title: Nonlinear excitations in DNA: aperiodic models versus actual genome sequences.
abstract: We study the effects of the genetic sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual data from the human genome. We show that kink propagation requires forces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Domínguez-Adame et al., Phys. Rev. E 52, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent on the specific sequence. Contrary to the conjecture advanced by Domínguez-Adame and co-workers, we find no evidence supporting the dependence of the kink dynamics on the information content of the genetic sequences considered. We discuss possible reasons for that result as well as its practical consequences. Physically, the results of our model are consistent with the stick-slip dynamics of the unzipping process observed in experiments. We also show that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A 193, 263 (1994)], is a useful tool to identify key regions in DNA that control the dynamical behavior of large segments. As a side result, we extend the previous studies on aperiodic sequences by analyzing the effect of the initial position of the kink, leading to further insight on the phenomenology observed in such systems.
authors.affiliation: Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganés, Madrid, Spain. scuenda@math.uc3m.es
authors.forename: Sara
authors.initials: S
authors.lastname: Cuenda
authors.forename: Angel
authors.initials: A
authors.lastname: Sánchez
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D015894:Genome, Human; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017711:Nonlinear Dynamics; D009690:Nucleic Acid Conformation; D010507:Periodicity; D010812:Physical Stimulation / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D013314:Stress, Mechanical
chemical_list: D004247:DNA