Unzipping DNA by a periodic force: Hysteresis loops, Dynamical order parameter, Correlations and Equilibrium curves

Abstract

The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as the time average extension between the end monomers of two strands of the DNA over a period, and its probability distributions $P(Q)$ at various force amplitudes and frequencies. We also study the time autocorrelations of extension and the dynamical order parameter for various chain lengths. The equilibrium force-distance isotherms were also obtained at various frequencies by using non-equilibrium work measurements.

10 pages, 7 figures, Published version