Two-dimensional discrete model for DNA dynamics: Longitudinal wave propagation and denaturation

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Abstract
In this paper, a simple, two-dimensional model of the deoxyribonucleic acid (DNA) is presented. In the model the two polynucleotide strands are linked together through the hydrogen bonds. The phosphodiester bridges in the backbone are described by the anharmonic potential of Toda kind, while the hydrogen bonds are described by the Lennard-Jones potential. Longitudinal wave propagation on ring-shaped DNA molecules is investigated. The model predicts a significant increase in the lifetime of the open states of the hydrogen bonds at physiological temperatures. Thus anharmonicity may play a role in DNA denaturation.