Nonlinear waves in double-stranded DNA

Natalia L. Komarova; Avy Soffer

doi:https://doi.org/10.1016/j.bulm.2004.09.008

Nonlinear waves in double-stranded DNA

Natalia L. Komarova, Avy Soffer

School of Arts and Sciences, Mathematics

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the propagating bubble, and we term this 'curvature dissipation'. The equations that we derive allow for stable pinned localized kinks which form the bubble. We perform the stability analysis and specify the energy requirements for the motion of the localized solutions. Our findings are consistent with properties of DNA dynamics, and can be used in models for denaturation bubbles, RNA and DNA transcription, nucleotide excision repair and meiotic recombination.

Original language	English (US)
Pages (from-to)	701-718
Number of pages	18
Journal	Bulletin of Mathematical Biology
Volume	67
Issue number	4
DOIs	https://doi.org/10.1016/j.bulm.2004.09.008
State	Published - Jul 2005

ASJC Scopus subject areas

Neuroscience(all)
Immunology
Mathematics(all)
Biochemistry, Genetics and Molecular Biology(all)
Environmental Science(all)
Pharmacology
Agricultural and Biological Sciences(all)
Computational Theory and Mathematics

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abstract = "We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the propagating bubble, and we term this 'curvature dissipation'. The equations that we derive allow for stable pinned localized kinks which form the bubble. We perform the stability analysis and specify the energy requirements for the motion of the localized solutions. Our findings are consistent with properties of DNA dynamics, and can be used in models for denaturation bubbles, RNA and DNA transcription, nucleotide excision repair and meiotic recombination.",

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AU - Soffer, Avy

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AB - We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the propagating bubble, and we term this 'curvature dissipation'. The equations that we derive allow for stable pinned localized kinks which form the bubble. We perform the stability analysis and specify the energy requirements for the motion of the localized solutions. Our findings are consistent with properties of DNA dynamics, and can be used in models for denaturation bubbles, RNA and DNA transcription, nucleotide excision repair and meiotic recombination.

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SP - 701

EP - 718

JO - Bulletin of Mathematical Biology

JF - Bulletin of Mathematical Biology

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ER -

Nonlinear waves in double-stranded DNA

Abstract

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