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Bubble dynamics in DNA | | Andreas Hanke
; Ralf Metzler
; | | Date: |
2 May 2003 | | Journal: | J. Phys. A: Math. Gen. 36, L473 (2003) | | Subject: | Soft Condensed Matter; Statistical Mechanics | cond-mat.soft cond-mat.stat-mech q-bio | | Abstract: | The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case. | | Source: | arXiv, cond-mat/0305049 | | Services: | Forum | Review | PDF | Favorites | |
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