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Journal Articles

Nonequilibrium friction and free energy estimates for kinetic coarse-graining—Driven particles in responsive media

Open Access
Sebastian Milster, Joachim Dzubiella, Gerhard Stock, Steffen Wolf
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 154113 (2025)
https://doi.org/10.1063/5.0261459
Published: April 2025
View articletitled, Nonequilibrium friction and free energy estimates for kinetic coarse-graining—Driven particles in responsive media
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Journal Articles

Atomistic analysis of nematic phase transition in 4-cyano-4′-n-alkyl biphenyl liquid crystals: Sampling for the first-order phase transition and the free-energy decomposition

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Shunsuke Ogita, Yoshiki Ishii, Go Watanabe, Hitoshi Washizu, Kang Kim, Nobuyuki Matubayasi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 054905 (2025)
https://doi.org/10.1063/5.0242416
Published: February 2025
View articletitled, Atomistic analysis of nematic phase transition in 4-cyano-4′-n-alkyl biphenyl liquid crystals: Sampling for the first-order phase transition and the free-energy decomposition
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Journal Articles

Flexible framework of computing binding free energy using the energy representation theory of solution

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Kazuya Okita, Yusei Maruyama, Kento Kasahara, Nobuyuki Matubayasi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 034103 (2025)
https://doi.org/10.1063/5.0242641
Published: January 2025
View articletitled, Flexible framework of computing binding free energy using the energy representation theory of solution
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Journal Articles

A partition function estimator

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Ying-Chih Chiang, Frank Otto, Jonathan W. Essex
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 024104 (2025)
https://doi.org/10.1063/5.0237340
Published: January 2025
View articletitled, A partition function estimator
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Journal Articles

Predicting solvation free energies with an implicit solvent machine learning potential

Open Access
Sebastien Röcken, Anton F. Burnet, Julija Zavadlav
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 234101 (2024)
https://doi.org/10.1063/5.0235189
Published: December 2024
View articletitled, Predicting solvation free energies with an implicit solvent machine learning potential
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Journal Articles

Mechanical and thermodynamic routes to the liquid–liquid interfacial tension and mixing free energy by molecular dynamics

Open Access
Rei Ogawa, Hiroki Kusudo, Takeshi Omori, Edward R. Smith, Laurent Joly, Samy Merabia, Yasutaka Yamaguchi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 224708 (2024)
https://doi.org/10.1063/5.0238862
Published: December 2024
View articletitled, Mechanical and thermodynamic routes to the liquid–liquid interfacial tension and mixing free energy by molecular dynamics
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Journal Articles

Predictions of the interfacial free energy along the coexistence line from single-state calculations

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Ignacio Sanchez-Burgos, Pablo Montero de Hijes, Eduardo Sanz, Carlos Vega, Jorge R. Espinosa
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 204701 (2024)
https://doi.org/10.1063/5.0233420
Published: November 2024
View articletitled, Predictions of the interfacial free energy along the coexistence line from single-state calculations
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Journal Articles

The spectrum of experimentally accessible states for melting and freezing transitions in mesoporous materials

Open Access
A. Alzaidi, D. Schneider, E. S. Kikkinides, R. Valiullin
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 194703 (2024)
https://doi.org/10.1063/5.0238552
Published: November 2024
View articletitled, The spectrum of experimentally accessible states for melting and freezing transitions in mesoporous materials
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Journal Articles

Simulation of the THF hydrate–water interfacial free energy from computer simulation

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Miguel J. Torrejón, Cristóbal Romero-Guzmán, Manuel M. Piñeiro, Felipe J. Blas, Jesús Algaba
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 064701 (2024)
https://doi.org/10.1063/5.0217798
Published: August 2024
View articletitled, Simulation of the THF hydrate–water interfacial free energy from computer simulation
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Journal Articles

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

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Yujun Tao, Timothy J. Giese, Şölen Ekesan, Jinzhe Zeng, Bálint Aradi, Ben Hourahine, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz, Jr., Darrin M. York
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 224104 (2024)
https://doi.org/10.1063/5.0211276
Published: June 2024
View articletitled, Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials
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Journal Articles

Ion solvation free energy calculations based on first-principles molecular dynamics thermodynamic integration

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Chao Lin, Xiaojun He, Cong Xi, Qianfan Zhang, Lin-Wang Wang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 184115 (2024)
https://doi.org/10.1063/5.0191068
Published: May 2024
View articletitled, Ion solvation free energy calculations based on first-principles molecular dynamics thermodynamic integration
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Includes: Supplementary data
Journal Articles

A new dynamic Monte Carlo method satisfying n-particle diffusion equation with position-dependent diffusion coefficient, free energy, and intermolecular interactions

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Susumu Okazaki
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 174111 (2024)
https://doi.org/10.1063/5.0204129
Published: May 2024
View articletitled, A new dynamic Monte Carlo method satisfying n-particle diffusion equation with position-dependent diffusion coefficient, free energy, and intermolecular interactions
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Journal Articles

Pseudo-marginal approximation to the free energy in a micro–macro Markov chain Monte Carlo method

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Hannes Vandecasteele, Giovanni Samaey
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 104702 (2024)
https://doi.org/10.1063/5.0199562
Published: March 2024
View articletitled, Pseudo-marginal approximation to the free energy in a micro–macro Markov chain Monte Carlo method
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Journal Articles

Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods

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Tadeáš Kalvoda, Tomas Martinek, Pavel Jungwirth, Lubomír Rulíšek
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 084308 (2024)
https://doi.org/10.1063/5.0192024
Published: February 2024
View articletitled, Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods
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Includes: Supplementary data
Journal Articles

Computing equilibrium free energies through a nonequilibrium quench

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Kangxin Liu, Grant M. Rotskoff, Eric Vanden-Eijnden, Glen M. Hocky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 034109 (2024)
https://doi.org/10.1063/5.0176700
Published: January 2024
View articletitled, Computing equilibrium free energies through a nonequilibrium quench
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Includes: Supplementary data
Journal Articles

Can a coarse-grained water model capture the key physical features of the hydrophobic effect?

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Kuntal Ghosh, Timothy D. Loose, Gregory A. Voth
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 224105 (2023)
https://doi.org/10.1063/5.0176716
Published: December 2023
View articletitled, Can a coarse-grained water model capture the key physical features of the hydrophobic effect?
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Includes: Supplementary data
Journal Articles

Analysis of probability of inserting a hard spherical particle with small diameter in hard-sphere fluid

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Ruslan L. Davidchack, Aisha Ahmed Elmajdoub, Brian B. Laird
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 184503 (2023)
https://doi.org/10.1063/5.0170928
Published: November 2023
View articletitled, Analysis of probability of inserting a hard spherical particle with small diameter in hard-sphere fluid
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Journal Articles

Counterion-controlled phase equilibria in a charge-regulated polymer solution

Open Access
Giulia L. Celora, Ralf Blossey, Andreas Münch, Barbara Wagner
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 184902 (2023)
https://doi.org/10.1063/5.0169610
Published: November 2023
View articletitled, Counterion-controlled phase equilibria in a charge-regulated polymer solution
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Journal Articles

Development of an analytical exponential-6 equation of state through Monte Carlo simulations

Open Access
Peter Hallstadius
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 164501 (2023)
https://doi.org/10.1063/5.0171319
Published: October 2023
View articletitled, Development of an analytical exponential-6 equation of state through Monte Carlo simulations
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Includes: Supplementary data
Journal Articles

Effect of wall free energy formulation on the wetting phenomenon: Conservative Allen–Cahn model

Open Access
Hongmin Zhang, Yanchen Wu, Fei Wang, Britta Nestler
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 164701 (2023)
https://doi.org/10.1063/5.0168394
Published: October 2023
View articletitled, Effect of wall free energy formulation on the wetting phenomenon: Conservative Allen–Cahn model
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Includes: Supplementary data