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Journal Articles

The role of structural heterogeneity in the homodimerization of transmembrane proteins

Ayan Majumder, John E. Straub
Journal: The Journal of Chemical Physics
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
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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
Journal: The Journal of Chemical Physics
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
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Includes: Supplementary data
Journal Articles

Deep learning collective variables from transition path ensemble

Dhiman Ray, Enrico Trizio, Michele Parrinello
Journal: The Journal of Chemical Physics
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
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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
Journal: The Journal of Chemical Physics
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?
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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
Journal: The Journal of Chemical Physics
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
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Includes: Supplementary data
Journal Articles

A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly

Akash Banerjee, Meenakshi Dutt
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 114105 (2023)
https://doi.org/10.1063/5.0138510
Published: March 2023
View article titled, A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly
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Includes: Supplementary data
Journal Articles

Free energy calculations and unbiased molecular dynamics targeting the liquid–liquid transition in water no man’s land

Alexandre Jedrecy, A. Marco Saitta, Fabio Pietrucci
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 014502 (2023)
https://doi.org/10.1063/5.0120789
Published: January 2023
View article titled, Free energy calculations and unbiased molecular dynamics targeting the liquid–liquid transition in water no man’s land
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Includes: Supplementary data
Journal Articles

Efficient exploration of complex free energy landscapes by stepwise multi-subphase space metadynamics

Ye-Guang Fang, Xiaojiao Li, Yurui Gao, Yan-Hong Cui, Joseph S. Francisco, Chongqin Zhu, Wei-Hai Fang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 214111 (2022)
https://doi.org/10.1063/5.0098269
Published: December 2022
View article titled, Efficient exploration of complex free energy landscapes by stepwise multi-subphase space metadynamics
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Includes: Supplementary data
Journal Articles

Computing committors via Mahalanobis diffusion maps with enhanced sampling data

L. Evans, M. K. Cameron, P. Tiwary
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 214107 (2022)
https://doi.org/10.1063/5.0122990
Published: December 2022
View article titled, Computing committors via Mahalanobis diffusion maps with enhanced sampling data
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Journal Articles

Computer simulation of the early stages of self-assembly and thermal decomposition of ZIF-8

S. R. G. Balestra, R. Semino
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 184502 (2022)
https://doi.org/10.1063/5.0128656
Published: November 2022
View article titled, Computer simulation of the early stages of self-assembly and thermal decomposition of ZIF-8
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Includes: Supplementary data
Journal Articles

Reduction pathway of glutaredoxin 1 investigated with QM/MM molecular dynamics using a neural network correction

Julian Böser, Tomáš Kubař, Marcus Elstner, Denis Maag
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 154104 (2022)
https://doi.org/10.1063/5.0123089
Published: October 2022
View article titled, Reduction pathway of glutaredoxin 1 investigated with QM/MM molecular dynamics using a neural network correction
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Includes: Supplementary data
Journal Articles

Effect of nitrogen molecules on the growth kinetics at the interface between a (111) plane of cubic ice and water

Hiroki Nada
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 124701 (2022)
https://doi.org/10.1063/5.0106842
Published: September 2022
View article titled, Effect of nitrogen molecules on the growth kinetics at the interface between a (111) plane of cubic ice and water
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Includes: Supplementary data
Journal Articles

Well-tempered metadynamics applied to field-theoretic simulations of diblock copolymer melts

Thomas M. Beardsley, Mark W. Matsen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 114902 (2022)
https://doi.org/10.1063/5.0112703
Published: September 2022
View article titled, Well-tempered metadynamics applied to field-theoretic simulations of diblock copolymer melts
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Includes: Supplementary data
Journal Articles

Statistically optimal analysis of the extended-system adaptive biasing force (eABF) method

Andreas Hulm, Johannes C. B. Dietschreit, Christian Ochsenfeld
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 024110 (2022)
https://doi.org/10.1063/5.0095554
Published: July 2022
View article titled, Statistically optimal analysis of the extended-system adaptive biasing force (eABF) method
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Includes: Supplementary data
Journal Articles

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters

Federica Lodesani, Maria Cristina Menziani, Shingo Urata, Alfonso Pedone
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 194501 (2022)
https://doi.org/10.1063/5.0089183
Published: May 2022
View article titled, Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters
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Includes: Supplementary data
Journal Articles

Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters

Daniel Sucerquia, Cristian Parra, Pilar Cossio, Olga Lopez-Acevedo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 154301 (2022)
https://doi.org/10.1063/5.0082332
Published: April 2022
View article titled, <em>Ab initio</em> metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters
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Includes: Supplementary data
Journal Articles

Two-step nucleation in confined geometry: Phase diagram of finite particles on a lattice gas model

Jacob Holder, Ralf Schmid, Peter Nielaba
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 124504 (2022)
https://doi.org/10.1063/5.0073043
Published: March 2022
View article titled, Two-step nucleation in confined geometry: Phase diagram of finite particles on a lattice gas model
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Journal Articles

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Willmor J. Peña Ccoa, Glen M. Hocky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 125102 (2022)
https://doi.org/10.1063/5.0081078
Published: March 2022
View article titled, Assessing models of force-dependent unbinding rates via infrequent metadynamics
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Includes: Supplementary data
Journal Articles

Impurity diffusion in magic-size icosahedral clusters

Diana Nelli, Fabio Pietrucci, Riccardo Ferrando
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 144304 (2021)
https://doi.org/10.1063/5.0060236
Published: October 2021
View article titled, Impurity diffusion in magic-size icosahedral clusters
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Journal Articles

Nucleation rates from small scale atomistic simulations and transition state theory

Kristof M. Bal
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 144111 (2021)
https://doi.org/10.1063/5.0063398
Published: October 2021
View article titled, Nucleation rates from small scale atomistic simulations and transition state theory
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