TY - JOUR
T1 - Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins
AU - D'ovidio, Francesco
AU - Bohr, Henrik
AU - Lindgård, Per-Anker
N1 - Copyright 2005 American Physical Society
PY - 2005
Y1 - 2005
N2 - We 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.
AB - We 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.
KW - 5-I nano
U2 - 10.1103/PhysRevE.71.026606
DO - 10.1103/PhysRevE.71.026606
M3 - Journal article
C2 - 15783440
SN - 1063-651X
VL - 71
SP - 026606
JO - Physical Review E. Statistical, Nonlinear, and Soft Matter Physics
JF - Physical Review E. Statistical, Nonlinear, and Soft Matter Physics
IS - 2
ER -