Testing the transition state theory in stochastic dynamics of a genetic switch

Abstract: Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching transition between those states are compared with the theoretical estimation of the switching rate derived from the idea similar to the transition state theory. Even though the circuit is kept far from equilibrium, the method gives a consistent explanation of the switching kinetics for a wide range of parameters. The transition state theory-like estimation, however, fails to describe transitions involving the state which has the extremely small numbers of protein molecules.