Coarse-graining DNA: Symmetry, non-local elasticity and persistence length
Abstract
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein interactions and the nucleosome diffusion mechanism. Here, by employing the rigid base pair model, we connect its microscopic parameters to the persistence length. Combined with all-atom molecular dynamic simulations, our scheme identifies relevant couplings between different degrees of freedom at each coarse-graining step. This allows us to clarify how the scale dependence of the elastic moduli is determined in a systematic way encompassing the role of previously unnoticed off site couplings between deformations with different parity.
Keywords
Cite
@article{arxiv.2206.01504,
title = {Coarse-graining DNA: Symmetry, non-local elasticity and persistence length},
author = {Yair Augusto Gutierrez Fosado and Fabio Landuzzi and Takahiro Sakaue},
journal= {arXiv preprint arXiv:2206.01504},
year = {2025}
}