Davydov soliton is a quantum
quasiparticle
In physics, quasiparticles and collective excitations are closely related emergent phenomena arising when a microscopically complicated system such as a solid behaves as if it contained different weakly interacting particles in vacuum.
For exa ...
representing an excitation propagating along the
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
α-helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ...
self-trapped
amide I. It is a solution of the Davydov
Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
. It is named for the Soviet and Ukrainian physicist
Alexander Davydov. The Davydov model describes the interaction of the amide I
vibration
Vibration is a mechanical phenomenon whereby oscillations occur about an equilibrium point. The word comes from Latin ''vibrationem'' ("shaking, brandishing"). The oscillations may be periodic, such as the motion of a pendulum—or random, su ...
s with the
hydrogen bonds that stabilize the
α-helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ...
of
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
s. 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
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 proposed by Lev Landau in 1933 and Solomon Pekar in 1946 to describe an electro ...
,
exciton) can be described as follows:
vibration
Vibration is a mechanical phenomenon whereby oscillations occur about an equilibrium point. The word comes from Latin ''vibrationem'' ("shaking, brandishing"). The oscillations may be periodic, such as the motion of a pendulum—or random, su ...
al
energy
In physics, energy (from Ancient Greek: ἐνέργεια, ''enérgeia'', “activity”) is the quantitative property that is transferred to a body or to a physical system, recognizable in the performance of work and in the form of hea ...
of the
C=O stretching
Stretching is a form of physical exercise in which a specific muscle or tendon (or muscle group) is deliberately flexed or stretched in order to improve the muscle's felt elasticity and achieve comfortable muscle tone. The result is a feeling ...
(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''.
[
] Soliton
In mathematics and physics, a soliton or solitary wave is a self-reinforcing wave packet that maintains its shape while it propagates at a constant velocity. Solitons are caused by a cancellation of nonlinear and dispersive effects in the medi ...
s in which the
energy
In physics, energy (from Ancient Greek: ἐνέργεια, ''enérgeia'', “activity”) is the quantitative property that is transferred to a body or to a physical system, recognizable in the performance of work and in the form of hea ...
is distributed in a fashion preserving the
helical
Helical may refer to:
* Helix, the mathematical concept for the shape
* Helical engine, a proposed spacecraft propulsion drive
* Helical spring, a coilspring
* Helical plc, a British property company, once a maker of steel bar stock
* Helicoil
A t ...
symmetry are dynamically unstable, and such
symmetric
Symmetry (from grc, συμμετρία "agreement in dimensions, due proportion, arrangement") in everyday language refers to a sense of harmonious and beautiful proportion and balance. In mathematics, "symmetry" has a more precise definiti ...
al 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.
[
]
Davydov Hamiltonian
Davydov
Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
is formally similar to the
Fröhlich-Holstein Hamiltonian for the interaction of electrons with a polarizable lattice. Thus the
Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
of the
energy operator is
:
where
is the
exciton Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
, which describes the motion of the amide I excitations between adjacent sites;
is the
phonon Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
, which describes
the
vibration
Vibration is a mechanical phenomenon whereby oscillations occur about an equilibrium point. The word comes from Latin ''vibrationem'' ("shaking, brandishing"). The oscillations may be periodic, such as the motion of a pendulum—or random, su ...
s of the
lattice
Lattice may refer to:
Arts and design
* Latticework, an ornamental criss-crossed framework, an arrangement of crossing laths or other thin strips of material
* Lattice (music), an organized grid model of pitch ratios
* Lattice (pastry), an orna ...
; and
is the
interaction
Interaction is action that occurs between two or more objects, with broad use in philosophy and the sciences. It may refer to:
Science
* Interaction hypothesis, a theory of second language acquisition
* Interaction (statistics)
* Interactions o ...
Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
, which describes the interaction of the amide I excitation with the lattice.
The
exciton Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
is
:
where the index
counts the peptide groups along the α-helix spine, the index
counts each α-helix spine,
z J is the energy of the amide I
vibration (CO stretching),
z J is the
dipole
In physics, a dipole () is an electromagnetic phenomenon which occurs in two ways:
*An electric dipole deals with the separation of the positive and negative electric charges found in any electromagnetic system. A simple example of this system ...
-
dipole
In physics, a dipole () is an electromagnetic phenomenon which occurs in two ways:
*An electric dipole deals with the separation of the positive and negative electric charges found in any electromagnetic system. A simple example of this system ...
coupling energy between a particular amide I bond and those ahead and behind along the same spine,
z J is the
dipole-dipole coupling energy between a particular amide I bond and those on adjacent spines in the same unit cell of the
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
α-helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ...
,
and
are respectively
the
boson
In particle physics, a boson ( ) is a subatomic particle whose spin quantum number has an integer value (0,1,2 ...). Bosons form one of the two fundamental classes of subatomic particle, the other being fermions, which have odd half-integer spi ...
creation and annihilation operator for an amide I exciton at the
peptide group .
[
][
][
]
The
phonon Hamiltonian
Hamiltonian may refer to:
* Hamiltonian mechanics, a function that represents the total energy of a system
* Hamiltonian (quantum mechanics), an operator corresponding to the total energy of that system
** Dyall Hamiltonian, a modified Hamiltonian ...
is
: