RT Journal Article
T1 Nonlinear excitatios in DNA: aperiodic models versus actual genome sequences
A1 Cuenda, Sara
A1 Sánchez, Angel
AB We study the effects of the genetic sequence on the propagation of nonlinear excitations in simple models ofDNA in which we incorporate actual data from the human genome. We show that kink propagation requiresforces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Domínguez-Adame etal., Phys. Rev. E 52, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent onthe specific sequence. Contrary to the conjecture advanced by Domínguez-Adame and co-workers, we find noevidence supporting the dependence of the kink dynamics on the information content of the genetic sequencesconsidered. We discuss possible reasons for that result as well as its practical consequences. Physically, theresults 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 andKivshar [Phys. Lett. A 193, 263 (1994)], is a useful tool to identify key regions in DNA that control thedynamical behavior of large segments. As a side result, we extend the previous studies on aperiodic sequencesby analyzing the effect of the initial position of the kink, leading to further insight on the phenomenologyobserved in such systems.
PB American Physical Society
SN 1539-3755 (print version)
SN 1550-2376 (online version)
YR 2004
FD 2004-11
LK https://hdl.handle.net/10016/15148
UL https://hdl.handle.net/10016/15148
LA eng
NO This 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.
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RD 1 sept. 2024