Nonlinear breathing modes at a defect

Wattis, Jonathan A.D.

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.

Citation

Wattis, J. A. (2004). Nonlinear breathing modes at a defect. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 362,

• Journal Article Type: Article
• Publication Date: Jan 1, 2004
• Deposit Date: Aug 15, 2008
• Publicly Available Date: Aug 15, 2008
• Journal: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
• Electronic ISSN: 1364-503X
• Publisher: The Royal Society
• Peer Reviewed: Peer Reviewed
• Volume: 362
• Keywords: Localisation, defect, lattice model, breathers
• Public URL: https://nottingham-repository.worktribe.com/output/1021840
• Publisher URL: http://journals.royalsociety.org/content/4qja9tmm6jnf9j8a/fulltext.pdf
• Additional Information: Published as: Nonlinear breathing modes due to a defect in a DNA chain.