2007/06/29 by Hans C. Fogedby, Ralf Metzler
Biochemistry, Genetics and Molecular Biology · Mathematics · Physics and Astronomy · #Diffusion and Search Dynamics #Spectroscopy and Quantum Chemical Studies #Stochastic processes and statistical mechanics #cond-mat.soft #cond-mat.stat-mech
paper · pdf · doi:10.1103/physreve.76.061915
published as Phys. Rev. E 76, 061915 (2007) · 12 pages, 10 figures, revtex
arxiv created 2007/06/29 · openalex publication_date 2007/12/21 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We show that long time distributions for the survival of DNA bubbles and the size autocorrelation function can be derived from an asymptotic weak noise approach. In particular, below the melting temperature the bubble closure corresponds to a noisy finite time singularity. We demonstrate that the associated Fokker-Planck equation is equivalent to a quantum 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.