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Journal Articles

Modeling of fluence-dependent hole-burned spectra and hole-growth kinetics using multiple two-level system model

Tonu Reinot, Ryszard Jankowiak

J. Chem. Phys. 161, 164106 (2024)

https://doi.org/10.1063/5.0222998

Published: October 2024

View article titled, Modeling of fluence-dependent hole-burned spectra and hole-growth kinetics using multiple two-level system model

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

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

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

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

Includes: Supplementary data

Journal Articles

Emergence of allostery through reorganization of protein residue network architecture

Riya Samanta, Neel Sanghvi, Dorothy Beckett, Silvina Matysiak

J. Chem. Phys. 158, 085104 (2023)

https://doi.org/10.1063/5.0136010

Published: February 2023

View article titled, Emergence of allostery through reorganization of protein residue network architecture

Includes: Supplementary data

Journal Articles

Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface

Santiago Gomez Melo, Dennis Wörthmüller, Pierre Gönczy, Niccolo Banterle, Ulrich S. Schwarz

J. Chem. Phys. 158, 085102 (2023)

https://doi.org/10.1063/5.0135349

Published: February 2023

View article titled, Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface

Includes: Supplementary data

Journal Articles

Structure-based model of fucoxanthin–chlorophyll protein complex: Calculations of chlorophyll electronic couplings

Austėja Mikalčiūtė, Andrius Gelzinis, Mindaugas Mačernis, Claudia Büchel, Bruno Robert, Leonas Valkunas, Jevgenij Chmeliov

J. Chem. Phys. 156, 234101 (2022)

https://doi.org/10.1063/5.0092154

Published: June 2022

View article titled, Structure-based model of fucoxanthin–chlorophyll protein complex: Calculations of chlorophyll electronic couplings

Includes: Supplementary data

Journal Articles

Combined contributions of carotenoids and chlorophylls in two-photon spectra of photosynthetic pigment–protein complexes—A new way to quantify carotenoid dark state to chlorophyll energy transfer?

Julia Nowak, Janin Füller, Peter Jomo Walla

J. Chem. Phys. 156, 191103 (2022)

https://doi.org/10.1063/5.0089420

Published: May 2022

View article titled, Combined contributions of carotenoids and chlorophylls in two-photon spectra of photosynthetic pigment–protein complexes—A new way to quantify carotenoid dark state to chlorophyll energy transfer?

Journal Articles

Ultrafast excitation quenching by the oxidized photosystem II reaction center

Parveen Akhtar, Gábor Sipka, Wenhui Han, Xingyue Li, Guangye Han, Jian-Ren Shen, Győző Garab, Howe-Siang Tan, Petar H. Lambrev

J. Chem. Phys. 156, 145101 (2022)

https://doi.org/10.1063/5.0086046

Published: April 2022

View article titled, Ultrafast excitation quenching by the oxidized photosystem II reaction center

Includes: Supplementary data

Journal Articles

Two-dimensional electronic spectroscopy of the Q_x to Q_y relaxation of chlorophylls a in photosystem II core complex

Thanh Nhut Do, Hoang Long Nguyen, Stefano Caffarri, Howe-Siang Tan

J. Chem. Phys. 156, 145102 (2022)

https://doi.org/10.1063/5.0079500

Published: April 2022

View article titled, Two-dimensional electronic spectroscopy of the Qx to Qy relaxation of chlorophylls a in photosystem II core complex

Journal Articles

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Willmor J. Peña Ccoa, Glen M. Hocky

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

Includes: Supplementary data

Journal Articles

Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded–double-stranded DNA junctions by 2D fluorescence spectroscopy

Dylan Heussman, Justin Kittell, Peter H. von Hippel, Andrew H. Marcus

J. Chem. Phys. 156, 045101 (2022)

https://doi.org/10.1063/5.0076261

Published: January 2022

View article titled, Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded–double-stranded DNA junctions by 2D fluorescence spectroscopy

Includes: Supplementary data

Journal Articles

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

Marcelo C. R. Melo, Rafael C. Bernardi, Cesar de la Fuente-Nunez, Zaida Luthey-Schulten

J. Chem. Phys. 153, 134104 (2020)

https://doi.org/10.1063/5.0018980

Published: October 2020

View article titled, Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

Includes: Supplementary data

Journal Articles

SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations

Tsung-Jen Liao, Hyunbum Jang, David Fushman, Ruth Nussinov

J. Chem. Phys. 153, 045106 (2020)

https://doi.org/10.1063/5.0013926

Published: July 2020

View article titled, SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations

Includes: Supplementary data

Journal Articles

Bayesian counting of photobleaching steps with physical priors

Jon Garry, Yuchong Li, Brandon Shew, Claudiu C. Gradinaru, Andrew D. Rutenberg

J. Chem. Phys. 152, 024110 (2020)

https://doi.org/10.1063/1.5132957

Published: January 2020

View article titled, Bayesian counting of photobleaching steps with physical priors

Includes: Supplementary data

Journal Articles

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure

Kei Terayama, Ai Shinobu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao

J. Chem. Phys. 151, 215104 (2019)

https://doi.org/10.1063/1.5129551

Published: December 2019

View article titled, evERdock BAI: Machine-learning-guided selection of protein-protein complex structure

Includes: Supplementary data

Journal Articles

Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2

Ingo Schelter, Johannes M. Foerster, Alastair T. Gardiner, Aleksander W. Roszak, Richard J. Cogdell, G. Matthias Ullmann, Thiago Branquinho de Queiroz, Stephan Kümmel

J. Chem. Phys. 151, 134114 (2019)

https://doi.org/10.1063/1.5116779

Published: October 2019

View article titled, Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2

Includes: Supplementary data

Journal Articles

Target search on DNA by interacting molecules: First-passage approach

Jaeoh Shin, Anatoly B. Kolomeisky

J. Chem. Phys. 151, 125101 (2019)

https://doi.org/10.1063/1.5123988

Published: September 2019

View article titled, Target search on DNA by interacting molecules: First-passage approach

Journal Articles

Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning

Ashley Z. Guo, Joshua Lequieu, Juan J. de Pablo

J. Chem. Phys. 150, 054902 (2019)

https://doi.org/10.1063/1.5063851

Published: February 2019

View article titled, Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning

Journal Articles

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao

J. Chem. Phys. 149, 195101 (2018)

https://doi.org/10.1063/1.5055799

Published: November 2018

View article titled, Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

Includes: Supplementary data

Journal Articles

Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations

Dominik Sidler, Simon Frasch, Michael Cristòfol-Clough, Sereina Riniker

J. Chem. Phys. 148, 234105 (2018)

https://doi.org/10.1063/1.5007132

Published: June 2018

View article titled, Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations

Includes: Supplementary data

NARROW

Topics

Modeling of fluence-dependent hole-burned spectra and hole-growth kinetics using multiple two-level system model

Inhibition mechanism of testis-expressed gene 14 (TEX14) in cytokinetic abscission: Well-tempered metadynamics simulation studies

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

Emergence of allostery through reorganization of protein residue network architecture

Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface

Structure-based model of fucoxanthin–chlorophyll protein complex: Calculations of chlorophyll electronic couplings

Combined contributions of carotenoids and chlorophylls in two-photon spectra of photosynthetic pigment–protein complexes—A new way to quantify carotenoid dark state to chlorophyll energy transfer?

Ultrafast excitation quenching by the oxidized photosystem II reaction center

Two-dimensional electronic spectroscopy of the Q_x to Q_y relaxation of chlorophylls a in photosystem II core complex

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded–double-stranded DNA junctions by 2D fluorescence spectroscopy

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations

Bayesian counting of photobleaching steps with physical priors

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure

Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2

Target search on DNA by interacting molecules: First-passage approach

Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations

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