Related papers: Nonlinear molecular excitations in a completely in…
We study nonlinear dynamics of a periodic inhomogeneous DNA double helical chain under dynamic plane-base rotator model by considering angular rotation of bases in a plane normal to the helical axis. The dynamics is governed by a perturbed…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
We investigate the nonlinear dynamics of the Peyrard-Bishop DNA model taking into account site dependent inhomogeneities. By means of the multiple-scale expansion in the semi-discrete approximation, the dynamics is governed by the perturbed…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
We investigate propagation of a kink soliton along inhomogeneous chains with two different constituents, arranged either periodically, aperiodically, or randomly. For the discrete sine-Gordon equation and the Fibonacci and Thue-Morse chains…
In this work we analyze the possibility that soliton dynamics in a simple nonlinear model allows functionally relevant predictions of the behaviour of DNA. This suggestion was first put forward by Salerno [Phys. Rev. A, vol. 44, p. 5292…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
We present an analytical and numerical study of the Klein-Gordon kink-soliton dynamics in inhomogeneous media. In particular, we study an external field that is almost constant for the whole system but that changes its sign at the center of…
In the present paper we investigate the influence of inhomogeneities in the dynamics and stability of DNA open states, modeled as propagating solitons in the spirit of a Generalized Yakushevish Model. It is a direct consecuence of our model…
We have examined the dynamical behavior of the kink solutions of the one-dimensional sine-Gordon equation in the presence of a spatially periodic parametric perturbation. Our study clarifies and extends the currently available knowledge on…
Nonlinear wave propagation plays a crucial role in the functioning of many physical and biophysical systems. In the propagation regime, disturbances due to the presence of local external perturbations, such as localised defects or boundary…
Nonlinear space-time dynamics, defined in terms of celebrated 'solitonic' equations, brings indispensable tools for understanding, prediction and control of complex behaviors in both physical and life sciences. In this paper, we review…
Nonlinear dynamics of two biomolecules is studied. These are a microtubule and DNA molecule. Two mathematical procedures are explained, yielding to three kinds of solitary waves moving through the systems. These waves are kinks, modulated…
In this paper we deal with a nonlinear Schr\"{o}dinger equation with chaotic, random, and nonperiodic cubic nonlinearity. Our goal is to study the soliton evolution, with the strength of the nonlinearity perturbed in the space and time…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a…
The sine-Gordon equation is a fundamental nonlinear partial differential equation that governs soliton dynamics and phase evolution in a variety of physical systems, including Josephson junctions and superconducting circuits. In this study,…
We study the evolution of fronts in the Klein-Gordon equation when the nonlinear term is non-homogeneous. Extending previous works on homogeneous nonlinear terms, we describe the derivation of an equation governing the front motion, which…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…