Physics – Condensed Matter – Statistical Mechanics
Scientific paper
2007-06-29
Phys. Rev. E 76, 061915 (2007)
Physics
Condensed Matter
Statistical Mechanics
12 pages, 10 figures, revtex
Scientific paper
10.1103/PhysRevE.76.061915
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.
Fogedby Hans C.
Metzler Ralf
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