title: An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations.
abstract: In the Ermak-McCammon algorithm for Brownian dynamics, the hydrodynamic interactions (HIs) between N spherical particles are described by a 3Nx3N diffusion tensor. This tensor has to be factorized at each time step with a runtime of O(N(3)), making the calculation of the correlated random displacements the bottleneck for many-particle simulations. Here we present a faster algorithm for this step, which is based on a truncated expansion of the hydrodynamic multiparticle correlations as two-body contributions. The comparison to the exact algorithm and to the Chebyshev approximation of Fixman verifies that for bead-spring polymers this approximation yields about 95% of the hydrodynamic correlations at an improved runtime scaling of O(N(2)) and a reduced memory footprint. The approximation is independent of the actual form of the hydrodynamic tensor and can be applied to arbitrary particle configurations. This now allows to include HI into large many-particle Brownian dynamics simulations, where until now the runtime scaling of the correlated random motion was prohibitive.
authors.affiliation: Zentrum fur Bioinformatik, Universitat des Saarlandes, D-66123 Saarbrucken, Germany. tihamer.geyer@bioinformatik.uni-saarland.de
authors.forename: Tihamér
authors.initials: T
authors.lastname: Geyer
authors.forename: Uwe
authors.initials: U
authors.lastname: Winter