Simulating Reactions and Diffusion: Lessons from Toy Models

Synopsis

Chemical systems can deviate from equilibrium for a variety of reasons: because they are kinetically trapped, because they are subject to a time-varying drive, or because they are simultaneously in contact with multiple incommensurate reservoirs. This last scenario, which generates a nonequilibrium steady state (NESS), yields a stationary distribution over microstates that is not Boltzmann and that sustains currents. I will describe my group’s efforts to build coarse-grained molecular motor models and to explicitly sample the NESS dynamics driven by a catalyzed “fuel” decomposition. The open-system molecular dynamics simulations can offer a new perspective on motor design, current reversals, and power strokes.