Effective Thermal Equilibrium for Switiching Polymer Model of Chromosome Dynamics

How the genome organizes and interacts within the cell can be understood through a polymer-like model of chromosome dynamics that combines Brownian motion with a stochastic switching force. The switching force, which follows a continuous-time Markov chain process, keeps the general overdamped Langevin system out of strict equilibrium. However, an effective energy landscape through the framework of quasipotentials helps us to understand the stability and transitions in the system. We show how this quasipotential changes as a function of switching rate which explains the difference in cluster-lifetimes observed in the large scale simulations of the experimental chromosome system.