slow modes from nonequilibrium metadynamics

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Jack Hanni, Dhiman Ray
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 164101 (2025)
https://doi.org/10.1063/5.0258483
Published: April 2025
View article titled, Data efficient learning of molecular slow modes from nonequilibrium metadynamics
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Journal Articles

Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model

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Nhung T. T. Nguyen, Pham Nam Phong, Duy Manh Le, Minh-Tien Tran, Trinh Xuan Hoang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 145104 (2025)
https://doi.org/10.1063/5.0257315
Published: April 2025
View article titled, Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model
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Journal Articles

Low-temperature nucleation rate calculations using the N-Fold way

Open Access
Federico Ettori, Dipanjan Mandal, David Quigley
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 124116 (2025)
https://doi.org/10.1063/5.0255066
Published: March 2025
View article titled, Low-temperature nucleation rate calculations using the N-Fold way
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Journal Articles

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence

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Hindol Chatterjee, Pallab Dutta, Martin Zacharias, Neelanjana Sengupta
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 104110 (2025)
https://doi.org/10.1063/5.0250082
Published: March 2025
View article titled, Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence
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Journal Articles

Efficient sampling of free energy landscapes with functions in Sobolev spaces

Open Access
Pablo F. Zubieta Rico, Gustavo R. Pérez-Lemus, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 084109 (2025)
https://doi.org/10.1063/5.0221263
Published: February 2025
View article titled, Efficient sampling of free energy landscapes with functions in Sobolev spaces
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Journal Articles

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

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

Evaluating multi-state free energy profiles from splitting probability

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Rohan Singh, Parbati Biswas
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 055102 (2025)
https://doi.org/10.1063/5.0246238
Published: February 2025
View article titled, Evaluating multi-state free energy profiles from splitting probability
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Journal Articles

The interplay of heterogeneity and product detachment in templated polymer copying

Open Access
Jeremy E. B. Guntoro, Benjamin J. Qureshi, Thomas E. Ouldridge
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 055103 (2025)
https://doi.org/10.1063/5.0245687
Published: February 2025
View article titled, The interplay of heterogeneity and product detachment in templated polymer copying
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