Nonequilibrium theory of polymer stretching based on the Master Equation

Single polymer pulling experiments such as protein unfolding measurements and dynamic force spectroscopy are increasingly done at high loading rates where equilibrium statistical mechanics is no longer applicable. I will present a theory that takes into account non-equilibrium effects using a Master Equation [PRE v. 72, 031805 (2005)]. If the molecular length is used as a stochastic variable, the transition probabilities have a simple analytic form. This theory predicts significant differences between experimental designs using controlled end-to-end positions and those that utilize a force-control mechanism. The most prominent non-equilibrium effect is a loading rate-dependent hysteresis in the force-extension curve. Molecular relaxation close to and far from equilibrium will also be discussed in the frame-work of the Master Equation theory.