title: ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units.
abstract: ReaDDy is a modular particle simulation package combining off-lattice reaction kinetics with arbitrary particle interaction forces. Here we present a graphical processing unit implementation of ReaDDy that employs the fast multiplatform molecular dynamics package OpenMM. A speedup of up to two orders of magnitude is demonstrated, giving us access to timescales of multiple seconds on single graphical processing units. This opens up the possibility of simulating cellular signal transduction events while resolving all protein copies.
authors: Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany.
authors: Johann
authors: J
authors: Biedermann
authors: Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany.
authors: Alexander
authors: A
authors: Ullrich
authors: Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany.
authors: Johannes
authors: J
authors: Schöneberg
authors: Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany. Electronic address: frank.noe@fu-berlin.de.
authors: Frank
authors: F
authors: Noé
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D004058:Diffusion; D007700:Kinetics; D012984:Software; D013997:Time Factors
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