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Journal Articles

Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures

Shivam Gupta, Jatin Soni, Awneesh Kumar, Taraknath Mandal
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 165102 (2023)
https://doi.org/10.1063/5.0167144
Published: October 2023
View article titled, Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures
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Includes: Supplementary data
Journal Articles

Signature of functional enzyme dynamics in quasielastic neutron scattering spectra: The case of phosphoglycerate kinase

Abir N. Hassani, Luman Haris, Markus Appel, Tilo Seydel, Andreas M. Stadler, Gerald R. Kneller
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 141102 (2023)
https://doi.org/10.1063/5.0166124
Published: October 2023
View article titled, Signature of functional enzyme dynamics in quasielastic neutron scattering spectra: The case of phosphoglycerate kinase
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Journal Articles

Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents

Cameron J. Shock, Mark J. Stevens, Amalie L. Frischknecht, Issei Nakamura
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 134507 (2023)
https://doi.org/10.1063/5.0165481
Published: October 2023
View article titled, Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents
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Journal Articles

Dynamic coarse-graining of linear and non-linear systems: Mori–Zwanzig formalism and beyond

Bernd Jung, Gerhard Jung
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 084110 (2023)
https://doi.org/10.1063/5.0165541
Published: August 2023
View article titled, Dynamic coarse-graining of linear and non-linear systems: Mori–Zwanzig formalism and beyond
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Journal Articles

Optimized reaction coordinates for analysis of enhanced sampling

Julian Widmer, Cassiano Langini, Andreas Vitalis, Amedeo Caflisch
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 015101 (2023)
https://doi.org/10.1063/5.0149207
Published: July 2023
View article titled, Optimized reaction coordinates for analysis of enhanced sampling
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Includes: Supplementary data
Journal Articles

Electrostatic hindrance to diffusion in flexible crosslinked gels: A coarse-grained simulation study

Luis Pérez-Mas, María del Mar Ramos-Tejada, Alberto Martín-Molina, José-Alberto Maroto-Centeno, Manuel Quesada-Pérez
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 014903 (2023)
https://doi.org/10.1063/5.0151353
Published: July 2023
View article titled, Electrostatic hindrance to diffusion in flexible crosslinked gels: A coarse-grained simulation study
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Journal Articles

MDiGest: A Python package for describing allostery from molecular dynamics simulations

Federica Maschietto, Brandon Allen, Gregory W. Kyro, Victor S. Batista
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 215103 (2023)
https://doi.org/10.1063/5.0140453
Published: June 2023
View article titled, MDiGest: A Python package for describing allostery from molecular dynamics simulations
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Journal Articles

Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A

Kirill A. Konovalov, Cheng-Guo Wu, Yunrui Qiu, Vijaya Kumar Balakrishnan, Pankaj Singh Parihar, Michael S. O’Connor, Yongna Xing, Xuhui Huang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 215101 (2023)
https://doi.org/10.1063/5.0150272
Published: June 2023
View article titled, Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A
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Includes: Supplementary data
Journal Articles

A theory of chemical reactions in biomolecules in solution: Generalized Langevin mode analysis (GLMA)

Fumio Hirata
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 144108 (2023)
https://doi.org/10.1063/5.0143849
Published: April 2023
View article titled, A theory of chemical reactions in biomolecules in solution: Generalized Langevin mode analysis (GLMA)
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Journal Articles

Sequence-dependent model of allosteric communication

Enrico Guarnera, Igor N. Berezovsky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 135101 (2023)
https://doi.org/10.1063/5.0139848
Published: April 2023
View article titled, Sequence-dependent model of allosteric communication
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Includes: Supplementary data
Journal Articles

Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes

Wenjun Zheng
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 124127 (2023)
https://doi.org/10.1063/5.0141630
Published: March 2023
View article titled, Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes
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Journal Articles

Interaction at a distance: Xenon migration in Mb

Haydar Taylan Turan, Eric Boittier, Markus Meuwly
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 125103 (2023)
https://doi.org/10.1063/5.0124502
Published: March 2023
View article titled, Interaction at a distance: Xenon migration in Mb
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Includes: Supplementary data
Journal Articles

Aggregation and crystallization of small alkanes

Timur Shakirov, Wolfgang Paul
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 094905 (2023)
https://doi.org/10.1063/5.0142692
Published: March 2023
View article titled, Aggregation and crystallization of small alkanes
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Includes: Supplementary data
Journal Articles

MCL-1 promiscuity and the structural resilience of its binding partners

Philipp J. Heckmeier, Jeannette Ruf, Brankica G. Janković, Peter Hamm
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 095101 (2023)
https://doi.org/10.1063/5.0137239
Published: March 2023
View article titled, MCL-1 promiscuity and the structural resilience of its binding partners
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Includes: Supplementary data
Journal Articles

Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G

Frank Hirschmann, Hender Lopez, Felix Roosen-Runge, Tilo Seydel, Frank Schreiber, Martin Oettel
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 084112 (2023)
https://doi.org/10.1063/5.0132493
Published: February 2023
View article titled, Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G
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Includes: Supplementary data
Journal Articles

The “violin model”: Looking at community networks for dynamic allostery

Lalima K. Madan, Colin L. Welsh, Alexandr P. Kornev, Susan S. Taylor
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 081001 (2023)
https://doi.org/10.1063/5.0138175
Published: February 2023
View article titled, The “violin model”: Looking at community networks for dynamic allostery
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Journal Articles

Effects of temperature and ionic strength on the microscopic structure and dynamics of egg white gels

Nafisa Begam, Sonja Timmermann, Anastasia Ragulskaya, Anita Girelli, Maximilian D. Senft, Sebastian Retzbach, Nimmi Das Anthuparambil, Mohammad Sayed Akhundzadeh, Marvin Kowalski, Mario Reiser, Fabian Westermeier, Michael Sprung, Fajun Zhang, Christian Gutt, Frank Schreiber
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 074903 (2023)
https://doi.org/10.1063/5.0130758
Published: February 2023
View article titled, Effects of temperature and ionic strength on the microscopic structure and dynamics of egg white gels
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Includes: Supplementary data
Journal Articles

Compact and complete description of non-Markovian dynamics

Thomas Sayer, Andrés Montoya-Castillo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 014105 (2023)
https://doi.org/10.1063/5.0132614
Published: January 2023
View article titled, Compact and complete description of non-Markovian dynamics
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Journal Articles

Multilayered allosteric modulation of coupled folding and binding by phosphorylation, peptidyl-prolyl cis/trans isomerization, and diversity of interaction partners

Karin J. Buholzer, Jordan McIvor, Franziska Zosel, Christian Teppich, Daniel Nettels, Davide Mercadante, Benjamin Schuler
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 235102 (2022)
https://doi.org/10.1063/5.0128273
Published: December 2022
View article titled, Multilayered allosteric modulation of coupled folding and binding by phosphorylation, peptidyl-prolyl <em>cis</em>/<em>trans</em> isomerization, and diversity of interaction partners
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Includes: Supplementary data
Journal Articles

Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage

Helen B. Belato, Carmelissa Norbrun, Jinping Luo, Chinmai Pindi, Souvik Sinha, Alexandra M. D’Ordine, Gerwald Jogl, Giulia Palermo, George P. Lisi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 225103 (2022)
https://doi.org/10.1063/5.0128815
Published: December 2022
View article titled, Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage
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Includes: Supplementary data