Related papers: Solitons in alpha-helical proteins
A model of two coupled Ablowitz-Ladik (AL) lattices is introduced. While the system as a whole is not integrable, it admits reduction to the integrable AL model for symmetric states. Stability and evolution of symmetric solitons are studied…
The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of…
Dynamics of the Davydov's soliton in an external oscillating in time magnetic field is studied analytically. It is shown that in a field perpendicular to the molecular chain axis, soliton wavefunction is a product of the electron plane wave…
Existence, stability and dynamics of soliton complexes, centered at the site of a single transverse link connecting two parallel 2D (two-dimensional) lattices, are investigated. The system with the on-site cubic self-focusing nonlinearity…
The emergence of confined structures and pattern formation are exceptional manifestations of concurring nonlinear interactions found in a variety of physical, chemical and biological systems[1]. Optical solitons are a hallmark of extreme…
Solitons in liquid crystals are spatially localised stable configuration of the liquid crystal orientational order parameter that exhibit emergent particle-like properties such as mutual interaction, translational motion and reconfigurable…
We consider an array of dual-core waveguides, which represent an optical realization of a chain of dimers, with an active (gain-loss) coupling between the cores, opposite signs of discrete diffraction in the parallel arrays, and a…
The lineshape of spectroscopic transitions offer windows into the local environment of a system. Here, we present a novel approach for connecting the lineshape of a molecular exciton to finite-temperature lattice vibrations within the…
Protein clamps provide the cell with effective mechanisms for sensing of environmental changes and triggering adaptations that maintain homeostasis. The general physical mechanism behind protein clamping action, however, is poorly…
It has been observed that certain classical chains admit topologically protected zero-energy modes that are localized on the boundaries. The static features of such localized modes are captured by linearized equations of motion, but the…
General asymptotic approach to the stability problem of multi-parameter solitons in Hamiltonian systems $i\partial E_n/\partial z=\delta H/\delta E_n^*$ has been developed. It has been shown that asymptotic study of the soliton stability…
Symbiotic vortex-bright soliton structures with non-trivial topological charge in one component are found to be robust in immiscibel two-component superfluids, due to the effective potential created by a stable vortex in the other…
We report on the existence and stability of freely moving solitons in a spatially inhomogeneous Bose- Einstein condensate with helicoidal spin-orbit (SO) coupling. In spite of the periodically varying parameters, the system allows for the…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
Stability of soliton families in one-dimensional nonlinear Schroedinger equations with non-parity-time (PT)-symmetric complex potentials is investigated numerically. It is shown that these solitons can be linearly stable in a wide range of…
The low-energy physics of (quasi)degenerate one-dimensional systems is typically understood as the particle-like dynamics of kinks between stable, ordered structures. Such dynamics, we show, becomes highly non-trivial when the ground states…
A fully analytical theory of a traveling soliton in a one-dimensional fermionic superfluid is developed within the framework of time-dependent self-consistent Bogoliubov-de Gennes equations, which are solved exactly in the Andreev…
The formation of unstaggered localized modes in dynamical lattices can be supported by the interplay of discreteness and nonlinearity with a finite relaxation time. In rapidly responding nonlinear media, on-site discrete solitons are…
Soliton crystals are periodic patterns of multi-spot optical fields formed from either time or space entanglements of equally separated identical high-intensity pulses. These specific nonlinear optical structures have gained interest in…