COLLOQUIUM
Department of Computer Science and Engineering
University of South Carolina
 
Multiscale Stochastic Simulation of Biochemical Systems
Yang Cao

Department of Computer Science 
University of California, Santa Barbara

Date: March 25, 2005
Time: 3:30-4:30PM
Place: Swearingen 1A03 (Faculty Lounge)

Abstract

Biochemical systems are inherently multiscale and stochastic. In
microscopic systems formed by living cells, the small numbers of
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), a numerical simulation procedure that is
essentially exact for chemical systems that are spatially homogeneous
or well stirred. 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)
stiffness, i.e. the presence of multiple timescales, the fastest of
which are stable; and (2) the need to include in the simulation both
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 (or at some scale in
between). Discrete stochastic simulation algorithms that can
efficiently solve the multiscale problem are highly desired. In this
talk I will introduce my recent work in multiscale stochastic
simulation methods for biochemical systems.

Yang Cao obtained his bachelor and master’s degrees from the
mathematical science department of Tsinghua University, Beijing,
China. He obtained his Ph. D in March, 2003 from the department of
computer science of University of California Santa Barbara. Currently
Dr. Cao is a postgraduate researcher at the University of California,
Santa Barbara. His research covers many areas of computational
science, including the numerical solution of differential-algebraic
system, sensitivity and uncertainty analysis and stochastic simulation
of biochemical systems. Dr. Cao has written about 20 journal papers in
these areas. His current research is focused on multiscale stochastic
simulation algorithms for biochemical systems.