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Journal Articles

Evaluating multi-state free energy profiles from splitting probability

Rohan Singh, Parbati Biswas

J. Chem. Phys. 162, 055102 (2025)

https://doi.org/10.1063/5.0246238

Published: February 2025

View articletitled, Evaluating multi-state free energy profiles from splitting probability

Journal Articles

Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation

Marco Oestereich, Jürgen Gauss, Gregor Diezemann

J. Chem. Phys. 161, 154903 (2024)

https://doi.org/10.1063/5.0228198

Published: October 2024

View articletitled, Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation

Journal Articles

Individual adsorption of low volatility pheromones: Amphiphilic molecules on a clean water–air interface

L. Jami, T. Zemb, J. Casas, J-F. Dufrêche

J. Chem. Phys. 157, 094708 (2022)

https://doi.org/10.1063/5.0110264

Published: September 2022

View articletitled, Individual adsorption of low volatility pheromones: Amphiphilic molecules on a clean water–air interface

Includes: Supplementary data

Journal Articles

Protein aggregation rate depends on mechanical stability of fibrillar structure

Tran Thi Minh Thu, Mai Suan Li

J. Chem. Phys. 157, 055101 (2022)

https://doi.org/10.1063/5.0088689

Published: August 2022

View articletitled, Protein aggregation rate depends on mechanical stability of fibrillar structure

Journal Articles

Effect of ligand binding on riboswitch folding: Theory and simulations

Shivangi Sharma, Vishal Singh, Parbati Biswas

J. Chem. Phys. 154, 185101 (2021)

https://doi.org/10.1063/5.0047684

Published: May 2021

View articletitled, Effect of ligand binding on riboswitch folding: Theory and simulations

Includes: Supplementary data

Journal Articles

Data-guided Multi-Map variables for ensemble refinement of molecular movies

John W. Vant, Daipayan Sarkar, Ellen Streitwieser, Giacomo Fiorin, Robert Skeel, Josh V. Vermaas, Abhishek Singharoy

J. Chem. Phys. 153, 214102 (2020)

https://doi.org/10.1063/5.0022433

Published: December 2020

View articletitled, Data-guided Multi-Map variables for ensemble refinement of molecular movies

Includes: Supplementary data

Journal Articles

Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers

Sang Young Noh, Rebecca Notman

J. Chem. Phys. 153, 034115 (2020)

https://doi.org/10.1063/5.0016114

Published: July 2020

View articletitled, Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers

Includes: Supplementary data

Journal Articles

Detection of single DNA mismatches by force spectroscopy in short DNA hairpins

F. Landuzzi, X. Viader-Godoy, F. Cleri, I. Pastor, F. Ritort

J. Chem. Phys. 152, 074204 (2020)

https://doi.org/10.1063/1.5139284

Published: February 2020

View articletitled, Detection of single DNA mismatches by force spectroscopy in short DNA hairpins

Includes: Supplementary data

Journal Articles

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Anil Kumar Sahoo, Biman Bagchi, Prabal K. Maiti

J. Chem. Phys. 151, 164902 (2019)

https://doi.org/10.1063/1.5117163

Published: October 2019

View articletitled, Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Includes: Supplementary data

Journal Articles

Enhancement of protein mechanical stability: Correlated deformations are handcuffed by ligand binding

Wei Bu Wang, Jian Zhuo Zhu, Xing Yuan Li, Chun Hua Li, Ji Guo Su, Jing Yuan Li

J. Chem. Phys. 150, 155102 (2019)

https://doi.org/10.1063/1.5054932

Published: April 2019

View articletitled, Enhancement of protein mechanical stability: Correlated deformations are handcuffed by ligand binding

Journal Articles

Uncertainty quantification for Markov state models of biomolecules constructed using rare event acceleration techniques

Swati Bhattacharya, Abhijit Chatterjee

J. Chem. Phys. 150, 044106 (2019)

https://doi.org/10.1063/1.5066278

Published: January 2019

View articletitled, Uncertainty quantification for Markov state models of biomolecules constructed using rare event acceleration techniques

Includes: Supplementary data

Journal Articles

Exploring the binding mechanism between human profilin (PFN1) and polyproline-10 through binding mode screening

Leili Zhang, David R. Bell, Binquan Luan, Ruhong Zhou

J. Chem. Phys. 150, 015102 (2019)

https://doi.org/10.1063/1.5053922

Published: January 2019

View articletitled, Exploring the binding mechanism between human profilin (PFN1) and polyproline-10 through binding mode screening

Includes: Supplementary data

Journal Articles

Effects of solvent quality and non-equilibrium conformations on polymer translocation

Seulki Kwon, Bong June Sung

J. Chem. Phys. 149, 244907 (2018)

https://doi.org/10.1063/1.5048059

Published: December 2018

View articletitled, Effects of solvent quality and non-equilibrium conformations on polymer translocation

Includes: Supplementary data

Journal Articles

Calculations of free energy of surface interactions in crystalline polyethylene

In-Chul Yeh, Jan W. Andzelm

J. Chem. Phys. 149, 014701 (2018)

https://doi.org/10.1063/1.5031026

Published: July 2018

View articletitled, Calculations of free energy of surface interactions in crystalline polyethylene

Journal Articles

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Maksim Kouza, Nguyen Truong Co, Mai Suan Li, Sebastian Kmiecik, Andrzej Kolinski, Andrzej Kloczkowski, Irina Alexandra Buhimschi

J. Chem. Phys. 148, 215106 (2018)

https://doi.org/10.1063/1.5028575

Published: June 2018

View articletitled, Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Includes: Supplementary data

Journal Articles

Force probe simulations using a hybrid scheme with virtual sites

Ken Schäfer, Marco Oestereich, Jürgen Gauss, Gregor Diezemann

J. Chem. Phys. 147, 134909 (2017)

https://doi.org/10.1063/1.4986194

Published: October 2017

View articletitled, Force probe simulations using a hybrid scheme with virtual sites

Includes: Supplementary data

Journal Articles

Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness

Stefan Jaschonek, Gregor Diezemann

J. Chem. Phys. 146, 124901 (2017)

https://doi.org/10.1063/1.4978678

Published: March 2017

View articletitled, Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness

Journal Articles

β-sheet-like formation during the mechanical unfolding of prion protein

Weiwei Tao, Gwonchan Yoon, Penghui Cao, Kilho Eom, Harold S. Park

J. Chem. Phys. 143, 125101 (2015)

https://doi.org/10.1063/1.4931819

Published: September 2015

View articletitled, β-sheet-like formation during the mechanical unfolding of prion protein

Includes: Supplementary data

Journal Articles

Computation of the binding free energy of peptides to graphene in explicit water

Corrinne M. Welch, Aerial N. Camden, Stephen A. Barr, Gary M. Leuty, Gary S. Kedziora, Rajiv J. Berry

J. Chem. Phys. 143, 045104 (2015)

https://doi.org/10.1063/1.4927344

Published: July 2015

View articletitled, Computation of the binding free energy of peptides to graphene in explicit water

Includes: Supplementary data

Journal Articles

Multiple branched adaptive steered molecular dynamics

Gungor Ozer, Thomas Keyes, Stephen Quirk, Rigoberto Hernandez

J. Chem. Phys. 141, 064101 (2014)

https://doi.org/10.1063/1.4891807

Published: August 2014

View articletitled, Multiple branched adaptive steered molecular dynamics

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Evaluating multi-state free energy profiles from splitting probability

Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation

Individual adsorption of low volatility pheromones: Amphiphilic molecules on a clean water–air interface

Protein aggregation rate depends on mechanical stability of fibrillar structure

Effect of ligand binding on riboswitch folding: Theory and simulations

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers

Detection of single DNA mismatches by force spectroscopy in short DNA hairpins

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Enhancement of protein mechanical stability: Correlated deformations are handcuffed by ligand binding

Uncertainty quantification for Markov state models of biomolecules constructed using rare event acceleration techniques

Exploring the binding mechanism between human profilin (PFN1) and polyproline-10 through binding mode screening

Effects of solvent quality and non-equilibrium conformations on polymer translocation

Calculations of free energy of surface interactions in crystalline polyethylene

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Force probe simulations using a hybrid scheme with virtual sites

Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness

β-sheet-like formation during the mechanical unfolding of prion protein

Computation of the binding free energy of peptides to graphene in explicit water

Multiple branched adaptive steered molecular dynamics

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