Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution

Ivan Korotkin; Dmitry Nerukh; Elvira Tarasova; Vladimir Farafonov; Sergey Karabasov

doi:10.1016/j.jocs.2016.03.012

Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution

Ivan Korotkin, Dmitry Nerukh, Elvira Tarasova, Vladimir Farafonov, Sergey Karabasov

Research output: Contribution to journal › Article › peer-review

Abstract

A hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework based on the analogy with two-phase hydrodynamics has been extended to dynamically tracking the feature of interest at all-atom resolution. In the model, the hydrodynamics description is used as an effective boundary condition to close the molecular dynamics solution without resorting to standard periodic boundary conditions. The approach is implemented in a popular Molecular Dynamics package GROMACS and results for two biomolecular systems are reported. A small peptide dialanine and a complete capsid of a virus porcine circovirus 2 in water are considered and shown to reproduce the structural and dynamic properties compared to those obtained in theory, purely atomistic simulations, and experiment.

Original language	English
Pages (from-to)	446-456
Number of pages	11
Journal	Journal of Computational Science
Volume	17
Issue number	part 2
Early online date	24 Mar 2016
DOIs	https://doi.org/10.1016/j.jocs.2016.03.012
Publication status	Published - Nov 2016

Bibliographical note

© 2016, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/

Funding: EPSRC (EP/J004308/1); Royal Society of London; Royal Society of Chemistry; Royal Academy of Engineering; and Leverhulme Trust.

Keywords

hybrid atomistic/continuum
multiscale
molecular dynamics
fluctuating hydrodynamics
dialanine
all-atom whole virus simulation
capsid
PCV2

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10.1016/j.jocs.2016.03.012

Modelling liquids at atomistic resolution
© 2016, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/
Accepted author manuscript, 381 KBLicence: CC BY-NC-ND 3.0

Cite this

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title = "Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution",

abstract = "A hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework based on the analogy with two-phase hydrodynamics has been extended to dynamically tracking the feature of interest at all-atom resolution. In the model, the hydrodynamics description is used as an effective boundary condition to close the molecular dynamics solution without resorting to standard periodic boundary conditions. The approach is implemented in a popular Molecular Dynamics package GROMACS and results for two biomolecular systems are reported. A small peptide dialanine and a complete capsid of a virus porcine circovirus 2 in water are considered and shown to reproduce the structural and dynamic properties compared to those obtained in theory, purely atomistic simulations, and experiment.",

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doi = "10.1016/j.jocs.2016.03.012",

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AU - Korotkin, Ivan

AU - Nerukh, Dmitry

AU - Tarasova, Elvira

AU - Farafonov, Vladimir

AU - Karabasov, Sergey

N1 - © 2016, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ Funding: EPSRC (EP/J004308/1); Royal Society of London; Royal Society of Chemistry; Royal Academy of Engineering; and Leverhulme Trust.

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N2 - A hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework based on the analogy with two-phase hydrodynamics has been extended to dynamically tracking the feature of interest at all-atom resolution. In the model, the hydrodynamics description is used as an effective boundary condition to close the molecular dynamics solution without resorting to standard periodic boundary conditions. The approach is implemented in a popular Molecular Dynamics package GROMACS and results for two biomolecular systems are reported. A small peptide dialanine and a complete capsid of a virus porcine circovirus 2 in water are considered and shown to reproduce the structural and dynamic properties compared to those obtained in theory, purely atomistic simulations, and experiment.

AB - A hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework based on the analogy with two-phase hydrodynamics has been extended to dynamically tracking the feature of interest at all-atom resolution. In the model, the hydrodynamics description is used as an effective boundary condition to close the molecular dynamics solution without resorting to standard periodic boundary conditions. The approach is implemented in a popular Molecular Dynamics package GROMACS and results for two biomolecular systems are reported. A small peptide dialanine and a complete capsid of a virus porcine circovirus 2 in water are considered and shown to reproduce the structural and dynamic properties compared to those obtained in theory, purely atomistic simulations, and experiment.

KW - hybrid atomistic/continuum

KW - multiscale

KW - molecular dynamics

KW - fluctuating hydrodynamics

KW - dialanine

KW - all-atom whole virus simulation

KW - capsid

KW - PCV2

UR - http://doi.org/10.17036/de4b474e-0497-4aa4-9676-439644b1eb48

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DO - 10.1016/j.jocs.2016.03.012

M3 - Article

SN - 1877-7503

VL - 17

SP - 446

EP - 456

JO - Journal of Computational Science

JF - Journal of Computational Science

IS - part 2

ER -

Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution

Abstract

Bibliographical note

Keywords

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