2002/11/30 by Francesco d'Ovidio, Francesco d Ovidio, Henrik Bohr +2 · 14 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Chemistry #Crystallography #Formalism (music) #Hydrogen bond #Integrable system #Laser #Lattice (music) #Mathematical physics #Molecular physics #Molecular spectroscopy and chirality #Molecule #Nonlinear Photonic Systems #Nonlinear system #Perturbation (astronomy) #Physics #Quantum mechanics #Soliton #Spectroscopy and Quantum Chemical Studies #Toda lattice #cond-mat #q-bio.BM
paper · pdf · doi:10.1088/0953-8984/15/18/304
published in Journal of Physics Condensed Matter 15(18), S1699-S1707 (IOP Publishing) · 6 pages, 7 figures
openalex publication_date 2003/04/28 · arxiv created 2003/09/16 · arxiv updated 2009/11/30 · openalex created_date 2016/06/24 · openalex updated_date 2026/08/05
A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs the formalism of fully integrable Toda lattices in three dimensions which admit phonons as well as solitons along the hydrogen bonds of the helices. A simulation of the three-dimensional Toda lattice system shows that the solitons are spontaneously created and are stable and moving along the helix axis. A perturbation on one of the three H-bond lines forms solitons on the other H bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm −1 which are found in recent x-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins.