A. Suma, V. Carnevale and C. Micheletti
Nonequilibrium thermodynamics of DNA nanopore unzipping
Phys. Rev. Lett., 2023, 130 048101
, Link to online article

Abstract
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, $f$: (i) heterogeneous DNA retraction and rezipping ($f < 17$pN), (ii) normal ($17$pN $< f < 60$pN) and (iii) anomalous ($f > 60$pN) drift-diffusive behavior. We show that the normal drift-diffusion regime can be effectively modelled as a one-dimensional stochastic process in a tilted periodic potential. We use the theory of stochastic processes to recover the potential from nonequilibrium unzipping trajectories and show that it corresponds to the free-energy landscape for single base-pairs unzipping. Applying this general approach to other single-molecule systems with periodic potentials ought to yield detailed free-energy landscapes from out-of-equilibrium trajectories.