title: Bubble nucleation and cooperativity in DNA melting.
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.
authors.affiliation: Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
authors.forename: S
authors.initials: S
authors.lastname: Ares
authors.forename: N K
authors.initials: NK
authors.lastname: Voulgarakis
authors.forename: K O
authors.initials: KO
authors.lastname: Rasmussen
authors.forename: A R
authors.initials: AR
authors.lastname: Bishop
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D044367:Phase Transition; D013329:Structure-Activity Relationship; D044366:Transition Temperature
chemical_list: D004247:DNA