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Journal Articles

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg²⁺ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme

Prabin Baral, Mert Y. Sengul, Alexander D. MacKerell, Jr.

J. Chem. Phys. 161, 225102 (2024)

https://doi.org/10.1063/5.0241246

Published: December 2024

View article titled, Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme

Journal Articles

Integrating path sampling with enhanced sampling for rare-event kinetics

Dhiman Ray

J. Chem. Phys. 161, 224106 (2024)

https://doi.org/10.1063/5.0239303

Published: December 2024

View article titled, Integrating path sampling with enhanced sampling for rare-event kinetics

Journal Articles

Inference of non-exponential kinetics through stochastic resetting

Ofir Blumer, Shlomi Reuveni, Barak Hirshberg

J. Chem. Phys. 161, 224104 (2024)

https://doi.org/10.1063/5.0243783

Published: December 2024

View article titled, Inference of non-exponential kinetics through stochastic resetting

Journal Articles

Structural transitions of calcium carbonate by molecular dynamics simulation

Elizaveta Sidler, Raffaela Cabriolu

J. Chem. Phys. 161, 214707 (2024)

https://doi.org/10.1063/5.0233713

Published: December 2024

View article titled, Structural transitions of calcium carbonate by molecular dynamics simulation

Journal Articles

Analysis of transition rates from variational flooding using analytical theory

David Cummins, Carter Longstreth, James McCarty

J. Chem. Phys. 161, 194104 (2024)

https://doi.org/10.1063/5.0238289

Published: November 2024

View article titled, Analysis of transition rates from variational flooding using analytical theory

Journal Articles

Collective molecular-scale carbonation path in aqueous solutions with sufficient structural sampling: From CO₂ to CaCO₃

Xinping Zhu, Romain Dupuis, Roland J.-M. Pellenq, Katerina Ioannidou

J. Chem. Phys. 161, 184502 (2024)

https://doi.org/10.1063/5.0228805

Published: November 2024

View article titled, Collective molecular-scale carbonation path in aqueous solutions with sufficient structural sampling: From CO2 to CaCO3

Journal Articles

DeepLNE++ leveraging knowledge distillation for accelerated multi-state path-like collective variables

Thorben Fröhlking, Valerio Rizzi, Simone Aureli, Francesco Luigi Gervasio

J. Chem. Phys. 161, 114102 (2024)

https://doi.org/10.1063/5.0226721

Published: September 2024

View article titled, DeepLNE++ leveraging knowledge distillation for accelerated multi-state path-like collective variables

Journal Articles

Adaptive accelerated reactive molecular dynamics driven by parallel collective variables overcoming dimensionality explosion

Rui Zhou, Luyao Bao, Weifeng Bu, Feng Zhou

J. Chem. Phys. 161, 054103 (2024)

https://doi.org/10.1063/5.0222514

Published: August 2024

View article titled, Adaptive accelerated reactive molecular dynamics driven by parallel collective variables overcoming dimensionality explosion

Journal Articles

Harvesting nucleating structures in nanoparticle crystallization: The example of gold, silver, and iron

Arthur France-Lanord, Sarath Menon, Julien Lam

J. Chem. Phys. 161, 044108 (2024)

https://doi.org/10.1063/5.0200850

Published: July 2024

View article titled, Harvesting nucleating structures in nanoparticle crystallization: The example of gold, silver, and iron

Journal Articles

Ion association behaviors in the initial stage of calcium carbonate formation: An ab initio study

Yue Li, Jiarui Zhang, Hongbo Zeng, Hao Zhang

J. Chem. Phys. 161, 014503 (2024)

https://doi.org/10.1063/5.0206841

Published: July 2024

View article titled, Ion association behaviors in the initial stage of calcium carbonate formation: An ab initio study

Journal Articles

Insights into the structure and dynamics of K⁺ ions at the muscovite–water interface from machine learning potential simulations

Abhinav S. Raman, Annabella Selloni

J. Chem. Phys. 160, 244708 (2024)

https://doi.org/10.1063/5.0217720

Published: June 2024

View article titled, Insights into the structure and dynamics of K+ ions at the muscovite–water interface from machine learning potential simulations

Journal Articles

Unknown crystal-like phases formed in an imidazolium ionic liquid: A metadynamics simulation study

Hiroki Nada

J. Chem. Phys. 160, 204501 (2024)

https://doi.org/10.1063/5.0206020

Published: May 2024

View article titled, Unknown crystal-like phases formed in an imidazolium ionic liquid: A metadynamics simulation study

Journal Articles

CREST—A program for the exploration of low-energy molecular chemical space

Philipp Pracht, Stefan Grimme, Christoph Bannwarth, Fabian Bohle, Sebastian Ehlert, Gereon Feldmann, Johannes Gorges, Marcel Müller, Tim Neudecker, Christoph Plett, Sebastian Spicher, Pit Steinbach, Patryk A. Wesołowski, Felix Zeller

J. Chem. Phys. 160, 114110 (2024)

https://doi.org/10.1063/5.0197592

Published: March 2024

View article titled, CREST—A program for the exploration of low-energy molecular chemical space

Includes: Supplementary data

Journal Articles

A slow feature analysis approach for the optimization of collective variables

Shuai Gong, Zheng Zheng

J. Chem. Phys. 160, 094104 (2024)

https://doi.org/10.1063/5.0191014

Published: March 2024

View article titled, A slow feature analysis approach for the optimization of collective variables

Includes: Supplementary data

Journal Articles

Computing equilibrium free energies through a nonequilibrium quench

Kangxin Liu, Grant M. Rotskoff, Eric Vanden-Eijnden, Glen M. Hocky

J. Chem. Phys. 160, 034109 (2024)

https://doi.org/10.1063/5.0176700

Published: January 2024

View article titled, Computing equilibrium free energies through a nonequilibrium quench

Includes: Supplementary data

Journal Articles

The role of structural heterogeneity in the homodimerization of transmembrane proteins

Ayan Majumder, John E. Straub

J. Chem. Phys. 159, 134101 (2023)

https://doi.org/10.1063/5.0159801

Published: October 2023

View article titled, The role of structural heterogeneity in the homodimerization of transmembrane proteins

Includes: Supplementary data

Journal Articles

Inhibition mechanism of testis-expressed gene 14 (TEX14) in cytokinetic abscission: Well-tempered metadynamics simulation studies

Yunju Cho, Youhyun Nam, Hyung Ho Lee, Rakwoo Chang

J. Chem. Phys. 159, 015102 (2023)

https://doi.org/10.1063/5.0153799

Published: July 2023

View article titled, Inhibition mechanism of testis-expressed gene 14 (TEX14) in cytokinetic abscission: Well-tempered metadynamics simulation studies

Includes: Supplementary data

Journal Articles

Deep learning collective variables from transition path ensemble

Dhiman Ray, Enrico Trizio, Michele Parrinello

J. Chem. Phys. 158, 204102 (2023)

https://doi.org/10.1063/5.0148872

Published: May 2023

View article titled, Deep learning collective variables from transition path ensemble

Includes: Supplementary data

Journal Articles

Can molecular dynamics be used to simulate biomolecular recognition?

Malin Lüking, David van der Spoel, Johan Elf, Gareth A. Tribello

J. Chem. Phys. 158, 184106 (2023)

https://doi.org/10.1063/5.0146899

Published: May 2023

View article titled, Can molecular dynamics be used to simulate biomolecular recognition?

Includes: Supplementary data

Journal Articles

Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach

Praveen Ranganath Prabhakar, Dhiman Ray, Ioan Andricioaei

J. Chem. Phys. 158, 134108 (2023)

https://doi.org/10.1063/5.0140113

Published: April 2023

View article titled, Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach

Includes: Supplementary data

NARROW

Topics

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg²⁺ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme

Integrating path sampling with enhanced sampling for rare-event kinetics

Inference of non-exponential kinetics through stochastic resetting

Structural transitions of calcium carbonate by molecular dynamics simulation

Analysis of transition rates from variational flooding using analytical theory

Collective molecular-scale carbonation path in aqueous solutions with sufficient structural sampling: From CO₂ to CaCO₃

DeepLNE++ leveraging knowledge distillation for accelerated multi-state path-like collective variables

Adaptive accelerated reactive molecular dynamics driven by parallel collective variables overcoming dimensionality explosion

Harvesting nucleating structures in nanoparticle crystallization: The example of gold, silver, and iron

Ion association behaviors in the initial stage of calcium carbonate formation: An ab initio study

Insights into the structure and dynamics of K⁺ ions at the muscovite–water interface from machine learning potential simulations

Unknown crystal-like phases formed in an imidazolium ionic liquid: A metadynamics simulation study

CREST—A program for the exploration of low-energy molecular chemical space

A slow feature analysis approach for the optimization of collective variables

Computing equilibrium free energies through a nonequilibrium quench

The role of structural heterogeneity in the homodimerization of transmembrane proteins

Inhibition mechanism of testis-expressed gene 14 (TEX14) in cytokinetic abscission: Well-tempered metadynamics simulation studies

Deep learning collective variables from transition path ensemble

Can molecular dynamics be used to simulate biomolecular recognition?

Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach

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