ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units

Johann Biedermann; Alexander Ullrich; Johannes Schöneberg; Frank Noé

doi:10.1016/j.bpj.2014.12.025

ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units

Biophys J. 2015 Feb 3;108(3):457-61. doi: 10.1016/j.bpj.2014.12.025.

Authors

Johann Biedermann¹, Alexander Ullrich¹, Johannes Schöneberg¹, Frank Noé²

Affiliations

¹ Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany.
² Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany. Electronic address: [email protected].

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computer Graphics*
Computer Simulation*
Diffusion
Kinetics
Software*
Time Factors