title: Dynamics of DNA breathing: weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem.
abstract: 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.
authors.affiliation: Department of Physics and Astronomy, University of Aarhus, Ny Munkegade, Aarhus C, Denmark. fogedby@phys.au.dk
authors.forename: Hans C
authors.initials: HC
authors.lastname: Fogedby
authors.forename: Ralf
authors.initials: R
authors.lastname: Metzler
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011789:Quantum Theory; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004247:DNA