Related papers: Nonlinear Localized Excitations and the Dynamics o…
Physico-mechanical properties of polymers in solid state, in particular conditions of their structural transformations, are substantially defined by existence and mobility of elementary nonlinear excitations. The localized oscillatory…
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…
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…
Discrete breathers, or intrinsic localized modes, are spatially localized, time--periodic, nonlinear excitations that can exist and propagate in systems of coupled dynamical units. Recently, some experiments show the sighting of a form of…
We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as…
Artificial intelligence in the form of deep learning is now very popular and directly implemented in many areas of science and technology. In the present work we study time evolution of Discrete Breathers in one-dimensional nonlinear chains…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
In this communication, we examine a nonlinear model with an impurity emulating a bend. We justify the geometric interpretation of the model and connect it with earlier work on models including geometric effects. We focus on both the…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
We consider time-periodic nonlinear localized excitations (NLEs) on one-dimensional translationally invariant Hamiltonian lattices with arbitrary finite interaction range and arbitrary finite number of degrees of freedom per unit cell. We…
In this paper we consider a 2D hexagonal crystal lattice model first proposed by Marin, Eilbeck and Russell in 1998. We perform a detailed numerical study of nonlinear propagating localized modes, that is, propagating discrete breathers and…
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 propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
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.…
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,…
We describe results concerning the existence proofs of Discrete Breathers (DBs) in the two classes of dynamical systems with optical linear phonons and with acoustic linear phonons. A standard approach is by continuation of DBs from an…
Nonlinear classical Hamiltonian lattices exhibit generic solutions in the form of discrete breathers. These solutions are time-periodic and (typically exponentially) localized in space. The lattices exhibit discrete translational symmetry.…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
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…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…