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Bubble Nucleation and Cooperativity in DNA Melting S. Ares,1,2

Summary: Bubble Nucleation and Cooperativity in DNA Melting
S. Ares,1,2
N. K. Voulgarakis,3
K. Ų. Rasmussen,1
and A. R. Bishop1
Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matema“ticas, Universidad Carlos III de Madrid,
Avenida de la Universidad 30, 28911 Legane“s, Madrid, Spain
Department of Physics, University of Crete and Foundation for Research and Technology-Hellas (FORTH), P.O. Box 2208,
71003 Heraklion, Crete, Greece
(Received 5 October 2004; published 27 January 2005)
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.
DOI: 10.1103/PhysRevLett.94.035504 PACS numbers: 63.20.Pw, 87.15.He


Source: Ares, Saśl - Max-Planck-Institut für Physik komplexer Systeme


Collections: Physics; Biology and Medicine