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

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 order...

Full description

Saved in:
Bibliographic Details
Published in:Biophysical journal 2015-02, Vol.108 (3), p.457-461
Main Authors: Biedermann, Johann, Ullrich, Alexander, Schöneberg, Johannes, Noé, Frank
Format: Article
Language:English
Subjects:
Computational Tools
Computer Graphics
Computer Simulation
Diffusion
Kinetics
Proteins
Reaction kinetics
Signal transduction
Simulation
Software
Time Factors
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0006-3495
1542-0086
DOI:10.1016/j.bpj.2014.12.025