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

Korotkin, Ivan, Karabasov, Sergey, Nerukh, Dmitry, Markesteijn, Anton, Scukins, Arturs, Farafonov, Vladimir and Pavlov, Evgen (2015). A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time. Journal of Chemical Physics, 143 (1),

Abstract

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.

Publication DOI: https://doi.org/10.1063/1.4923011
Divisions: Engineering & Applied Sciences > Systems analytics research institute (SARI)
Engineering & Applied Sciences > Mathematics
Additional Information: © 2015 AIP Publishing LLC Funding: EPSRC (No. EP/J004308/1) in the framework of the G8 Research Councils Initiative on Multilateral Research Funding.
Uncontrolled Keywords: Physics and Astronomy(all),Physical and Theoretical Chemistry
Full Text Link: http://scitation.aip.org/content/aip/journal/jcp/143/1/10.1063/1.4923011
Related URLs: http://www.scopus.com/inward/record.url?scp=84936876921&partnerID=8YFLogxK (Scopus URL)
Published Date: 2015
Authors: Korotkin, Ivan
Karabasov, Sergey
Nerukh, Dmitry ( 0000-0001-9005-9919)
Markesteijn, Anton
Scukins, Arturs
Farafonov, Vladimir
Pavlov, Evgen

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Version: Accepted Version


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