Statistical mechanics of a nonlinear model for DNA denaturation

Peyrard, Michel; Bishop, A. R.

doi:10.1103/physrevlett.62.2755

Cited by 988 publications

(1,001 citation statements)

References 20 publications

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“…Thus, the distance between the bases changes as the sites oscillate, which fact is assumed not to reflect on the exchange matrix elements. However this assumption is only valid for weak oscillations and fails to describe such phenomena as formation of open states and denaturation of a DNA [27].…”

Section: Discussion Of the Resultsmentioning

confidence: 99%

Sequence Dependent Hole Evolution in DNA

Лахно

2004

Journal of Biological Physics

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Abstract. The paper examines the dynamical behavior of a radical cation (G + * ) generated in a double stranded DNA for different oligonucleotide sequences. The resonance hole tunneling through an oligonucleotide sequence is studied by the method of numerical integration of self-consistent quantum-mechanical equations. The hole motion is considered quantum mechanically and nucleotide base oscillations are treated classically. The results obtained demonstrate a strong dependence of charge transfer on the type of nucleotide sequence. The rates of the hole transfer are calculated for different nucleotide sequences and compared with experimental data on the transfer from (G + * ) to a GGG unit.

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Section: Discussion Of the Resultsmentioning

confidence: 99%

Sequence Dependent Hole Evolution in DNA

Лахно

2004

Journal of Biological Physics

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“…Recentemente, o interesse pelo tratamento clássico desse potencial tem aumentado bastante, em particular, devido a ele ser usado para simular as interações de ponte de hidrogênio em modelos mecânicos do DNA. Essa abordagem, proposta inicialmente no final da década de 1980 [8,9], tem sido muito utilizada desde então. Para uma revisão recente veja a Ref.…”

Section: Introductionunclassified

Solução analítica do potencial de Morse em mecânica clássica

Barboza¹,

Costa²,

Ribeiro³

et al. 2007

Rev. Bras. Ens. Fis.

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Usualmente o potencial de Morseé estudado em contextos de mecânica quântica. Por outro lado, eleé relativamente pouco aplicado em problemas clássicos. Neste trabalho uma solução completaé encontrada para as equações de movimento clássicas para uma partícula submetida a esse potencial. Exemplos numéricos são apresentados para alguns valores fixos dos parâmetros. Palavras-chave: mecânica clássica, potencial de Morse, equação de movimento.Usually the Morse potential is studied in the quantum mechanics context. On the other hand, there are relatively few applications for classical problems. In this work, a complete solution for the classical equation of motion is found for a particle subject to this potential. Numerical examples are presented for a fixed set of parameters.

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“…Surprisingly, the passage of the DNA kinks through the CDS region was not modeled by investigators, though the necessary mathematical formalism has been already developed. We can point out the model of Peyrard and Bishop [10] that takes into account the transverse motions of nucleotides, the Y-model [11][12][13] that takes into account the angular displacements of nitrous bases, the combined model [14] that takes into account both the angular and the transverse displacements, and numerous modifications of these models [15][16][17][18][19][20]. Any of them could be used for the purpose.…”

Section: Introductionmentioning

confidence: 99%

Траектории Кинков ДНК В Последовательностях, Содержащих Кодирующие Области Генов

Якушевич¹,

Yakushevich²

2017

Math.Biol.Bioinf.

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Coding regions (CDS) being an integral part of any gene sequence, play an important role in the process of transcription. One of the tasks associated with the CDS regions, consists in the modeling of the passage of transcription bubbles named also open states or DNA kinks through the coding regions. In this paper, we present a simple and convenient approach to the modeling of the passage. It includes the calculation of the energy profile of the sequence and reducing the initial task to the modeling of the movement of a quasi particle in the field with this energy profile. To illustrate the method, we present the results of the calculations of the trajectories of the DNA kinks moving in the sequence of gene coding interferon alpha 17 (IFNA17) that consists of the three regions: the coding region and the two regions with unknown functional properties. To analyze the kink dynamics, we apply approximation where the DNA parameters are being averaged separately over each of the three regions. In the absences of dissipation, the total kink energy is constant. At the same time the kink velocity is constant only inside each of the regions. In the presence of dissipation, the total kink energy decreases. It is shown that the greater the total initial energy of the kink, the faster the energy decrease. It is suggested that the proposed approach could be useful in finding the ways to govern the movement of transcription bubbles at the first stage of the process of transcription.

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Statistical mechanics of a nonlinear model for DNA denaturation

Cited by 988 publications

References 20 publications

Sequence Dependent Hole Evolution in DNA

Sequence Dependent Hole Evolution in DNA

Solução analítica do potencial de Morse em mecânica clássica

Траектории Кинков ДНК В Последовательностях, Содержащих Кодирующие Области Генов

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