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Journal Articles

Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems

Jaehyeok Jin, Gregory A. Voth

J. Chem. Phys. 162, 124114 (2025)

https://doi.org/10.1063/5.0254388

Published: March 2025

View articletitled, Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems

Journal Articles

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Blake I. Armstrong, Andrea Arsiccio, Simone Aureli, Federico Ballabio, Mattia Bernetti, Luigi Bonati, Samuel G. H. Brookes, Z. Faidon Brotzakis, Riccardo Capelli, Michele Ceriotti, Kam-Tung Chan, Pilar Cossio, Siva Dasetty, Davide Donadio, Bernd Ensing, Andrew L. Ferguson, Guillaume Fraux, Julian D. Gale, Francesco Luigi Gervasio, Toni Giorgino, Nicholas S. M. Herringer, Glen M. Hocky, Samuel E. Hoff, Michele Invernizzi, Olivier Languin-Cattoën, Vanessa Leone, Vittorio Limongelli, Olga Lopez-Acevedo, Fabrizio Marinelli, Pedro Febrer Martinez, Matteo Masetti, Shams Mehdi, Angelos Michaelides, Mhd Hussein Murtada, Michele Parrinello, Pablo M. Piaggi, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Claire Pritchard, Paolo Raiteri, Stefano Raniolo, Daniele Rapetti, Valerio Rizzi, Jakub Rydzewski, Matteo Salvalaglio, Christoph Schran, Aniruddha Seal, Armin Shayesteh Zadeh, Tomás F. D. Silva, Vojtěch Spiwok, Guillaume Stirnemann, Daniel Sucerquia, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A. Voth, Andrew D. White, Jiangbo Wu

J. Chem. Phys. 162, 092501 (2025)

https://doi.org/10.1063/5.0251501

Published: March 2025

View articletitled, PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Journal Articles

Entropy-based methods for formulating bottom-up ultra-coarse-grained models

Patrick G. Sahrmann, Gregory A. Voth

J. Chem. Phys. 162, 044102 (2025)

https://doi.org/10.1063/5.0244427

Published: January 2025

View articletitled, Entropy-based methods for formulating bottom-up ultra-coarse-grained models

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

J. Chem. Phys. 161, 034114 (2024)

https://doi.org/10.1063/5.0212973

Published: July 2024

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

Journal Articles

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

Kuntal Ghosh, Timothy D. Loose, Gregory A. Voth

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?

Includes: Supplementary data

Journal Articles

Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability

Jaehyeok Jin, Jisung Hwang, Gregory A. Voth

J. Chem. Phys. 159, 184105 (2023)

https://doi.org/10.1063/5.0160567

Published: November 2023

View articletitled, Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability

Includes: Supplementary data

Journal Articles

Understanding dynamics in coarse-grained models. III. Roles of rotational motion and translation-rotation coupling in coarse-grained dynamics

Jaehyeok Jin, Eok Kyun Lee, Gregory A. Voth

J. Chem. Phys. 159, 164102 (2023)

https://doi.org/10.1063/5.0167158

Published: October 2023

View articletitled, Understanding dynamics in coarse-grained models. III. Roles of rotational motion and translation-rotation coupling in coarse-grained dynamics

Journal Articles

Using classifiers to understand coarse-grained models and their fidelity with the underlying all-atom systems

Aleksander E. P. Durumeric, Gregory A. Voth

J. Chem. Phys. 158, 234101 (2023)

https://doi.org/10.1063/5.0146812

Published: June 2023

View articletitled, Using classifiers to understand coarse-grained models and their fidelity with the underlying all-atom systems

Includes: Supplementary data

Journal Articles

Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory

Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth

J. Chem. Phys. 158, 034104 (2023)

https://doi.org/10.1063/5.0116300

Published: January 2023

View articletitled, Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory

Journal Articles

Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship

Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth

J. Chem. Phys. 158, 034103 (2023)

https://doi.org/10.1063/5.0116299

Published: January 2023

View articletitled, Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship

Journal Articles

The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water

Christopher Arntsen, Chen Chen, Paul B. Calio, Chenghan Li, Gregory A. Voth

J. Chem. Phys. 154, 194506 (2021)

https://doi.org/10.1063/5.0040758

Published: May 2021

View articletitled, The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water

Includes: Supplementary data

Journal Articles

Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining

Yining Han, Jaehyeok Jin, Gregory A. Voth

J. Chem. Phys. 154, 084122 (2021)

https://doi.org/10.1063/5.0035184

Published: February 2021

View articletitled, Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining

Journal Articles

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature

Jaehyeok Jin, Alexander J. Pak, Yining Han, Gregory A. Voth

J. Chem. Phys. 154, 044105 (2021)

https://doi.org/10.1063/5.0026652

Published: January 2021

View articletitled, A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature

Journal Articles

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model

Jaehyeok Jin, Yining Han, Alexander J. Pak, Gregory A. Voth

J. Chem. Phys. 154, 044104 (2021)

https://doi.org/10.1063/5.0026651

Published: January 2021

View articletitled, A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model

Journal Articles

Compatible observable decompositions for coarse-grained representations of real molecular systems

Thomas Dannenhoffer-Lafage, Jacob W. Wagner, Aleksander E. P. Durumeric, Gregory A. Voth

J. Chem. Phys. 151, 134115 (2019)

https://doi.org/10.1063/1.5116027

Published: October 2019

View articletitled, Compatible observable decompositions for coarse-grained representations of real molecular systems

Includes: Supplementary data

Journal Articles

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

Aleksander E. P. Durumeric, Gregory A. Voth

J. Chem. Phys. 151, 124110 (2019)

https://doi.org/10.1063/1.5097559

Published: September 2019

View articletitled, Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

Journal Articles

Coarse-graining of many-body path integrals: Theory and numerical approximations

Won Hee Ryu, Yining Han, Gregory A. Voth

J. Chem. Phys. 150, 244103 (2019)

https://doi.org/10.1063/1.5097141

Published: June 2019

View articletitled, Coarse-graining of many-body path integrals: Theory and numerical approximations

Includes: Supplementary data

Journal Articles

Coarse-graining involving virtual sites: Centers of symmetry coarse-graining

Jaehyeok Jin, Yining Han, Gregory A. Voth

J. Chem. Phys. 150, 154103 (2019)

https://doi.org/10.1063/1.5067274

Published: April 2019

View articletitled, Coarse-graining involving virtual sites: Centers of symmetry coarse-graining

Journal Articles

Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models

Yining Han, James F. Dama, Gregory A. Voth

J. Chem. Phys. 149, 044104 (2018)

https://doi.org/10.1063/1.5039738

Published: July 2018

View articletitled, Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models

Journal Articles

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

Rui Sun, Yining Han, Jessica M. J. Swanson, Jeffrey S. Tan, John P. Rose, Gregory A. Voth

J. Chem. Phys. 149, 072310 (2018)

https://doi.org/10.1063/1.5027004

Published: May 2018

View articletitled, Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

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Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Entropy-based methods for formulating bottom-up ultra-coarse-grained models

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

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

Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability

Understanding dynamics in coarse-grained models. III. Roles of rotational motion and translation-rotation coupling in coarse-grained dynamics

Using classifiers to understand coarse-grained models and their fidelity with the underlying all-atom systems

Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory

Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship

The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water

Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model

Compatible observable decompositions for coarse-grained representations of real molecular systems

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

Coarse-graining of many-body path integrals: Theory and numerical approximations

Coarse-graining involving virtual sites: Centers of symmetry coarse-graining

Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

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