Friday, January 27, 2006
4:30 pm
5130 Upson Hall

Computer Science
Spring 2006

Linda Petzold

University of California, Santa Barbara


Multiscale Simulation of 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). Despite recent improvements, as a procedure that simulates every reaction event, the SSA is necessarily inefficient for most realistic problems. There are two main reasons for this, both arising from the multiscale nature of the underlying problem: (1) the presence of multiple timescales (both fast and slow reactions); and (2) the need to include in the simulation both chemical species that are present in relatively small quantities and should be modeled by a discrete stochastic process, and species that are present in larger quantities and are more efficiently modeled by a deterministic differential equation. We will describe several recently developed techniques for multiscale simulation of biochemical systems, along with some biological applications and a new software toolkit.