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We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for the cases where the force is applied to only one strand or to both. Different assumptions on the monomer size of single and double stranded DNA lead to opposite conclusions as to whether DNA melts or not as it overstretches.
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which mimic the
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs, subject to
We study the effect of rapid quench to zero temperature in a model with competing interactions, evolving through conserved spin dynamics. In a certain regime of model parameters, we find that the model belongs to the broader class of kinetically cons
Relaxation in glasses is often approximated by a stretched-exponential form: $f(t) = A exp [-(t/tau)^{beta}]$. Here, we show that the relaxation in a model of sheared non-Brownian suspensions developed by Corte et al. [Nature Phys. 4, 420 (2008)] can
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built fro