Institute Colloquium
Topic: Bridging the Scales in Biochemical Simulation
Speaker: Prof. Linda Petzold
Day & Date: Friday, 22nd July, 2005
Time: 3.00 PM
Venue: Institute Auditorium
ABOUT THE SPEAKER
Prof. Linda Petzold, Director, Computational Science and Engineering Program, University of California, Santa Barbara, is also a Professor and Chair, Department of Computer Science,Professor, Department of Mechanical and Environmental Engineering. Prof. Petzold completed her Ph.D. in Computer Science, Mathematics minor, from University of Illinois, Urbana, Illinois, in 1978. She is B.S. in Mathematics, from University of Illinois, Urbana, Illinois, 1974. Her awards and accolades includes prestigious honours such as Membership of National Academy of Engineering, 2004, (First) AWM/SIAM Kovalevsky Prize in 2003, Dahlquist Prize (for numerical solution of differential equations) in 1999, (First) Wilkinson Prize for Numerical Software in 1991, and JSPS Fellowship for Research in Japan in 1994.
ABSTRACT
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). We will describe several recently developed techniques for multiscale simulation of biochemical systems, and outline some of the technical challenges that still need to be addressed.
