Related papers: Nonlinear molecular excitations in a completely in…
A couple of models are explained. Helicoidal PB model is studied in more details. It is shown that semi-discrete approximation yields to breather-type soliton moving along the chain. The model can explain local opening as a resonance mode.…
We consider the continuum version of an elastic chain supporting topological and non-topological degrees of freedom; this generalizes a model for the dynamics of DNA recently proposed and investigated by ourselves. In a certain limit, the…
We investigate the dynamics of the sine-Gordon solitons perturbed by spatiotemporal external forces. We prove the existence of internal (shape) modes of sine-Gordon solitons when they are in the presence of inhomogeneous space-dependent…
This paper examines the effects of a thin layer of inhomogeneity on periodic solutions of the Multiple-sine-Gordon (MsG) model. We investigate the dynamics of the perturbed Double-sine-Gordon (DsG) system as a significant and more practical…
The problem of stability and spectrum of linear excitations of a soliton (kink) of the dispersive sine-Gordon and $\varphi^4$ - equations is solved exactly. It is shown that the total spectrum consists of a discrete set of frequencies of…
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…
The transition from integrable to non-integrable highly-dispersive nonlinear models is investigated. The sine-Gordon and $\phi^4$-equations with the additional fourth-order spatial and spatio-temporal derivatives, describing the higher…
In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure…
In the present work, we study, by means of a one-dimensional lattice model, the collective excitations corresponding to intra molecular ones of a chain like proteins. It is shown that such excitations are described by the Nonlinear…
We study inhomogeneous quantum quenches in the attractive regime of the sine-Gordon model. In our protocol, the system is prepared in an inhomogeneous initial state in finite volume by coupling the topological charge density operator to a…
We use quantum sine-Gordon model to describe the low energy dynamics of a pair of coupled one-dimensional condensates of interacting atoms. We show that the nontrivial excitation spectrum of the quantum sine-Gordon model, which includes…
In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…
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…
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
We show that soliton interaction with finite-width inhomogeneities can activate a great number of soliton internal modes. We obtain the exact stationary soliton solution in the presence of inhomogeneities and solve exactly the stability…
We investigate the dynamics of the sine-Gordon solitons perturbed by spatiotemporal external forces. We prove the existence of internal (shape) modes of sine-Gordon solitons when they are in the presence of inhomogeneous space-dependent…
We theoretically analyse the equation of topological solitons in a chain of particles interacting via a repulsive power-law potential and confined by a periodic lattice. Starting from the discrete model, we perform a gradient expansion and…
In this paper, modulation instability and nonlinear supratransmission are investigated in a one-dimensional chain of atoms using cubic-quartic nonlinearity coefficients. As a result, we establish the discrete nonlinear evolution equation by…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
We prove the existence of an infinite number of internal (shape) modes of sine-Gordon solitons in the presence of some inhomogeneous long-range forces, provided some conditions are satisfied.