Some of the most challenging and exciting opportunities for physical geometric computation arise in developing and applying computational approaches to understand the molecular machinery of the cell. Computer simulation of molecular motion is a prime example. Classic simulation techniques, such as the Monte Carlo and molecular dynamics methods, generate individual motion pathways one at a time and spend most of their time trying to escape from the local minima of the energy landscape of a molecule. Their high computational cost prevents them from being used to analyze many pathways. We introduce Stochastic Roadmap Simulation (SRS), a new approach for exploring the kinetics of molecular motion by examining multiple pathways simultaneously. The computation does not suffer from the local-minima problem encountered with existing methods. By viewing the roadmap as a Markov chain, we can efficiently compute kinetic properties of molecular motion over the entire molecular energy landscape

To test the effectiveness of our approach, we have applied it to the computation of the transmission coefficients for protein folding, an important order parameter that measures the ``kinetic distance'' of a protein's conformation to its native state. Our computational studies show that SRS obtains more accurate results and reduces the computation time by several orders of magnitude, compared with Monte Carlo simulation.

Wednesday, February 27, 2002 at 3:00pm in DH 1070
A reception in Martel Hall will follow the talk.

About David Hsu

David Hsu is currently a post-doctoral research associate at the University of North Carolina at Chapell Hill. His research interests include motion planning and geometric computation, with emphasis on applications in computational biology and robotics.

He received the B.Sc. degree in computer science & mathematics in 1995 from the University of British Columbia in Canada, and the M.S. and Ph.D. degrees in computer science in 1998 and 2000 from Stanford University. He worked at Compaq's Cambridge Research Laboratory in Cambridge, MA, where he initiiated work to apply motion planning to computer animation.