Bubble Nucleation and Cooperativity in DNA Melting

S. Ares, N. K. Voulgarakis, K. Ø. Rasmussen, and A. R. Bishop
Phys. Rev. Lett. 94, 035504 – Published 27 January 2005

Abstract

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles, and the possibility of a two-state transition are studied.

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  • Received 5 October 2004

DOI:https://doi.org/10.1103/PhysRevLett.94.035504

©2005 American Physical Society

Authors & Affiliations

S. Ares1,2, N. K. Voulgarakis3, K. Ø. Rasmussen1, and A. R. Bishop1

  • 1Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
  • 2Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganés, Madrid, Spain
  • 3Department of Physics, University of Crete and Foundation for Research and Technology-Hellas (FORTH), P.O. Box 2208, 71003 Heraklion, Crete, Greece

Comments & Replies

Comment on “Bubble Nucleation and Cooperativity in DNA Melting”

Michaël Sanrey and Marc Joyeux
Phys. Rev. Lett. 102, 029601 (2009)

Ares et al. Reply:

S. Ares, N. K. Voulgarakis, K. Ø. Rasmussen, and Alan R. Bishop
Phys. Rev. Lett. 102, 029602 (2009)

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Vol. 94, Iss. 3 — 28 January 2005

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