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

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.
Authors:
; ;  [1] ; ;  [2] ;  [3] ;  [2] ;  [4]
  1. The School of Engineering and Material Science, Queen Mary University of London, Mile End Road, E1 4NS London (United Kingdom)
  2. Institute of Systems Analytics, Aston University, Birmingham B4 7ET (United Kingdom)
  3. Department of Physical Chemistry, V. N. Karazin Kharkiv National University, Svobody Square 4, 61022 Kharkiv (Ukraine)
  4. (Ukraine)
Publication Date:
OSTI Identifier:
22490863
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 1; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; COMPARATIVE EVALUATIONS; CONSERVATION LAWS; DIFFUSION; HYBRIDIZATION; HYDRODYNAMICS; LIQUIDS; MOLECULAR DYNAMICS METHOD; PEPTIDES; SIMULATION; WATER