2009 PIMS-CSC Seminar - 05

  • Date: 03/13/2009
Linda Petzold (University of California Santa Barbara)

Simon Fraser University


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, and outline some of the future challenges.