Jump to main content
Jump to site search
PLANNED MAINTENANCE Close the message box

Scheduled maintenance work on Wednesday 22nd May 2019 from 11:00 AM to 1:00 PM (GMT).

During this time our website performance may be temporarily affected. We apologise for any inconvenience this might cause and thank you for your patience.


Volume 169, 2014
Previous Article Next Article

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

Author affiliations

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.

Back to tab navigation

Publication details

The article was received on 24 Dec 2013, accepted on 31 Jan 2014 and first published on 31 Jan 2014


Article type: Paper
DOI: 10.1039/C3FD00159H
Author version
available:
Download author version (PDF)
Faraday Discuss., 2014,169, 285-302

  •   Request permissions

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

    E. Pavlov, M. Taiji, A. Scukins, A. Markesteijn, S. Karabasov and D. Nerukh, Faraday Discuss., 2014, 169, 285
    DOI: 10.1039/C3FD00159H

Search articles by author

Spotlight

Advertisements