- published: 10 Sep 2015
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Davydov soliton is a quantum quasiparticle representing an excitation propagating along the protein α-helix self-trapped amide I. It is a solution of the Davydov Hamiltonian. It is named for the Soviet and Ukrainian physicist Alexander Davydov. The Davydov model describes the interaction of the amide I vibrations with the hydrogen bonds that stabilize the α-helix of proteins. The elementary excitations within the α-helix are given by the phonons which correspond to the deformational oscillations of the lattice, and the excitons which describe the internal amide I excitations of the peptide groups. Referring to the atomic structure of an α-helix region of protein the mechanism that creates the Davydov soliton (polaron, exciton) can be described as follows: vibrational energy of the C=O stretching (or amide I) oscillators that is localized on the α-helix acts through a phonon coupling effect to distort the structure of the α-helix, while the helical distortion reacts again through phonon coupling to trap the amide I oscillation energy and prevent its dispersion. This effect is called self-localization or self-trapping.Solitons in which the energy is distributed in a fashion preserving the helical symmetry are dynamically unstable, and such symmetrical solitons once formed decay rapidly when they propagate. On the other hand, an asymmetric soliton which spontaneously breaks the local translational and helical symmetries possesses the lowest energy and is a robust localized entity.
A "polaron" is a quasiparticle used in condensed matter physics to understand the interactions between electrons and atoms in a solid material. The polaron concept was first proposed by Lev Landau in 1933 to describe an electron moving in a dielectric crystal where the atoms move from their equilibrium positions to effectively screen the charge of an electron, known as a phonon cloud. This lowers the electron mobility and increases the electron's effective mass. The general concept of a polaron has been extended to describe other interactions between the electrons and ions in metals that result in a bound state, or a lowering of energy compared to the non-interacting system. Major theoretical work has focused on solving Fröhlich and Holstein Hamiltonians. This is still an active field o...