DNA bubble dynamics as a quantum Coulomb problem

TL;DR

This paper models DNA bubble dynamics using a Coulomb problem analogy, revealing different behaviors below, at, and above melting temperature, with implications for understanding DNA denaturation processes.

Contribution

It introduces a novel mapping of DNA bubble dynamics to a quantum Coulomb problem, providing new insights into the temperature-dependent behavior of DNA denaturation.

Findings

Below melting temperature, bubble lifetime relates to scattering states.

At melting temperature, the Coulomb potential vanishes, leading to power law tail dynamics.

Above melting temperature, bound states dominate long-term behavior.

Abstract

We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the bubble lifetime is associated with the continuum of scattering states of the repulsive Coulomb potential, at the melting temperature the Coulomb potential vanishes and the underlying first exit dynamics exhibits a long time power law tail, above the melting temperature, corresponding to an attractive Coulomb potential, the long time dynamics is controlled by the lowest bound state. Correlations and finite size effects are discussed.