Solitary waves dynamic for Davydov α-helical protein model: Effects of localized and periodic inhomogeneities.

Abstract

We describe the dynamic of excitons through single inhomogeneous α-helical proteins with off-diagonal and diagonal couplings. Inhomogeneities considered are either localized or periodic. Intensive numerical simulations carried show stable structures and allow us to single out important features of excitons dynamic. In the absence of inhomogeneities, the interplay between off-diagonal and diagonal couplings leads to two distinct types of solitary waves. Bright solitary waves correspond to an off-diagonal coupling constant lower than a critical diagonal coupling constant, while dark solitary waves are obtained in the opposite case. Inclusion of inhomogeneities profoundly affects the profiles, amplitudes, and energies transported by the waves. For relatively small strength of inhomogeneities, only the profiles of the waves significantly change, the other properties remaining almost unchanged. Large strength inhomogeneities sensitively twist the profiles and increase amplitudes and energies of the waves. Our study suggests that small strength inhomogeneities allow a coherent transport of energy and the biological functions remain unchanged, but large strengths of inhomogeneities affect the biological functioning of the α-helical protein chains. Hence, large strengths of inhomogeneities may amplify the energy of the molecule and could be used to treat some diseases.