dorsal/arxiv
View SchemaA composite model for DNA torsion dynamics
| Authors | M. Cadoni, R. De Leo, G. Gaeta |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0604014 |
| URL | https://arxiv.org/abs/q-bio/0604014 |
| DOI | 10.1103/PhysRevE.75.021919 |
| Journal | Phys. Rev. E75 (2007), 021919 |
Abstract
DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits made of a nucleoside and the attached nitrogen bases are described by a single degree of freedom. In this paper we propose and investigate, both analytically and numerically, a ``composite'' version of the Y model, in which the nucleoside and the base are described by separate degrees of freedom. The model proposed here contains as a particular case the Y model and shares with it many features and results, but represents an improvement from both the conceptual and the phenomenological point of view. It provides a more realistic description of DNA and possibly a justification for the use of models which consider the DNA chain as uniform. It shows that the existence of solitons is a generic feature of the underlying nonlinear dynamics and is to a large extent independent of the detailed modelling of DNA. The model we consider supports solitonic solutions, qualitatively and quantitatively very similar to the Y solitons, in a fully realistic range of all the physical parameters characterizing the DNA.
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"abstract": "DNA torsion dynamics is essential in the transcription process; a simple\nmodel for it, in reasonable agreement with experimental observations, has been\nproposed by Yakushevich (Y) and developed by several authors; in this, the DNA\nsubunits made of a nucleoside and the attached nitrogen bases are described by\na single degree of freedom. In this paper we propose and investigate, both\nanalytically and numerically, a ``composite\u0027\u0027 version of the Y model, in which\nthe nucleoside and the base are described by separate degrees of freedom. The\nmodel proposed here contains as a particular case the Y model and shares with\nit many features and results, but represents an improvement from both the\nconceptual and the phenomenological point of view. It provides a more realistic\ndescription of DNA and possibly a justification for the use of models which\nconsider the DNA chain as uniform. It shows that the existence of solitons is a\ngeneric feature of the underlying nonlinear dynamics and is to a large extent\nindependent of the detailed modelling of DNA. The model we consider supports\nsolitonic solutions, qualitatively and quantitatively very similar to the Y\nsolitons, in a fully realistic range of all the physical parameters\ncharacterizing the DNA.",
"arxiv_id": "q-bio/0604014",
"authors": [
"M. Cadoni",
"R. De Leo",
"G. Gaeta"
],
"categories": [
"q-bio.BM",
"physics.bio-ph"
],
"doi": "10.1103/PhysRevE.75.021919",
"journal_ref": "Phys. Rev. E75 (2007), 021919",
"title": "A composite model for DNA torsion dynamics",
"url": "https://arxiv.org/abs/q-bio/0604014"
},
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