title: Bubble statistics and dynamics in double-stranded DNA.
abstract: The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two distribution functions describing localized separations ("bubbles") of the double strand. The result that the bubble distributions are more sharply peaked at the active sites than thermodynamically obtained distributions is ascribed to the fact that the bubble lifetimes affect the distributions. Certain base-pair sequences are found to promote long-lived bubbles, and we argue that this is a result of length scale competition between the nonlinearity and disorder present in the system.
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
authors.forename: B S
authors.initials: BS
authors.lastname: Alexandrov
authors.forename: L T
authors.initials: LT
authors.lastname: Wille
authors.forename: K Ø
authors.initials: KØ
authors.lastname: Rasmussen
authors.forename: A R
authors.initials: AR
authors.lastname: Bishop
authors.forename: K B
authors.initials: KB
authors.lastname: Blagoev
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D013696:Temperature
chemical_list: D009711:Nucleotides; D004247:DNA