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Journal Articles

Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations

Phuong H. Nguyen, Philippe Derreumaux
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 235101 (2023)
https://doi.org/10.1063/5.0149419
Published: June 2023
View article titled, Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations
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Journal Articles

On the allosteric puzzle and pocket crosstalk through computational means

Riccardo Aguti, Mattia Bernetti, Stefano Bosio, Sergio Decherchi, Andrea Cavalli
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 165101 (2023)
https://doi.org/10.1063/5.0145364
Published: April 2023
View article titled, On the allosteric puzzle and pocket crosstalk through computational means
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Includes: Supplementary data
Journal Articles

Fast conformational clustering of extensive molecular dynamics simulation data

Simon Hunkler, Kay Diederichs, Oleksandra Kukharenko, Christine Peter
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 144109 (2023)
https://doi.org/10.1063/5.0142797
Published: April 2023
View article titled, Fast conformational clustering of extensive molecular dynamics simulation data
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Includes: Supplementary data
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

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

Hemoglycin visible fluorescence induced by x rays

M. W. McGeoch, R. L. Owen, S. Jaho, J. E. M. McGeoch
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 114901 (2023)
https://doi.org/10.1063/5.0143945
Published: March 2023
View article titled, Hemoglycin visible fluorescence induced by x rays
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Includes: Supplementary data
Journal Articles

How protein topology controls allosteric regulations

Juan Xie, Gaoxiang Pan, Yibo Li, Luhua Lai
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 105102 (2023)
https://doi.org/10.1063/5.0138279
Published: March 2023
View article titled, How protein topology controls allosteric regulations
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Includes: Supplementary data
Journal Articles

Determining the impact of gold nanoparticles on amyloid aggregation with 2D IR spectroscopy

Kayla A. Hess, Nathan J. Spear, Sophia A. Vogelsang, Janet E. Macdonald, Lauren E. Buchanan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 091101 (2023)
https://doi.org/10.1063/5.0136376
Published: March 2023
View article titled, Determining the impact of gold nanoparticles on amyloid aggregation with 2D IR spectroscopy
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Includes: Supplementary data
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

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Thomas J. Summers, Reza Hemmati, Justin E. Miller, Donatus A. Agbaglo, Qianyi Cheng, Nathan J. DeYonker
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 065101 (2023)
https://doi.org/10.1063/5.0127106
Published: February 2023
View article titled, Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase
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Includes: Supplementary data
Journal Articles

Simulation of two-dimensional infrared Raman spectroscopy with application to proteins

Carleen D. N. van Hengel, Kim E. van Adrichem, Thomas L. C. Jansen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 064106 (2023)
https://doi.org/10.1063/5.0138958
Published: February 2023
View article titled, Simulation of two-dimensional infrared Raman spectroscopy with application to proteins
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Journal Articles

Water dynamics around T vs R4 of hemoglobin from local hydrophobicity analysis

Seyedeh Maryam Salehi, Marco Pezzella, Adam Willard, Markus Meuwly, Martin Karplus
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 025101 (2023)
https://doi.org/10.1063/5.0129990
Published: January 2023
View article titled, Water dynamics around T<sub /> vs R<sub>4</sub> of hemoglobin from local hydrophobicity analysis
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Includes: Supplementary data
Journal Articles

Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials

Keerthi Krishnan, Hao Tian, Peng Tao, Gennady M. Verkhivker
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 245101 (2022)
https://doi.org/10.1063/5.0133826
Published: December 2022
View article titled, Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials
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Journal Articles

Optimization of non-equilibrium self-assembly protocols using Markov state models

Anthony Trubiano, Michael F. Hagan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 244901 (2022)
https://doi.org/10.1063/5.0130407
Published: December 2022
View article titled, Optimization of non-equilibrium self-assembly protocols using Markov state models
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Journal Articles

Essential collective dynamics analysis reveals nonlocal interactions of alpha-synuclein38-95 monomers with fibrillar seeds

Min Wu, Holger Wille, Maria Stepanova
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 235101 (2022)
https://doi.org/10.1063/5.0116032
Published: December 2022
View article titled, Essential collective dynamics analysis reveals nonlocal interactions of alpha-synuclein<sub>38-95</sub> monomers with fibrillar seeds
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Includes: Supplementary data
Journal Articles

Impact of A2T and D23N mutations on C99 homodimer conformations

Yan Lu, Freddie R. Salsbury, Jr., Philippe Derreumaux
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 085102 (2022)
https://doi.org/10.1063/5.0101622
Published: August 2022
View article titled, Impact of A2T and D23N mutations on C99 homodimer conformations
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Includes: Supplementary data
Journal Articles

Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood

Mao Oide, Yuji Sugita
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 075101 (2022)
https://doi.org/10.1063/5.0099094
Published: August 2022
View article titled, Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood
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Includes: Supplementary data
Journal Articles

Heteronuclear decoupling with rotor-synchronized phase-alternated cycles

Andrea Simion, Tobias Schubeis, Tanguy Le Marchand, Mihai Vasilescu, Guido Pintacuda, Anne Lesage, Claudiu Filip
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 014202 (2022)
https://doi.org/10.1063/5.0098135
Published: July 2022
View article titled, Heteronuclear decoupling with rotor-synchronized phase-alternated cycles
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Includes: Supplementary data
Journal Articles

Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Sukolsak Sakshuwong, Hayley Weir, Umberto Raucci, Todd J. Martínez
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 204801 (2022)
https://doi.org/10.1063/5.0090482
Published: May 2022
View article titled, Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry
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Includes: Supplementary data
Journal Articles

Reorganization free energy of copper proteins in solution, in vacuum, and on metal surfaces

Outi Vilhelmiina Kontkanen, Denys Biriukov, Zdenek Futera
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 175101 (2022)
https://doi.org/10.1063/5.0085141
Published: May 2022
View article titled, Reorganization free energy of copper proteins in solution, in vacuum, and on metal surfaces
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Includes: Supplementary data