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Nonlinear excitatios in DNA: aperiodic models versus actual genome sequences

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dc.affiliation.dptoUC3M. Departamento de Matemáticases
dc.affiliation.grupoinvUC3M. Grupo de Investigación: Interdisciplinar de Sistemas Complejos (GISC)es
dc.contributor.authorCuenda, Sara
dc.contributor.authorSánchez, Angel
dc.date.accessioned2012-08-30T08:10:26Z
dc.date.available2012-08-30T08:10:26Z
dc.date.issued2004-11
dc.description.abstractWe 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.es
dc.description.sponsorshipThis work has been supported by the Ministerio de Ciencia y Tecnología of Spain through Grant No. BFM2003-07749-C05-01. S.C. is supported by the Consejería de Educación de la Comunidad Autónoma de Madrid and the Fondo Social Europeo.es
dc.description.statusPublicadoes
dc.format.mimetypeapplication/pdf
dc.identifier.bibliographicCitationPhysical Review E, vol. 70, n. 5, nov. 2004. Pp. 1-8es
dc.identifier.doi10.1103/PhysRevE.70.051903
dc.identifier.issn1539-3755 (print version)
dc.identifier.issn1550-2376 (online version)
dc.identifier.urihttps://hdl.handle.net/10016/15148
dc.language.isoenges
dc.publisherAmerican Physical Societyes
dc.relation.publisherversionhttp://dx.doi.org/10.1103/PhysRevE.70.051903
dc.rights.accessRightsopen accesses
dc.subject.ecienciaMatemáticases
dc.titleNonlinear excitatios in DNA: aperiodic models versus actual genome sequenceses
dc.typeresearch article*
dc.type.hasVersionVoR*
dspace.entity.typePublication
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