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 ω 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. arXiv:1811.08082v2 [cond-mat.soft]

Hysteresis loop area scaling exponents in DNA unzipping by a periodic force: A Langevin dynamics simulation study

“…In this paper, we study the unzipping transition of a ds-DNA subjected to a periodic force using LD simulations on a model that is very much similar to a well established DSAW model of a DNA on a D = 1 + 1 square lattice. The later model has been studied extensively, for over two decades, using the generating function, exact transfer matrix, and Monte Carlo techniques [1,2,[7][8][9][25][26][27][28][29]. Furthermore, the length of the DNA, having up to 184 monomers with N = 96 base pairs, simulated here, for the periodic case, are six times longer than the earlier BD/LD simulation studies [20][21][22][23][24].…”

“…In recent years, the behavior of a dsDNA under a periodic force with frequency ω and amplitude G has been studied by using Brownian dynamics (BD) or Langevin dynamics (LD) simulation of an off-lattice coarse-grained model for short chains which are limited to a maximum number of N = 16 base pairs and 32 monomers [20][21][22][23][24], and by using Monte Carlo (MC) simulations of DNA chains having 1024 monomers with N = 512 base pairs on a (d = 1 + 1)-dimensional square lattice [1,2,25,26]. Both LD and MC simulation studies show the existence of a dynamical phase transition, where the DNA can be taken from the zipped state to an unzipped state via a new dynamical state.…”

“…One end of the chain is anchored at the origin and an external time dependent periodic force g(t) is applied on the free end along x direction and its distance from the origin, x(t), is monitored. In MC simulation studies [1,2,25,26], the strands of DNA are represented by two directed selfavoiding walks (DSAWs), which do not cross each other, on a (d = 1 + 1)-dimensional square lattice. Whenever the ith monomers of walks (mimicking complementary bases) are unit distance apart, there is a gain in energy (base-pairing).…”

Quantifying molecular tension—classifications, interpretations and limitations of force sensors

“…The severity of hysteresis depends on both the timescale of the force change as well as the folding characteristics of the force-sensing domain. For instance, the hysteresis of a DNA hairpin is significantly smaller than that of most proteins due to its larger distance to unfolding transition barrier, making it less affected by loading rate differences [120]. In general, the force-sensing domain should have a refolding rate under zero-force condition that is much faster than the timescale of the force dynamics of the biological system under investigation.…”