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Article Dans Une Revue Physical Review E : Statistical, Nonlinear, and Soft Matter Physics Année : 2005

Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

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We study the propagation of solitons along the hydrogen bonds of an α helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jones potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons. The soliton phenomena described in the simulations of α helices may help to explain recent x-ray experiments on long α helices in Rhodopsin where a long lifetime of the vibrational modes has been observed.
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hal-00770747 , version 1 (17-03-2022)

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Francesco d'Ovidio, Henrik Georg Bohr, Per-Anker Lindgård. Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins. Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2005, 71, pp.26606. ⟨10.1103/PHYSREVE.71.026606⟩. ⟨hal-00770747⟩
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