Abstract
Structural transitions in some rod-like biological macromolecules under tension are known to proceed by the propagation through the length of the molecule of an interface separating two phases. A continuum mechanical description of the motion of this interface, or phase boundary, takes the form of a kinetic law which relates the thermodynamic driving force across it with its velocity in the reference configuration. For biological macromolecules immersed in a heat bath, thermally activated kinetics described by the Arrhenius law is often a good choice. Here we show that 'stick-slip' kinetics, characteristic of friction, can also arise in an overdamped bistable bar immersed in a heat bath. To mimic a rod-like biomolecule we model the bar as a chain of masses and bistable springs moving in a viscous fluid. We conduct Langevin dynamics calculations on the chain and extract a temperature dependent kinetic relation by observing that the dissipation at a phase boundary can be estimated by performing an energy balance. Using this kinetic relation we solve boundary value problems for a bistable bar immersed in a constant temperature bath and show that the resultant force-extension relation matches very well with the Langevin dynamics results. We estimate the force fluctuations at the pulled end of the bar due to thermal kicks from the bath by using a partition function. We also show rate dependence of hysteresis in cyclic loading of the bar arising from the stick-slip kinetics. Our kinetic relation could be applied to rod-like biomolecules, such as, DNA and coiled-coil proteins which exhibit structural transitions that depend on both temperature and loading rate.