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Journal Articles

The synergy between compartmentalization and motorization in chromatin architecture

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Ronaldo J. Oliveira, Antonio B. Oliveira Junior, Vinícius G. Contessoto, José N. Onuchic
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 114116 (2025)
https://doi.org/10.1063/5.0239634
Published: March 2025
View articletitled, The synergy between compartmentalization and motorization in chromatin architecture
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Journal Articles

Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers

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Zilong Li, Stephanie Portillo-Ledesma, Moshe Janani, Tamar Schlick
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 094107 (2025)
https://doi.org/10.1063/5.0242199
Published: March 2025
View articletitled, Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers
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Journal Articles

Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function

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Shingo Tsukamoto, Mohammad R. K. Mofrad
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 054122 (2025)
https://doi.org/10.1063/5.0232328
Published: February 2025
View articletitled, Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function
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Journal Articles

Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells

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Loucif Remini, Midas Segers, Andrea Parmeggiani, Enrico Carlon
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 054110 (2025)
https://doi.org/10.1063/5.0236067
Published: February 2025
View articletitled, Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells
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Journal Articles

Thermodynamics of nucleosome breathing and positioning

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Kharerin Hungyo, Benjamin Audit, Cédric Vaillant, Alexandre V. Morozov
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 025101 (2025)
https://doi.org/10.1063/5.0245457
Published: January 2025
View articletitled, Thermodynamics of nucleosome breathing and positioning
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Journal Articles

Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics

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Andrea Fontana, Simona Bianco, Fabrizio Tafuri, Andrea Esposito, Alex Abraham, Mattia Conte, Francesca Vercellone, Florinda Di Pierno, Sumanta Kundu, Sougata Guha, Ciro Di Carluccio, Antonella Prisco, Mario Nicodemi, Andrea M. Chiariello
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 014903 (2025)
https://doi.org/10.1063/5.0243454
Published: January 2025
View articletitled, Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics
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Journal Articles

Deciphering single-cell 3D chromatin structure using scCTG

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Ran Jiang, Yue Xue, Yanyi Huang, Yi Qin Gao
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 245101 (2024)
https://doi.org/10.1063/5.0241334
Published: December 2024
View articletitled, Deciphering single-cell 3D chromatin structure using scCTG
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Journal Articles

Extrinsic fluctuations in the p53 cycle

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Manuel Eduardo Hernández-García, Mariana Gómez-Schiavon, Jorge Velázquez-Castro
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 184103 (2024)
https://doi.org/10.1063/5.0227728
Published: November 2024
View articletitled, Extrinsic fluctuations in the p53 cycle
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Journal Articles

Predicting p53-dependent cell transitions from thermodynamic models

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Pankaj Gautam, Isabella Ciuta, Vladimir B. Teif, Sudipta Kumar Sinha
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 135101 (2024)
https://doi.org/10.1063/5.0225166
Published: October 2024
View articletitled, Predicting p53-dependent cell transitions from thermodynamic models
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Journal Articles

Heat capacity changes associated with G-quadruplex unfolding

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Arees Garabet, Lutan Liu, Tigran V. Chalikian
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 055101 (2023)
https://doi.org/10.1063/5.0157749
Published: August 2023
View articletitled, Heat capacity changes associated with G-quadruplex unfolding
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Includes: Supplementary data
Journal Articles

Dynamics of single-base editing: Theoretical analysis

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Vardan Hoviki Vardanyan, Qian Wang, Anatoly B. Kolomeisky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 245101 (2023)
https://doi.org/10.1063/5.0157193
Published: June 2023
View articletitled, Dynamics of single-base editing: Theoretical analysis
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Journal Articles

Derivable genetic programming for two-dimensional colloidal materials

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Nathan A. Mahynski, Bliss Han, Daniel Markiewitz, Vincent K. Shen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 114112 (2022)
https://doi.org/10.1063/5.0106131
Published: September 2022
View articletitled, Derivable genetic programming for two-dimensional colloidal materials
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Includes: Supplementary data
Journal Articles

How capture affects polymer translocation in a solitary nanopore

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Swarnadeep Seth, Aniket Bhattacharya
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 244902 (2022)
https://doi.org/10.1063/5.0094221
Published: June 2022
View articletitled, How capture affects polymer translocation in a solitary nanopore
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Includes: Supplementary data
Journal Articles

Multiscale modeling of genome organization with maximum entropy optimization

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Xingcheng Lin, Yifeng Qi, Andrew P. Latham, Bin Zhang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 010901 (2021)
https://doi.org/10.1063/5.0044150
Published: July 2021
View articletitled, Multiscale modeling of genome organization with maximum entropy optimization
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Journal Articles

Novel high voltage polymer insulators using computational and data-driven techniques

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Deepak Kamal, Huan Tran, Chiho Kim, Yifei Wang, Lihua Chen, Yang Cao, V. Roshan Joseph, Rampi Ramprasad
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 174906 (2021)
https://doi.org/10.1063/5.0044306
Published: May 2021
View articletitled, Novel high voltage polymer insulators using computational and data-driven techniques
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Includes: Supplementary data
Journal Articles

Deep learning for nanopore ionic current blockades

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Ángel Díaz Carral, Magnus Ostertag, Maria Fyta
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 044111 (2021)
https://doi.org/10.1063/5.0037938
Published: January 2021
View articletitled, Deep learning for nanopore ionic current blockades
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Journal Articles

The effect of obstacles in multi-site protein target search with DNA looping

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Cayke Felipe, Jaeoh Shin, Yulia Loginova, Anatoly B. Kolomeisky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 025101 (2020)
https://doi.org/10.1063/1.5135917
Published: January 2020
View articletitled, The effect of obstacles in multi-site protein target search with DNA looping
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Journal Articles

1CPN: A coarse-grained multi-scale model of chromatin

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Joshua Lequieu, Andrés Córdoba, Joshua Moller, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 215102 (2019)
https://doi.org/10.1063/1.5092976
Published: June 2019
View articletitled, 1CPN: A coarse-grained multi-scale model of chromatin
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Includes: Supplementary data
Journal Articles

Erratum: “Measuring the wall depletion length of nanoconfined DNA” [J. Chem. Phys. 149, 104901 (2018)]

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Aditya Bikram Bhandari, Jeffrey G. Reifenberger, Hui-Min Chuang, Han Cao, Kevin D. Dorfman
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 219901 (2019)
https://doi.org/10.1063/1.5108718
Published: June 2019
View articletitled, Erratum: “Measuring the wall depletion length of nanoconfined DNA” [J. Chem. Phys. 149, 104901 (2018)]
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Journal Articles

wACSF—Weighted atom-centered symmetry functions as descriptors in machine learning potentials

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M. Gastegger, L. Schwiedrzik, M. Bittermann, F. Berzsenyi, P. Marquetand
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 241709 (2018)
https://doi.org/10.1063/1.5019667
Published: March 2018
View articletitled, wACSF—Weighted atom-centered symmetry functions as descriptors in machine learning potentials
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Includes: Supplementary data