Issue
EPL
Volume 85, Number 3, February 2009
Article Number 38001
Number of page(s) 5
Section Interdisciplinary Physics and Related Areas of Science and Technology
DOI http://dx.doi.org/10.1209/0295-5075/85/38001
Published online 04 February 2009
EPL, 85 (2009) 38001
DOI: 10.1209/0295-5075/85/38001

Dynamics of a bubble formed in double-stranded DNA

Shikha Srivastava and Yashwant Singh

Department of Physics, Banaras Hindu University - Varanasi-221 005, India

singhyas_in@yahoo.co.in

received 8 October 2008; accepted in final form 8 January 2009; published February 2009
published online 4 February 2009

Abstract
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 et al. (Phys. Rev. Lett., 90 (2003) 138101) 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.

PACS
87.14.gk - DNA.
87.15.Ya - Fluctuations.
87.15.ad - Analytical theories.

© EPLA 2009