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

Evgen Pavlov*, Makoto Taiji, Arturs Scukins, Anton Markesteijn, Sergey Karabasov, Dmitry Nerukh

*Corresponding author for this work

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)285-302
Number of pages18
JournalFaraday Discussions
Volume169
Early online date31 Jan 2014
DOIs
Publication statusPublished - 2014

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Molecular dynamics
Hydrodynamics
hydrodynamics
molecular dynamics
Atoms
continuums
atoms
Computer hardware
hardware
Feedback
Computer simulation
simulation

Bibliographical note

Funding: 8 Research Councils Initiative on Multilateral Research Funding (Engineering and Physical Sciences Research Council Grant No. EP/J004308/1)

Cite this

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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.",
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Visualising and controlling the flow in biomolecular systems at and between multiple scales : from atoms to hydrodynamics at different locations in time and space. / Pavlov, Evgen; Taiji, Makoto; Scukins, Arturs; Markesteijn, Anton; Karabasov, Sergey; Nerukh, Dmitry.

In: Faraday Discussions, Vol. 169, 2014, p. 285-302.

Research output: Contribution to journalArticle

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AU - Pavlov, Evgen

AU - Taiji, Makoto

AU - Scukins, Arturs

AU - Markesteijn, Anton

AU - Karabasov, Sergey

AU - Nerukh, Dmitry

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