Abstract
We study the propagation of solitons along the hydrogen bonds of an 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 helices may help to explain recent x-ray experiments on long helices in Rhodopsin where a long lifetime of the vibrational modes has been observed.
6 More- Received 20 May 2004
DOI:https://doi.org/10.1103/PhysRevE.71.026606
©2005 American Physical Society