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

被引：25

作者：

Biedermann, Johann ^{[1
]}

Ullrich, Alexander ^{[1
]}

Schoeneberg, Johannes ^{[1
]}

Noe, Frank ^{[1
]}

机构：

[1] Free Univ Berlin, Dept Math Comp Sci & Bioinformat, Berlin, Germany

来源：

BIOPHYSICAL JOURNAL | 2015年 / 108卷 / 03期

基金：

欧洲研究理事会;

关键词：

SPACE; DYNAMICS; TIME;

D O I：

10.1016/j.bpj.2014.12.025

中图分类号：

Q6 [生物物理学];

学科分类号：

071011 ;

摘要：

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.

引用

页码：457 / 461

页数：5

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