Dynamics of the Davydov model in<i>alpha</i>-helical proteins: Effects of the coupling parameter and temperature

Abstract

A model incorporating exciton-phonon interactions has been proposed as a mechanism for localizing and stabilizing energy transport in long-chain proteins. Previous analytical and numerical studies have not adequately addressed the effects of thermal phonons, which may act to disperse exciton energy. We have performed numerical calculations which indicate that excitons are strongly dispersed at biologically relevant temperatures. Furthermore, the propagation of the exciton-phonon system at low temperatures makes a transition from a solitary-wave mode to a stationary, self-trapped mode as the coupling between excitons and phonons is increased. We also report new calculations of exciton--normal-mode coupling in the formamide dimer, which indicate that more sophisticated models are necessary to yield the true coupling constant in proteins.