Mathematical Biology Seminar

Dan Gillespie
Friday April 4, 2008
3:05pm in LCB 225
"The Slow-Scale Stochastic Simulation Algorithm" "

Abstract: Reactions in real chemical systems often take place on vastly different time scales, with "fast" reaction channels firing very much more frequently than "slow" ones. These firings will be interdependent if, as is usually the case, the fast and slow reactions involve some of the same species. An exact stochastic simulation of such a system will spend most of its time on the more numerous fast reaction events. This will be a frustratingly inefficient allocation of computational effort when "dynamical stiffness" is present, since in that case a fast reaction event will usually be much less important to the system's evolution than a slow reaction event. For such situations, we derive a systematic approximate procedure that allows one to stochastically advance the system in time by simulating the firings of only the slow reactions. Implementing this procedure poses some challenges, but as shown by several simple examples (such as the enzyme-substrate reaction), when those challenges can be overcome, substantial increases in simulation speed can be realized.