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
Many biochemical reaction networks inside of a living cell operate with only a few copies of key proteins and/or RNAs, which introduces a stochastic component to the reaction dynamics. Computational modeling of in vivo biochemistry must account for such stochastic effects if it is to accurately describe populations of cells. Here, the Lattice Microbes software suite is presented for studying spatially resolved, stochastic models of cellular reaction networks operating inside a modeled cell.
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