Solitons in a nonlinear DNA model

González, Jorge A.; Martı́n-Landrove, Miguel

doi:10.1016/0375-9601(94)90795-1

Cited by 35 publications

(29 citation statements)

References 8 publications

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“…(1.8) 3 It should be stressed that -as remarked by Gonzalez and Martin-Landrove [15] -if we expand this in a power series for ϑ1, ϑ2 around ϑ1 = ϑ2 = 0, and assuming ℓ0 = 0, the quadratic term vanishes and…”

Section: Yakushevich Modelmentioning

confidence: 90%

Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

Gaeta¹

2007

JNMP

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The Yakushevich model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Yakushevich model, the interaction between bases of a pair is modelled by a harmonic potential, which becomes anharmonic when described in terms of the rotation angles; here we substitute to this different types of improved potentials, providing a more physical description of the H-bond mediated interactions between the bases. We focus in particular on soliton solutions; the Yakushevich model predicts the correct size of the nonlinear excitations supposed to model the "transcription bubbles", and this is essentially unchanged with the improved potential. Other features of soliton dynamics, in particular curvature of soliton field configurations and the Peierls-Nabarro barrier, are instead significantly changed.

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Section: Yakushevich Modelmentioning

confidence: 90%

Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

Gaeta¹

2007

JNMP

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“…In the standard Yakushevich model, one considers the approximation ℓ 0 → 0; it is known that this approximation has a strong impact on linearized dynamics and dispersion relations [20], but for what concerns fully nonlinear dynamics it has been observed that -at least in the framework of the Yakushevich model -the approximation has a very little impact on travelling solitons [17]. This suggests the possibility of considering the same approximation ℓ 0 = 0, hence A = R + r, here as well.…”

Section: The Modelmentioning

confidence: 99%

Solitons in a double pendulums chain model, and DNA roto-torsional dynamics

Cadoni

Лео

Gaeta

2007

JNMP

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It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [4] we argued for the advantages of an extension of this approach based on considering a chain of double pendulums with certain characteristics. Here we study a simplified model of this kind, focusing on its general features and nonlinear travelling wave excitations; in particular, we show that some of the degrees of freedom are actually slaved to others, allowing for an effective reduction of the relevant equations.

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“…The Y model has been studied in a number of paper, in particular for what concerns its solitonic solutions; here we will quote in particular [20,21,29,53,54,57]. It has been shown that it gives a correct prediction of quantities related to small amplitude dynamics, such as the frequency of small torsional oscillations; as well as of quantities related to fully nonlinear dynamics, such as the size of solitonic excitations describing transcription bubbles [26,56].…”

Section: Introductionmentioning

confidence: 99%

Composite model for DNA torsion dynamics

2007

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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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Solitons in a nonlinear DNA model

Cited by 35 publications

References 8 publications

Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

Solitons in a double pendulums chain model, and DNA roto-torsional dynamics

Composite model for DNA torsion dynamics

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