Issue |
EPL
Volume 96, Number 6, December 2011
|
|
---|---|---|
Article Number | 68003 | |
Number of page(s) | 6 | |
Section | Interdisciplinary Physics and Related Areas of Science and Technology | |
DOI | https://doi.org/10.1209/0295-5075/96/68003 | |
Published online | 09 December 2011 |
Mean bubble formation time in DNA denaturation
1
School of Physics, University of Hyderabad, Central University P.O. - Hyderabad 500 046, Andhra Pradesh, India
2
Theoretical Soft Matter and Biophysics, Institute of Complex Systems, Forschungszentrum Jülich Jülich, Germany, EU
Received:
15
August
2011
Accepted:
3
November
2011
Using the Poland-Scheraga free energy of the bubble size in a double-stranded DNA we propose a discrete stochastic dynamics for the number of base pairs N of an unzipped bubble. We derive a universal subdiffusive growth TN∼A/Γ(b+2)N1+b for the mean formation time (MBFT) TN of a bubble of size N. The amplitude A is determined by the bubble initiation rate and time spent in the denaturated state. We examine critically the significance of these results for experiments. We find: i) Our results provide a new method to determine whether the order of the denaturation transition is discontinuous (b>2) or not. ii) The asymptotic growth law of TN is reached with 10% precision already for small bubbles of sizes >20. However, the amplitude is very sensitive to modeling details for small bubbles. iii) In an equilibrium sample of bubbles up to size N the averaged MBFT grows diffusively, TN*∝N2, irrespective of b.
PACS: 87.15.H- – Dynamics of biomolecules / 87.14.gk – DNA / 05.40.Fb – Random walks and Levy flights
© EPLA, 2011
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