FIGURE 1.

Illustration of the asymmetry of melting-hybridization dynamics. We show microscopic configurations (vertical) as a function of time (horizontal) for a 500-basepair toy model of DNA having two phases, hybridized (gray) and molten (black). The sequence is homogeneous. (Top panel) Heating-cooling cycle for c = 1 (a) and c = 2 (b). We increase the temperature linearly with time until well above coexistence, and then reverse the protocol until the original temperature is recovered. Molten bubbles grow via nucleation, and close via nucleation when the parameter c is small (left panel). When c is large (right panel), cooling is sufficiently rapid that bubbles are constrained to close via domain wall drift. This asymmetry can give rise to melting-driven asymmetric hysteresis in pulling simulations, in which the varying control parameter is tension rather than temperature (see Simulation Results). (Bottom panel, c) Equilibrium dynamics for c = 2 at a fixed temperature near coexistence. With no external driving, dynamical symmetry is restored.