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

AuthorsD'Ovidio, Francesco; Bohr, Henrik Georg; Lindgaard, Per-Anker
Lennard-Jones potential
Hydrogen bonds
Vibrational modes
Molecular biophysics
Issue Date15-Feb-2005
PublisherAmerican Physical Society
CitationPhysical Review E 71, 026606 (1-9) (2005)
AbstractWe study the propagation of solitons along the hydrogen bonds of an alpha 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 alpha helices may help to explain recent x-ray experiments on long alpha helices in Rhodopsin where a long lifetime of the vibrational modes has been observed.
Description9 pages, 13 figures.-- PACS nrs.: 05.45.Yv, 87.15.-v.-- PMID: 15783440 [PubMed].
Publisher version (URL)http://dx.doi.org/10.1103/PhysRevE.71.026606
Appears in Collections:(IFISC) Artículos
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