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.

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Divisions: College of Engineering & Physical Sciences > Systems analytics research institute (SARI)
Additional Information: © 2016, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Funding: EPSRC (EP/J004308/1); Royal Society of London; Royal Society of Chemistry; Royal Academy of Engineering; and Leverhulme Trust.
Uncontrolled Keywords: hybrid atomistic/continuum,multiscale,molecular dynamics,fluctuating hydrodynamics,dialanine,all-atom whole virus simulation,capsid,PCV2
Publication ISSN: 1877-7511
Last Modified: 24 Apr 2024 07:12
Date Deposited: 31 Mar 2016 14:40
PURE Output Type: Article
Published Date: 2016-11
Published Online Date: 2016-03-24
Accepted Date: 2016-03-21
Submitted Date: 2015-11-29
Authors: Korotkin, Ivan
Nerukh, Dmitry (ORCID Profile 0000-0001-9005-9919)
Tarasova, Elvira
Farafonov, Vladimir
Karabasov, Sergey

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