Pavlov, Evgen, Taiji, Makoto, Scukins, Arturs, Markesteijn, Anton, Karabasov, Sergey and Nerukh, Dmitry (2014). Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space. Faraday Discussions, 169 , pp. 285-302.
Abstract
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: | https://doi.org/10.1039/c3fd00159h |
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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: | 30 Sep 2024 10:33 |
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 ( 0000-0001-9005-9919) |