Interfacing Brownian dynamics simulations.
Starting from the flux of particles in a Brownian dynamics simulation we derive boundary conditions, which allow us (i) to couple a Brownian dynamics calculation to a reservoir of particles of a given density, i.e., setting up constant density boundary conditions, and (ii) to build an interface between Brownian dynamics and a diffusional treatment of adjacent simulation volumes. With these algorithms it is sometimes possible to dramatically reduce the system size--and therefore the necessary resources--of multiparticle Brownian dynamics calculations. In this paper we give one-dimensional examples which illustrate potential applications and savings.
Geyer
T
T
Center for Bioinformatics, Saarland University, D-66041 Saarbrucken, Germany. tihamer.gyer@bioinformatik.uni-saarland.de
Gorba
C
C
Helms
V
V