Speaker: Zan Luthey-Schulten (University of Illinois)
Title: 4D simulations of a growing and dividing minimal cell: Mathematical approaches used and needed for modeling the virtual human cell
Abstract: I will describe our research into constructing 4D (x,y,z + time) models of a living minimal cell. The 4D simulations integrate data from -omics, cryo-electron tomograms,DNA contact maps, fluorescent imaging, and kinetic experiments to initialize a realistic cell state. The states are propagated in time through hybrid stochastic-deterministic methods: reaction-diffusion master equations, chemical master equations, and ordinary differential equations. Fundamental behaviors emerge from these simulations that reveal how the cell balances the demands of its metabolism, genetic information processes, growth and morphological changes. Validation by coarse-grained atomistic MD simulations and experiments are critical steps in building the whole-cell models for the genetically minimized bacterium JCVI-Syn3A. Improvements in the hybrid algorithms are needed to treat large human cells, and I will attempt to identify the principle bottlenecks.