Related papers: Hysteresis loop area scaling exponents in DNA unzi…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency ($\omega$) and amplitude ($G$). For the static force, i.e., $\omega \to…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
Using Langevin Dynamics simulations, we study a simple model of interacting-polymer under a periodic force. The force-extension curve strongly depends on the magnitude of the amplitude $(F)$ and the frequency ($\nu$) of the applied force.…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
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…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
Experiments on ferromagnetic thin films have measured the dependence of the hysteresis loop area on the amplitude and frequency of the external field, $A$=$A(H_{0},\omega)$, and approximate agreement with numerical simulations of Ising…
We investigate the properties of hysteresis cycles produced by a one-dimensional, periodically forced Langevin equation. We show that depending on amplitude and frequency of the forcing and on noise intensity, there are three qualitatively…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
Dynamic quantities related to hysteresis have been measured in micromagnetic simulations of single-domain nanoscale magnets at nonzero temperature. The hysteresis-loop area and magnetization-field correlation display the characteristics of…
DNA loop extrusion is arguably one of the most important players in genome organization. The precise mechanism by which loop extruding factors (LEFs) work is still unresolved and much debated. One of the major open questions in this field…
The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for…
Dynamic hysteresis, viz., delay in switching of a bistable system on account of the finite sweep rate of the drive has been extensively studied in dynamical and thermodynamic systems. Dynamic hysteresis results from slowing of the response…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
We consider three mechanisms of hysteresis phenomena in alternating magnetic field: the domain wall motion in a random medium, the nucleation and the retardation of magnetization due to slow (critical) fluctuations. We construct…