Phase boundaries as agents of structural change in macromolecules

We model long rod-like molecules, such as DNA and coiled-coil proteins, as one-dimensional continua with a multi-well stored energy function. These molecules suffer a structural change in response to large forces, characterized by highly typical force-extension behavior. We assume that the structural change proceeds via a moving folded/unfolded interface, or phase boundary, that represents a jump in strain and is governed by the Abeyaratne–Knowles theory of phase transitions. We solve the governing equations using a finite difference method with moving nodes to represent phase boundaries. Our model can reproduce the experimental observations on the overstretching transition in DNA and coiled-coils and makes predictions for the speed at which the interface moves. We employ different types of kinetic relations to describe the mobility of the interface and show that this leads to different classes of experimentally observed force-extension curves. We make connections with several existing theories, experiments and simulation studies, thus demonstrating the effectiveness of the phase transitions-based approach in a biological setting.