Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten.
Lattice microbes: High-performance stochastic simulation method for
the reaction-diffusion master equation.
Journal of Computational Chemistry, 34:245-255, 2013.
ROBE2012-ZLS
Spatial stochastic simulation is a valuable technique for
studying reactions in biological systems. With the availability
of high-performance computing (HPC), the method is poised
to allow integration of data from structural, single-molecule
and biochemical studies into coherent computational models
of cells. Here, we introduce the Lattice Microbes software
package for simulating such cell models on HPC systems. The
software performs either well-stirred or spatially resolved
stochastic simulations with approximated cytoplasmic
crowding in a fast and efficient manner. Our new algorithm
efficiently samples the reaction-diffusion master equation
using NVIDIA graphics processing units and is shown to be
two orders of magnitude faster than exact sampling for large
systems while maintaining an accuracy of %0.1cell models and animation of reaction trajectories involving
millions of molecules is facilitated using a plug-in to the
popular VMD visualization platform. The Lattice Microbes
software is open source and available for download at http://
www.scs.illinois.edu/schulten/lm VC 2012 Wiley Periodicals, Inc.
