Dynamics and kinetics of single-molecule pulling experiments

The response of a single molecule to an applied force is important for many biological processes. This response is often investigated via single-molecule pulling experiments, where a tension force is applied to the opposite ends of a biological chain molecule. In equilibrium conditions, the system follows a trajectory that may be predicted from a free-energy landscape. In non-equilibrium experiments, the pulling force varies too rapidly for the chain to explore all available configurations resulting in a deviation from the equilibrium trajectory. To gain a better understanding of the relationship between equilibrium and non-equilibrium processes, we investigate the effect of the pulling speed on the system's trajectory with two types of computer simulations of single-molecule experiments. We perform Wang-Landau simulations to determine the energy landscape and Langevin dynamics simulations to probe the dynamic response of the same bead-spring model of a biopolymer. After verifying that both simulation methods yield consistent equilibrium results, we study the effect of the pulling protocol on the free-energy landscape trajectories and compare kinetic predictions with dynamic simulation results.