2025/08/10 by Chari, S. Siva Nasarayya, Maiti, Prabal K.
#Biological Physics (physics.bio-ph) #FOS: Physical sciences #Soft Condensed Matter (cond-mat.soft)
paper · doi:10.48550/arxiv.2508.07354
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force f acting on it. After equilibration, a switching experiment is performed over the system by pulling one end of the DNA while restraining its other end. The finite time pulling process is performed at a constant rate of the applied force until a maximum value of 400 pN. The associated nonequilibrium work done (W) during this process is determined by numerically integrating the force-extension curve as a function of the applied force. An ensemble of the work values, P(W), is obtained by repeating the pulling experiment a large number of times. We determine the free energy difference (ΔF) between the equilibrium and force-induced melted states of the DNA by employing the Jarzynski equality. The value of ΔF is found to be in close agreement with the conventional equilibrium methods.