Dynamic stability in an isothermal molecular machine

This work presents a dynamic stability analysis of a generic model for a molecular motor, namely, a twostate machine operating along a one-dimensional reaction coordinate. The states correspond to two minima of an appropriate free energy landscape. While a physical energy landscape is expected to be very complicated and high dimensional, the thermally activated transitions between the two states will typically follow a preferred pathway that connect these states via the lowest lying saddle point which is the so called activated state. Previous studies on thermal engine models and energy converting biological systems have shown that some of the paramétrés affecting their thermodynamic performance also affect their stability. Indeed, the system stability usually weakens as its thermodynamic properties improve. Stability is important because it allows the system to maintain its function despite internal and external perturbations. This means all sufficiently small disturbances away from it damp out in time. Our results indicate that the global free energy gap affects the stability of the steady state.