Nonlinear breathing modes at a defect

Wattis, Jonathan A.D. (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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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.
Keywords: Localisation, defect, lattice model, breathers
Schools/Departments: University of Nottingham, UK > Faculty of Science > School of Mathematical Sciences
Depositing User: Wattis, Jonathan
Date Deposited: 15 Aug 2008 15:06
Last Modified: 04 May 2020 20:31

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