Spatially resolved stochastic simulation is a valuable technique for studying reactions on time and size scales relevant for biological systems. Here, CPLC faculty ZLS and postdoc ER introduce the Lattice Microbes GPU-based software package for simulating complex biochemical reaction networks on the level of the whole cell. Our approach integrates data from cyroelectron tomography, proteomics, and single molecule spectroscopy to capture the molecular crowding within cells. 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. Lattice Microbe has been implemented on Blue Waters and other NSF/DOE supercomputers.