Parallel in time steady state averaging of multi-scale biochemical reaction kinetics
Wednesday, June 6, 2018 - 11:30am - 12:00pm
Stochastic reaction kinetics that exhibits multiple time scales is an important tool for modelling cellular systems in biology. Sampling of the stationary distribution of such multiscale systems is often computationally demanding due to the existence of rare events. On top of the parallel replica (ParRep) dynamics originally designed by Art Voter, we developed a parallel in time method for steady state sampling of continuous time Markov chain that includes the stochastic reaction kinetics model. We also provide theoretical analysis of ParRep using the theory of quasi-stationary distribution.Finally, the application of ParRep to several biological examples such as the genetic switch will be discussed.