@article { , title = {Nonlinear breathing modes at a defect}, 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.}, eissn = {1364-503X}, journal = {Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences}, publicationstatus = {Published}, publisher = {The Royal Society}, url = {https://nottingham-repository.worktribe.com/output/1021840}, volume = {362}, keyword = {Localisation, defect, lattice model, breathers}, year = {2004}, author = {Wattis, Jonathan A.D.} }