Discrete Stochastic Simulation of Spatially Inhomogeneous Biochemical Systems

In microscopic systems formed by living cells, the small numbers of some reactant molecules can result in dynamical behavior that is discrete and stochastic rather than continuous and deterministic. An analysis tool that respects these dynamical characteristics is the stochastic simulation algorithm (SSA), which applies to well-stirred chemically reacting systems. However, cells are hardly homogeneous! Spatio-temporal gradients and patterns play an important role in many biochemical processes. In this lecture we report on recent progress in the development of methods for spatial stochastic and multiscale simulation, and outline some of the many interesting complications that arise in the modeling and simulation of spatially inhomogeneous biochemical systems.

Bio: Dr. Linda Petzold is currently Professor in the Department of Computer Science (Chair 2003-2007) and the Department of Mechanical Engineering, and Director of the Computational Science and Engineering Graduate Emphasis at the University of California Santa Barbara. She received her Ph.D. in Computer Science in 1978 from the University of Illinois. Dr. Petzold is a member of the US National Academy of Engineering and a Fellow of the ASME, SIAM and AAAS. Her research focuses on modeling, simulation and analysis of multiscale systems in systems biology.