Coarse-graining DNA: Symmetry, non-local elasticity and persistence length

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...

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Bibliographic Details
Published in:arXiv.org 2022-06
Main Authors: Yair Augusto Gutierrez Fosado, Landuzzi, Fabio, Sakaue, Takahiro
Format: Article
Language:English
Subjects:
Couplings
Granulation
Mechanical properties
Modulus of elasticity
Molecular dynamics
Online Access:Get full text
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Summary: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.
ISSN:2331-8422
DOI:10.48550/arxiv.2206.01504