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Acoustic and Optical Soliton Excitations in the Peyrard-Bishop Model of DNA Dynamics with Alternating A-T and G-C Base Pairs

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Abstract:

With an attempt to describe DNA dynamics in a more realistic way, we introduce an extended Peyrard-Bishop (PB) model which takes into account the possible alternation between AT and GC pairs. The out-of-phase motion is then described by a set of coupled discrete differential equations which implies the existence of optical and acoustic modes. Through the semi-discrete approximation, a complex Ginzburg-Landau (CGL) equation describes the dynamics of the base pairs. It is shown that, the more probable DNA dynamics occurs in the optical mode, since it has a deep influence in energy exchange and collision phenomena.

Keywords: BUBBLE; COMPLEX GINZBURG-LANDAU (CGL) EQUATION; HIROTA'S METHOD; REPLICATION

Document Type: Research Article

DOI: http://dx.doi.org/10.1166/jctn.2008.1120

Publication date: November 1, 2008

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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