title: Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.
abstract: 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 !0.1%. Display of cell 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
authors.affiliation: Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Elijah
authors.initials: E
authors.lastname: Roberts
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.forename: Zaida
authors.initials: Z
authors.lastname: Luthey-Schulten
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism; D004058:Diffusion; D004926:Escherichia coli / Q000166:cytology; D005786:Gene Expression Regulation; D008954:Models, Biological; D011485:Protein Binding; D012984:Software; D013269:Stochastic Processes; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D004247:DNA