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

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 (part 2), pp. 446-456.

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.

Publication DOI: https://doi.org/10.1016/j.jocs.2016.03.012
Dataset DOI: https://doi.org/10.17036/de4b474e-0497-4aa4-9676-439644b1eb48
Divisions: Engineering & Applied Sciences > Non-linearity and complexity research group
Engineering & Applied Sciences > Mathematics
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Additional Information: © 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.
Uncontrolled Keywords: hybrid atomistic/continuum,multiscale,molecular dynamics,fluctuating hydrodynamics,dialanine,all-atom whole virus simulation,capsid,PCV2
Published Date: 2016-11
Authors: Korotkin, Ivan
Nerukh, Dmitry ( 0000-0001-9005-9919)
Tarasova, Elvira
Farafonov, Vladimir
Karabasov, Sergey

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