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Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Biophysical journal, 2015-03, Vol.108 (5), p.1153-1164

2015

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Partially Assembled Nucleosome Structures at Atomic Detail

Biophysical journal, 2017-02, Vol.112 (3), p.460-472

2017

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The Role of Correlation and Solvation in Ion Interactions with B-DNA

Biophysical journal, 2016-01, Vol.110 (2), p.315-326

2016

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Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Biophysical journal, 2010-09, Vol.99 (5), p.1577-1585

2010

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Spermine Condenses DNA, but Not RNA Duplexes

Biophysical journal, 2017-01, Vol.112 (1), p.22-30

2017

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Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei

Biophysical journal, 2023-02, Vol.122 (3), p.69a-69a

2023

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Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

Biophysical journal, 2010-03, Vol.98 (5), p.872-880

2010

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The Curious Case of Strongly Bent DNA

Biophysical journal, 2020-02, Vol.118 (3), p.377a-377a

Onufriev, Alexey V.

2020

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Modulation of the DNA Accessibility in the Nucleosome -- Insights from Physics Models

Biophysical journal, 2019-02, Vol.116 (3), p.71

Onufriev, Alexey V.

2019

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Stretching of long double-stranded DNA and RNA described by the same model

Biophysical journal, 2022-02, Vol.121 (3), p.65a-65a

2022

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From Small to Large to Very Large: Modeling of Biomolecular Structures in Implicit Solvent

Biophysical journal, 2015-01, Vol.108 (2), p.208a-208a

Onufriev, Alexey V.

2015

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3D architecture of Drosophila interphase chromatin is stabilized by relatively strong attractive interactions between highly-dynamic lamina-associated domains and nuclear envelope

Biophysical journal, 2022-02, Vol.121 (3), p.362a-362a

2022

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Proximity of chromatin to the nuclear envelope, does not, by itself, affect gene expression in drosophila

Biophysical journal, 2022-02, Vol.121 (3), p.160a-160a

2022

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Single-cell Hi-C: how modeling can augment experiment?

Biophysical journal, 2022-02, Vol.121 (3), p.362a-362a

2022

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The Effect of Nuclear Envelope on Chromatin Architecture in Drosophila Melanogaster: Modeling of Three-Dimensional Interphase Chromosome Organization

Biophysical journal, 2020-02, Vol.118 (3), p.551a-551a

2020

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Insights from All-Atom Molecular Dynamics Simulations of 40 Nucleosome Chromatin Fiber

Biophysical journal, 2015-01, Vol.108 (2), p.319a-319a

2015

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Chromosome-Nuclear Envelope Interactions Have Multiple Effects on Chromosome Folding Dynamics in Simulation

Biophysical journal, 2015-01, Vol.108 (2), p.537a-537a

2015

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Molecular Dynamics Study of Cobalt(III) Hexammine Counter-Ion Distributions around B-DNA and A-RNA Duplexes

Biophysical journal, 2013-01, Vol.104 (2), p.423a-423a

2013

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Nucleosome Stability is Controlled by the Charge of its Globular Core: Implications for the Biological Function

Biophysical journal, 2014-01, Vol.106 (2), p.75a-75a

2014

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A Model of Nuclear Organization Demonstrates the Effect of Nuclear Envelope - Chromosome Contacts on 3D Organization of Chromosomes

Biophysical journal, 2013-01, Vol.104 (2), p.551a-551a

2013

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Condensation of Nucleic Acids by Multivalent Ions: Sequence Dependence and the Curious Case of RNA

Biophysical journal, 2016-02, Vol.110 (3), p.409a-409a

2016

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The Role of Correlation and Solvation in Ion Interactions with B-DNA

Biophysical journal, 2016-01, Vol.110 (2)

2016

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Introducing Charge Hydration Asymmetry in the Realm of Continuum Solvation

Biophysical journal, 2013-01, Vol.104 (2), p.35a-35a

2013

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Statistics and Physical Origins of pK and Ionization State Changes Upon Protein-Ligand Binding

Biophysical journal, 2010-01, Vol.98 (3), p.429a-429a

2010

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Estimating Persistence Length of DNA from Molecular Dynamics Simulations

Biophysical journal, 2015-01, Vol.108 (2), p.233a-233a

2015

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Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Partially Assembled Nucleosome Structures at Atomic Detail

The Role of Correlation and Solvation in Ion Interactions with B-DNA

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

Spermine Condenses DNA, but Not RNA Duplexes

Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

The Curious Case of Strongly Bent DNA

Modulation of the DNA Accessibility in the Nucleosome -- Insights from Physics Models

Stretching of long double-stranded DNA and RNA described by the same model

From Small to Large to Very Large: Modeling of Biomolecular Structures in Implicit Solvent

3D architecture of Drosophila interphase chromatin is stabilized by relatively strong attractive interactions between highly-dynamic lamina-associated domains and nuclear envelope

Proximity of chromatin to the nuclear envelope, does not, by itself, affect gene expression in drosophila

Single-cell Hi-C: how modeling can augment experiment?

The Effect of Nuclear Envelope on Chromatin Architecture in Drosophila Melanogaster: Modeling of Three-Dimensional Interphase Chromosome Organization

Insights from All-Atom Molecular Dynamics Simulations of 40 Nucleosome Chromatin Fiber

Chromosome-Nuclear Envelope Interactions Have Multiple Effects on Chromosome Folding Dynamics in Simulation

Molecular Dynamics Study of Cobalt(III) Hexammine Counter-Ion Distributions around B-DNA and A-RNA Duplexes

Nucleosome Stability is Controlled by the Charge of its Globular Core: Implications for the Biological Function

A Model of Nuclear Organization Demonstrates the Effect of Nuclear Envelope - Chromosome Contacts on 3D Organization of Chromosomes

Condensation of Nucleic Acids by Multivalent Ions: Sequence Dependence and the Curious Case of RNA

The Role of Correlation and Solvation in Ion Interactions with B-DNA

Introducing Charge Hydration Asymmetry in the Realm of Continuum Solvation

Statistics and Physical Origins of pK and Ionization State Changes Upon Protein-Ligand Binding

Estimating Persistence Length of DNA from Molecular Dynamics Simulations

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