PMID: 11308512Apr 20, 2001Paper

Bubble propagation in a helicoidal molecular chain

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
A Campa

Abstract

We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the "transcription bubble," where the hydrogen bonds between complementary bases are disrupted, allowing access to the genetic code. We propose these kinds of excitations in alternative to kinks and breathers. The model has been introduced by Barbi et al. [Phys. Lett. A 253, 358 (1999)], and up to now it has been used to study on the one hand low amplitude breather solutions, and on the other hand the DNA melting transition. We extend the model to include the case of heterogeneous chains, in order to get closer to a description of real DNA; in fact, the Morse potential representing the interaction between complementary bases has two possible depths, one for A-T and one for G-C base pairs. We first compute the equilibrium configurations of a chain with a degree of uncoiling, and we find that a static bubble is among them; then we show, by molecular dynamics simulations, that these bubbles, once generated, can move along the chain. We find that also in the most unfavorable case, that of a heterogeneous DNA in the presence of thermal noise, the excitation ...Continue Reading

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Citations

May 17, 2005·Bulletin of Mathematical Biology·Natalia L Komarova, Avy Soffer
Sep 29, 2011·The Journal of Chemical Physics·Marco Zoli
Oct 24, 2007·The Journal of Chemical Physics·Debarati ChatterjeeBinny J Cherayil
Nov 5, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·P V LarsenYu B Gaididei
Mar 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Mariano CadoniGiuseppe Gaeta
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·V Vasumathi, M Daniel
Nov 9, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·S BehniaM Ghaderian
Jun 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M Vanitha, M Daniel
Nov 9, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M Daniel, M Vanitha
Mar 5, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M Daniel, V Vasumathi
Apr 12, 2003·Physical Review Letters·Grégoire Altan-BonnetOleg Krichevsky
Feb 3, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Maria BarbiNikos Theodorakopoulos
Jun 19, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Anil Kumar DasannaManoel Manghi
Sep 21, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·L V YakushevichL I Manevitch
Feb 1, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Elías Zamora-SilleroFrancisco J Esteban

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