4.5 Article

ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units

期刊

BIOPHYSICAL JOURNAL
卷 108, 期 3, 页码 457-461

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CELL PRESS
DOI: 10.1016/j.bpj.2014.12.025

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资金

  1. German Science Foundation (Deutsche Forschungsgemeinschaft (DFG) [SFB 740, SFB 958]
  2. European Commission through the European Research Council Starting Grant pcCell

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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.

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