Unzipping of a double-stranded block copolymer DNA by a periodic force

TL;DR

This study uses Monte Carlo simulations to analyze how periodic forces cause hysteresis in unzipping double-stranded block copolymer DNA, revealing sequence-dependent effects and scaling behaviors.

Contribution

It introduces a detailed simulation of hysteresis in block copolymer DNA unzipping under periodic force, highlighting sequence dependence and dynamic scaling.

Findings

Hysteresis loops vary with force frequency and sequence.

Loop area scales differently at low and high frequencies.

Equilibrium phase diagram is sequence-independent.

Abstract

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, respectively, and $2n$ represents the number of such base pairs in a unit. The end of the DNA are subjected to a time dependent periodic force with frequency ($\omega$) and amplitude ($g_0$) keeping the other end fixed. We find that the equilibrium force-temperature phase diagram for the static force is independent of the DNA sequence. For the periodic force case, the results are found to be dependent on the block copolymer DNA sequence and also on the base pair type on which the periodic force is acting. We observe hysteresis loops of various shapes and sizes and obtain the scaling of loop area both at low and high frequency regimes.