Statistical Mechanics of DNA Rupture: Theory and Simulations

Abstract

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the iterature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.Comment: 18 pages, 9 figures. Accepted in J. Chem. Phys. (2013). arXiv admin note: text overlap with arXiv:1104.305