A COUPLED MOLECULAR-CONTINUUM HYBRID MODEL FOR THE SIMULATION OF MACROMOLECULAR DYNAMICS

Giovanni Giupponi (), Gianni de Fabritiis () and Peter V. Coveney ()
Additional contact information
Giovanni Giupponi: Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon street, London WC1H 0AJ, UK
Gianni de Fabritiis: Computational Biochemistry and Biophysics Lab (GRIB-IMIM/UPF), Barcelona Biomedical Research Park, C/Doctor Aiguader 88, 08003 Barcelona, Spain
Peter V. Coveney: Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon street, London WC1H 0AJ, UK

International Journal of Modern Physics C (IJMPC), 2007, vol. 18, issue 04, 520-527

Abstract: We describe a hybrid simulation method that captures the combined effects of molecular and hydrodynamic forces which influence macromolecules in solution. In this method, the solvent contribution is accounted for implicitly as the Navier-Stokes equations are solved on a grid using a finite volume method, while we use coarse-grained molecular dynamics to describe the macromolecule. The two systems are coupled by a dissipative Stokesian force. We show that our method correctly captures the hydrodynamically enhanced self-diffusion of a single monomer for different fluids and grid sizes. Moreover, the monomer diffusion does not depend on the monomer mass for the mass range used, as postulated by polymer dynamics theories. We also show that the dynamical properties of the chain do not depend on the grid sizeawhen the chain radius of gyrationRg≫ a.

Keywords: Macromolecular dynamics; simulation; hybrid coupled models; 61.25.Hq; 61.82.Pv (search for similar items in EconPapers)
Date: 2007
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.worldscientific.com/doi/abs/10.1142/S0129183107010759
Access to full text is restricted to subscribers

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:wsi:ijmpcx:v:18:y:2007:i:04:n:s0129183107010759

Ordering information: This journal article can be ordered from

DOI: 10.1142/S0129183107010759

Access Statistics for this article

International Journal of Modern Physics C (IJMPC) is currently edited by H. J. Herrmann

More articles in International Journal of Modern Physics C (IJMPC) from World Scientific Publishing Co. Pte. Ltd.
Bibliographic data for series maintained by Tai Tone Lim ().