Dynamics of a bubble formed in double stranded DNA

Details Dynamics of a bubble formed in double stranded DNA Dynamics of a bubble formed in double stranded DNA

2008-09-26

arxiv.org/abs/0809.4602v1

Europhys. Lett. 85,38001 (2009)

Physics

Condensed Matter

Soft Condensed Matter

11 pages, 4 figures. submitted to Phys. Rev. Lett

Scientific paper

10.1209/0295-5075/85/38001

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.

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