Numerical computation of effective thermal equilibria in stochastically switching Langevin systems.

Stochastically switching force terms appear frequently in models of biological systems under the action of active agents such as proteins. The interaction of switching forces and Brownian motion can create an "effective thermal equilibrium," even though the system does not obey a potential function. In order to extend the field of energy landscape analysis to understand stability and transitions in switching systems, we derive the quasipotential that defines this effective equilibrium for a general overdamped Langevin system with a force switching according to a continuous-time Markov chain process. Combined with the string method for computing most-probable transition paths, we apply our method to an idealized system and show the appearance of previously unreported numerical challenges. We present modifications to the algorithms to overcome these challenges and show validity by demonstrating agreement between our computed quasipotential barrier and asymptotic Monte Carlo transition times in the system.