DNA melting: intra base-pair dynamics and a vector generalization of the Peyrard-Bishop-Dauxois model
Biological Physics
2026-04-28 v1 Soft Condensed Matter
Abstract
The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces and dynamical properties, e.g. hairpin dynamics. The paper presents an atomistic "toy model" of the intra base-pair motion which suggests that the thermodynamics may be better described by a planar vector - rather than a scalar - order parameter. This leads to correct estimates of melting entropy, unzipping force, hairpin opening rates, and the equilibrium constant of open/closed base pair states during imino proton exchange.
Keywords
Cite
@article{arxiv.2604.23771,
title = {DNA melting: intra base-pair dynamics and a vector generalization of the Peyrard-Bishop-Dauxois model},
author = {Nikos Theodorakopoulos},
journal= {arXiv preprint arXiv:2604.23771},
year = {2026}
}
Comments
8 pages, 4 figures, to be published in Phys. Rev. E