Join us for the QCB Seminar featuring QCB Director and Murchison-Mallory Endowed Chair in Chemistry Zan Luthey-Schulten, University of Illinois
Title: 4D simulations of a growing and dividing minimal cell
Abstract: We present a whole-cell spatial and kinetic model for the ∼100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. The 4D simulations include genetic information processes, metabolism, growth and cell division. Using hybrid stochastic-deterministic methods, dynamics of the morphological transformations are achieved. Growth is driven by synthesis of lipids and membrane proteins and constrained by fluorescence imaging data. Chromosome replication and segregation is controlled by essential SMC and topoisomerase proteins through Brownian dynamics simulations. The model captures the origin to terminus ratio measured in DNA sequencing and recovers other experimental measurements like doubling time, mRNA half-lives, protein distributions, and ribosome counts. Because of stochasticity, each replicate cell is unique. Not only do we predict average behavior for partitioning to daughter cells, we predict the heterogeneity among them. If time permits, I will discuss progress towards 4D simulations of a simple galactose switch functioning in yeast to demonstrate how we handle stochastic gene regulation.