Nonlinear breathing modes at a defect

Wattis, Jonathan AD (2004) Nonlinear breathing modes at a defect. Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences, 362 . pp. 1461-1477. ISSN 1364-503X

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Official URL: http://journals.royalsociety.org/content/4qja9tmm6jnf9j8a/fulltext.pdf

Abstract

Recent molecular dynamics (MD) simulations of Cubero et al (1999) of a DNA duplex containing the 'rogue' base difluorotoluene (F) in place of a thymine (T) base show that breathing events can occur on the nanosecond timescale, whereas breathing events in a normal DNA duplex take place on the microsecond timescale. The main aim of this paper is to analyse a nonlinear Klein-Gordon lattice model of the DNA duplex including both nonlinear interactions between opposing bases and a defect in the interaction at one lattice site; each of which can cause localisation of energy. Solutions for a breather mode either side of the defect are derived using multiple-scales asymptotics and are pieced together across the defect to form a solution which includes the effects of the nonlinearity and the defect. We consider defects in the inter-chain interactions and in the along chain interactions. In most cases we find in-phase breather modes and/or out-of-phase breather modes, with one case displaying a shifted mode.

Item Type:Article
Additional Information:Published as: Nonlinear breathing modes due to a defect in a DNA chain.
Uncontrolled Keywords:Localisation, defect, lattice model, breathers
Schools/Departments:Faculty of Science > School of Mathematical Sciences
ID Code:938
Deposited By:Wattis, Jonathan
Deposited On:15 Aug 2008 16:06
Last Modified:27 Jun 2011 11:22

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