Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space


A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Publication DOI:
Additional Information: Funding: 8 Research Councils Initiative on Multilateral Research Funding (Engineering and Physical Sciences Research Council Grant No. EP/J004308/1)
Uncontrolled Keywords: Physical and Theoretical Chemistry
Publication ISSN: 1364-5498
Last Modified: 23 Feb 2024 08:08
Date Deposited: 03 Jun 2015 09:00
Full Text Link: http://pubs.rsc ... 9H#!divAbstract
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
PURE Output Type: Article
Published Date: 2014-01-31
Authors: Pavlov, Evgen
Taiji, Makoto
Scukins, Arturs
Markesteijn, Anton
Karabasov, Sergey
Nerukh, Dmitry (ORCID Profile 0000-0001-9005-9919)



Version: Accepted Version

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