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

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

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.

All-atom whole virus simulation, Capsid, Dialanine, Fluctuating hydrodynamics, Hybrid atomistic/continuum, Molecular dynamics, Multiscale, PCV2
1877-7503
446-456
Korotkin, Ivan
1ca96363-075e-41d9-a0c1-153c8c0cc31a
Nerukh, Dmitry
75d91f2c-d211-469d-b13b-d0fc7fe2b219
Tarasova, Elvira
41aef7af-8878-4340-b7b7-398f3536e7fe
Farafonov, Vladimir
207a6c3e-4af2-4f1e-8a8c-7db7dc00ed17
Karabasov, Sergey
39acae29-1474-4567-a51c-af177ad0fe72
Korotkin, Ivan
1ca96363-075e-41d9-a0c1-153c8c0cc31a
Nerukh, Dmitry
75d91f2c-d211-469d-b13b-d0fc7fe2b219
Tarasova, Elvira
41aef7af-8878-4340-b7b7-398f3536e7fe
Farafonov, Vladimir
207a6c3e-4af2-4f1e-8a8c-7db7dc00ed17
Karabasov, Sergey
39acae29-1474-4567-a51c-af177ad0fe72

Korotkin, Ivan, Nerukh, Dmitry, Tarasova, Elvira, Farafonov, Vladimir and Karabasov, Sergey (2016) Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution. Journal of Computational Science, 17, 446-456. (doi:10.1016/j.jocs.2016.03.012).

Record type: Article

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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More information

Published date: 1 November 2016
Additional Information: Funding Information: Sergey Karabasov is a Reader in Computational Modelling in Queen Mary University of London, School of Engineering and Materials Science (SEMS). Prior to joining SEMS as a Senior Lecturer in 2012, SK was a Royal Society University Research Fellow in Cambridge University Engineering Department. His research is devoted to high-resolution and multiscale modelling in computational aero and hydrodynamics. Over the years, his research has been supported by the leading UK industry as well as UK Research Councils and the Royal Society of London. Internationally, his research into multiscale modelling methods for sound generated by jet turbulence in collaboration with Ohio Aerospace Institute was supported by Aero Acoustics Research Consortium (AARC). He was an organiser of the Royal Society Scientific Seminars in 2011, 2013 and a guest editor of the Royal Society PhilTrans A special issue “Multiscale systems in fluids and soft matter: approaches, numerics, and applications” in 2014. Funding Information: Dr Korotkin is a Senior Research Fellow at Moscow Institute for Nuclear Safety and also in the Laboratory of Industrial Mathematics at Lomonosov Moscow State University. He has been studying and working in top Russian institutions (Moscow Institute of Physics and Technology, the alma mater of the two recent Nobel Prize laureates in physics, and Moscow State University) as well as in Queen Mary University of London. His work has been recognised by several prestigious awards in Russia, e.g. the medal of Russian Academy of Sciences for the best scientific publication among students (2003), the Moscow Government award for scientific research (2005), the “New Generation” Contest award by RAO UES Russia (2007) and, internationally, by a CRDF Grant Assistance Program of Department of Energy, USA. Funding Information: The work has been supported by Engineering and Physical Sciences Research Council (EP/J004308/1) in the framework of the G8 Research Councils Initiative on Multilateral Research Funding. SK is grateful to the Royal Society of London for their support. DN thanks the Royal Society of Chemistry for the JWT fellowship and Royal Academy of Engineering and Leverhulme Trust for Senior Research Fellowship. The supporting data of this study are stored at the University of Aston. Details of how to request access to these data are provided in the documentation available from the University of Aston research data repository at http://doi.org/10.17036/de4b474e-0497-4aa4-9676-439644b1eb48 . Publisher Copyright: © 2016 Elsevier B.V. Copyright: Copyright 2016 Elsevier B.V., All rights reserved.
Keywords: All-atom whole virus simulation, Capsid, Dialanine, Fluctuating hydrodynamics, Hybrid atomistic/continuum, Molecular dynamics, Multiscale, PCV2

Identifiers

Local EPrints ID: 457494
URI: http://eprints.soton.ac.uk/id/eprint/457494
ISSN: 1877-7503
PURE UUID: baa8de9f-ef42-4149-b168-1c36d0f2936f
ORCID for Ivan Korotkin: ORCID iD orcid.org/0000-0002-5023-3684

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Date deposited: 09 Jun 2022 17:05
Last modified: 18 Mar 2024 03:50

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Contributors

Author: Ivan Korotkin ORCID iD
Author: Dmitry Nerukh
Author: Elvira Tarasova
Author: Vladimir Farafonov
Author: Sergey Karabasov

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