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Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome

Journal of chemical theory and computation, 2023-11, Vol.19 (21), p.7924-7933

2023

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The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model

Scientific reports, 2023-06, Vol.13 (1), p.9077-9077, Article 9077

2023

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Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes I: In Silico Implementation for Surfactant Micelles

The journal of physical chemistry. B, 2023-02, Vol.127 (4), p.1022-1030

2023

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Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes II: Insight from Atomistic Simulations of Micelles

The journal of physical chemistry. B, 2023-02, Vol.127 (4), p.1031-1038

2023

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Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices

Nature communications, 2020-03, Vol.11 (1), p.1182-1182, Article 1182

2020

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In Vitro and In Silico Investigation of Water-Soluble Fullerenol C60(OH)24: Bioactivity and Biocompatibility

The journal of physical chemistry. B, 2021-08, Vol.125 (32), p.9197-9212

2021

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Covalent conjugates based on nanodiamonds with doxorubicin and a cytostatic drug from the group of 1,3,5-triazines: Synthesis, biocompatibility and biological activity

Biochimica et biophysica acta. General subjects, 2023-09, Vol.1867 (9), p.130384-130384, Article 130384

2023

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Water–Peptide Dynamics during Conformational Transitions

The journal of physical chemistry letters, 2013-03, Vol.4 (5), p.815-819

2013

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Graphene Oxide of Extra High Oxidation: A Wafer for Loading Guest Molecules

The journal of physical chemistry letters, 2021-10, Vol.12 (41), p.10015-10024

2021

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Time-spatial drift of decelerating electromagnetic pulses

Optics express, 2013-07, Vol.21 (14), p.17366-17371

2013

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In search of an optimal acid-base indicator for examining surfactant micelles: Spectrophotometric studies and molecular dynamics simulations

Colloids and surfaces. A, Physicochemical and engineering aspects, 2019-03, Vol.565, p.97-107

2019

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A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

The Journal of chemical physics, 2015-07, Vol.143 (1), p.014110-014110

2015

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All-Atom Molecular Dynamics Simulations of Whole Viruses

The journal of physical chemistry letters, 2018-10, Vol.9 (19), p.5805-5809

2018

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Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density

Faraday discussions, 2022-11, Vol.24, p.152-167

2022

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Non-Markov state model of peptide dynamics

Journal of molecular liquids, 2012-12, Vol.176, p.65-70

Nerukh, Dmitry

2012

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Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface

The journal of physical chemistry. B, 2022-10, Vol.126 (41), p.8166-8176

2022

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Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation

Journal of biomolecular structure & dynamics, 2021-11, Vol.39 (16), p.5920-5939

2021

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Water dynamics and stability of major blood proteins at pre-denaturation stage

Atti della Accademia peloritana dei pericolanti. Classe I di scienze fis., mat. e naturali, 2019-01, Vol.97 (S2), p.A16

2019

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Alkali metal decorated BC3 monolayer as sensing material for warfare agents

Computational and theoretical chemistry, 2024-04, Vol.1234, Article 114531

2024

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Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Journal of molecular liquids, 2017-11, Vol.245, p.109-114

2017

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Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly

Physical chemistry chemical physics : PCCP, 2021-11, Vol.23 (43), p.24617-24626

2021

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All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid’s Stability

The journal of physical chemistry letters, 2017-02, Vol.8 (4), p.779-784

2017

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MS2 bacteriophage capsid studied using all-atom molecular dynamics

Interface focus, 2019-06, Vol.9 (3), p.20180081-20180081

2019

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Details of charge distribution in stable viral capsid

Journal of molecular liquids, 2018-09, Vol.265, p.585-591

2018

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Protein–Ligand Dissociation Rate Constant from All-Atom Simulation

The journal of physical chemistry letters, 2021-11, Vol.12 (43), p.10631-10636

2021

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Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome

The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model

Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes I: In Silico Implementation for Surfactant Micelles

Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes II: Insight from Atomistic Simulations of Micelles

Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices

In Vitro and In Silico Investigation of Water-Soluble Fullerenol C60(OH)24: Bioactivity and Biocompatibility

Covalent conjugates based on nanodiamonds with doxorubicin and a cytostatic drug from the group of 1,3,5-triazines: Synthesis, biocompatibility and biological activity

Water–Peptide Dynamics during Conformational Transitions

Graphene Oxide of Extra High Oxidation: A Wafer for Loading Guest Molecules

Time-spatial drift of decelerating electromagnetic pulses

In search of an optimal acid-base indicator for examining surfactant micelles: Spectrophotometric studies and molecular dynamics simulations

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

All-Atom Molecular Dynamics Simulations of Whole Viruses

Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density

Non-Markov state model of peptide dynamics

Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface

Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation

Water dynamics and stability of major blood proteins at pre-denaturation stage

Alkali metal decorated BC3 monolayer as sensing material for warfare agents

Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid’s Stability

MS2 bacteriophage capsid studied using all-atom molecular dynamics

Details of charge distribution in stable viral capsid

Protein–Ligand Dissociation Rate Constant from All-Atom Simulation

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