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Phys. Rev. E 70, 036609 (2004) [6 pages]

Bubble generation in a twisted and bent DNA-like model

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P. V. Larsen*
Informatics and Mathematical Modelling and Department of Mathematics, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

P. L. Christiansen
Informatics and Mathematical Modelling and Department of Physics, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

O. Bang
Research Center COM and Informatics and Mathematical Modelling, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

J. F. R. Archilla
Departamento de Fisica Aplicada I, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain

Yu. B. Gaididei
Bogolyubov Institute for Theoretical Physics, 03143 Kiev, Ukraine

Received 15 January 2004; revised 14 June 2004; published 21 September 2004

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.

© 2004 The American Physical Society

URL:
http://link.aps.org/doi/10.1103/PhysRevE.70.036609
DOI:
10.1103/PhysRevE.70.036609
PACS:
05.45.Yv, 63.20.Ry, 63.20.Pw, 87.15.Aa

*Electronic address: p.v.larsen@mat.dtu.dk

 
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