2004/11/24 by Natalia L. Komarova, Natalia Komarova, Avy Soffer +2
Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Physical sciences #Nonlinear Dynamics and Pattern Formation #Nonlinear Photonic Systems #Soft Condensed Matter (cond-mat.soft) #Spectroscopy and Quantum Chemical Studies #cond-mat.soft #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.cond-mat/0411621
to appear in Bull. Math. Biology
openalex publication_date 2004/11/24 · arxiv created 2004/12/21 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 it "curvature dissipation". The equations 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.