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DNA melting: Intra-base-pair dynamics and a vector generalization of the Peyrard-Bishop-Dauxois model

Nikos Theodorakopoulos

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Phys. Rev. E 113, 054405 – Published 11 May, 2026

DOI: https://doi.org/10.1103/7mtw-wvkx

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.

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Phys. Rev. E 113, 054405– Published 11 May, 2026
  • Received 6 October 2025
  • Revised 12 December 2025
  • Accepted 24 April 2026
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Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

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