Simulation of
macromolecules dynamics: an implicit solvent method
Centre
for Computational Science, Department of Chemistry
When studying
the dynamics of macromolecules, solvent molecules are responsible of the long
range hydrodynamic interactions. Unfortunately, simulations of such systems
which explicitily include solvent particles, even if coarse grained, are often computationally unaffordable. We
use an implicit solvent
method, in which an hydrodynamics solver replaces the
solvent particles and is coupled to the macromolecular dynamics. In our model,
fluctuating hydrodynamic equations are solved by a recently developed finite-volume
method [1], which ensures thermodynamic consistency and readily allows
variations of temperature and viscosity of the fluid. Following Alhrics and Dunweg [2], a Stokesian term is responsible for the coupling of the
macromolecule to the fluid. In this paper, we present results of Zimm like dynamics for a polymer in good solvent and for
the collapse of a polymer in poor solvent.
References
[1] G. De Fabritiis, R. Delgado-Buscaglioni,
P.V. Coveney, Submitted (2006).
[2] P. Ahlrichs, B. Duenweg,J. Chem. Phys. 111 8225
(1999).