Nonlinear breathing modes at a defect
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 o...
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| Format: | Article |
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Royal Society
2004
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| Online Access: | https://eprints.nottingham.ac.uk/938/ |
| _version_ | 1848790507044470784 |
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| author | Wattis, Jonathan A.D. |
| author_facet | Wattis, Jonathan A.D. |
| author_sort | Wattis, Jonathan A.D. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T18:13:42Z |
| format | Article |
| id | nottingham-938 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T18:13:42Z |
| publishDate | 2004 |
| publisher | Royal Society |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-9382020-05-04T20:31:43Z https://eprints.nottingham.ac.uk/938/ Nonlinear breathing modes at a defect Wattis, Jonathan A.D. 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. Royal Society 2004 Article PeerReviewed 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 Localisation defect lattice model breathers http://journals.royalsociety.org/content/4qja9tmm6jnf9j8a/fulltext.pdf |
| spellingShingle | Localisation defect lattice model breathers Wattis, Jonathan A.D. Nonlinear breathing modes at a defect |
| title | Nonlinear breathing modes at a defect |
| title_full | Nonlinear breathing modes at a defect |
| title_fullStr | Nonlinear breathing modes at a defect |
| title_full_unstemmed | Nonlinear breathing modes at a defect |
| title_short | Nonlinear breathing modes at a defect |
| title_sort | nonlinear breathing modes at a defect |
| topic | Localisation defect lattice model breathers |
| url | https://eprints.nottingham.ac.uk/938/ https://eprints.nottingham.ac.uk/938/ |