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Phys. Rev. E 70, 010902 (2004) [4 pages]

Bubble relaxation dynamics in double-stranded DNA

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D. J. Bicout1,2 and E. Kats1,3
1Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble, France
2Biomathematics and Epidemiology, ENVL, B.P. 83, 69280 Marcy l’Etoile, France
3L. D. Landau Institute for Theoretical Physics, RAS, 117940 GSP-1, Moscow, Russia

Rapid Communication Received 17 November 2003; revised 27 February 2004; published 28 July 2004

This paper deals with the two-state (opening–closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that includes end effects and derive analytic expressions of the correlation function, survival probability, and lifetimes for the bubble relaxation dynamics. It is shown that the continuous and semi-infinite limit of the model becomes a good approximation to an exact result when aN⪡1 , where N is bubble size and a , the ratio of opening to closing rates of base pairs, is the control parameter of DNA melting.


©2004 The American Physical Society

URL: http://link.aps.org/doi/10.1103/PhysRevE.70.010902
DOI: 10.1103/PhysRevE.70.010902
PACS: 87.14.Gg, 02.50.Ga, 82.39.Jn, 87.15.−v

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