Bubble relaxation dynamics in double-stranded DNA
Abstract
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.
- Publication:
-
Physical Review E
- Pub Date:
- July 2004
- DOI:
- 10.1103/PhysRevE.70.010902
- arXiv:
- arXiv:cond-mat/0406028
- Bibcode:
- 2004PhRvE..70a0902B
- Keywords:
-
- 87.14.Gg;
- 02.50.Ga;
- 82.39.Jn;
- 87.15.-v;
- DNA RNA;
- Markov processes;
- Charge transfer in biological systems;
- Biomolecules: structure and physical properties;
- Condensed Matter - Soft Condensed Matter;
- Condensed Matter - Statistical Mechanics
- E-Print:
- 4 pages, 2 figures, submitted to Physical Review E as a rapid communication