dorsal/arxiv
View SchemaDisorder and fluctuations in nonlinear excitations in DNA
| Authors | Sara Cuenda, Angel Sanchez |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0403003 |
| URL | https://arxiv.org/abs/q-bio/0403003 |
| DOI | 10.1117/12.548346 |
Abstract
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic potentials, [F. Dom\'\i nguez-Adame {\em et al.}, Phys. Rev. E {\bf 52}, 2183 (1995)], we analyze the behavior of lattices built from real DNA sequences obtained from human genome data. We confirm the existence of threshold forces, already found in Fibonacci sequences, and of stop positions highly dependent on the specific sequence. Another relevant conclusion is that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A {\bf 193}, 263 (1994)] is a useful tool to identify key regions that control the behaviour of a larger sequence. We then study how the fluctuations can assist the propagation process by helping the excitations to escape the stop positions. Our conclusions point out to improvements of the model which look promising to describe mechanical denaturation of DNA. Finally, we also consider how randomly distributed energy focus on the chain as a function of the sequence.
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"abstract": "We study the effects of the sequence on the propagation of nonlinear\nexcitations in simple models of DNA, and how those effects are modified by\nnoise. Starting from previous results on soliton dynamics on lattices defined\nby aperiodic potentials, [F. Dom\\\u0027\\i nguez-Adame {\\em et al.}, Phys. Rev. E\n{\\bf 52}, 2183 (1995)], we analyze the behavior of lattices built from real DNA\nsequences obtained from human genome data. We confirm the existence of\nthreshold forces, already found in Fibonacci sequences, and of stop positions\nhighly dependent on the specific sequence. Another relevant conclusion is that\nthe effective potential, a collective coordinate formalism introduced by\nSalerno and Kivshar [Phys. Lett. A {\\bf 193}, 263 (1994)] is a useful tool to\nidentify key regions that control the behaviour of a larger sequence. We then\nstudy how the fluctuations can assist the propagation process by helping the\nexcitations to escape the stop positions. Our conclusions point out to\nimprovements of the model which look promising to describe mechanical\ndenaturation of DNA. Finally, we also consider how randomly distributed energy\nfocus on the chain as a function of the sequence.",
"arxiv_id": "q-bio/0403003",
"authors": [
"Sara Cuenda",
"Angel Sanchez"
],
"categories": [
"q-bio.BM",
"cond-mat.dis-nn",
"math-ph",
"math.MP",
"nlin.PS",
"q-bio.GN"
],
"doi": "10.1117/12.548346",
"title": "Disorder and fluctuations in nonlinear excitations in DNA",
"url": "https://arxiv.org/abs/q-bio/0403003"
},
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