Moving discrete breathers in a Klein Gordon chain with an impurity

Taming intrinsic localized modes in a DNA lattice with damping, external force, and inhomogeneity

The dynamics of DNA in the presence of uniform damping and periodic force is studied. The damped and driven Joyeux-Buyukdagli model is used to investigate the formation of intrinsic localized modes (ILMs). Branches of ILMs are identified as well as their orbital stabilities. A study of the effect of inhomogeneity introduced into the DNA lattice and its ability to control chaotic behavior is conducted. It is seen that a single defect in the chain can induce synchronized spatiotemporal patterns, despite the fact that the entire set of oscillators and the impurity are chaotic when uncoupled. It is also shown that the periodic excitation applied on a specific site can drive the whole lattice into chaotic or regular spatial and temporal patterns.

Extreme events due to localization of energy

We study a one-dimensional chain of harmonically coupled units in an asymmetric anharmonic soft potential. Due to nonlinear localization of energy, this system exhibits extreme events in the sense that individual elements of the chain show very large excitations. A detailed statistical analysis of extremes in this system reveals some unexpected properties, e.g., a pronounced pattern in the interevent interval statistics. We relate these statistical properties to underlying system dynamics and notice that often when extreme events occur the system dynamics adopts (at least locally) an oscillatory behavior, resulting in, for example, a quick succession of such events. The model therefore might serve as a paradigmatic model for the study of the interplay of nonlinearity, energy transport, and extreme events.

LOCALIZED BREATHER-LIKE EXCITATIONS IN THE HELICOIDAL PEYRARD–BISHOP MODEL OF DNA

We consider the one-dimensional helicoidal Peyrard–Bishop (PB) model of DNA dynamics. By means of a method based on the Jacobian elliptic functions, we obtain the exact analytical solution which describes the modulational instability and the propagation of a bright solitary wave on a continuous wave background. It is shown that these solutions depend on the modulational (or Benjamin-Feir) instability criterion. Numerical simulations of their propagation show these excitations to be long-lived and suggest that they are physically relevant for DNA.

Traveling and stationary intrinsic localized modes and their spatial control in electrical lattices

This work focuses on the production of both stationary and traveling intrinsic localized modes (ILMs), also known as discrete breathers, in two closely related electrical lattices; we demonstrate experimentally that the interplay between these two ILM types can be utilized for the purpose of spatial control. We describe a novel mechanism that is responsible for the motion of driven ILMs in this system, and quantify this effect by modeling in some detail the electrical components comprising the lattice.

Solitons in one-dimensional nonlinear Schrödinger lattices with a local inhomogeneity

In this paper we analyze the existence, stability, dynamical formation, and mobility properties of localized solutions in a one-dimensional system described by the discrete nonlinear Schrödinger equation with a linear point defect. We consider both attractive and repulsive defects in a focusing lattice. Among our main findings are (a) the destabilization of the on-site mode centered at the defect in the repulsive case, (b) the disappearance of localized modes in the vicinity of the defect due to saddle-node bifurcations for sufficiently strong defects of either type, (c) the decrease of the amplitude formation threshold for attractive and its increase for repulsive defects, and (d) the detailed elucidation as a function of initial speed and defect strength of the different regimes (trapping, trapping and reflection, pure reflection, and pure transmission) of interaction of a moving localized mode with the defect.

Formation, control, and dynamics of N localized structures in the Peyrard-Bishop model

We explore in detail the creation of stable localized structures in the form of localized energy distributions that arise from general initial conditions in the Peyrard-Bishop (PB) model. By means of a method based on the inverse scattering transform we study the solutions of PB model equations obtained in the form of planar waves whose amplitudes are described by the nonlinear Schrödinger equation (NLS). For localized initial conditions different from the pure N-soliton shape, we have obtained analytical results that predict and control the number, amplitude, and velocity of the NLS solitary waves. To verify the validity of these results we have carried out numerical simulations of the PB model with the use of realistic values of parameters and the initial conditions in the form of planar waves whose modulated amplitudes are given by the examples studied in the NLS. In the simulations we have found that N localized structures arise in agreement with the prediction of the analytical results obtained in the NLS.

Bubble generation in a twisted and bent DNA-like model

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.

Breather statics and dynamics in Klein-Gordon chains with a bend

In this paper, 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 bifurcation and stability analysis of the modes that emerge as a function of the strength of the bend angle, but we also examine dynamical effects including the scattering of mobile localized modes (discrete breathers) off of such a geometric structure. The potential outcomes of such numerical experiments (including transmission, trapping within the bend as well as reflection) are highlighted and qualitatively explained. Such models are of interest both theoretically in understanding the interplay of breathers with curvature, but also practically in simple models of photonic crystals or of bent chains of DNA.

Energy funneling in a bent chain of Morse oscillators with long-range coupling

A bent chain of coupled Morse oscillators with long-range dispersive interaction is considered. Moving localized excitations may be trapped in the bending region. Thus chain geometry acts like an impurity. An energy funneling effect is observed in the case of random initial conditions.

Resonant scattering of solitons

We study the scattering of solitons in the nonlinear Schrödinger equation on local inhomogeneities which may give rise to resonant transmission and reflection. In both cases, we derive resonance conditions for the soliton's velocity. The analytical predictions are tested numerically in regimes characterized by various time scales. Special attention is paid to intermode interactions and their effect on coherence, decoherence, and dephasing of plane-wave modes which build up the soliton.

Instabilities and bifurcations of nonlinear impurity modes

We study the structure and stability of nonlinear impurity modes in the discrete nonlinear Schrödinger equation with a single on-site nonlinear impurity emphasizing the effects of interplay between discreteness, nonlinearity, and disorder. We show how the interaction of a nonlinear localized mode (a discrete soliton or discrete breather) with a repulsive impurity generates a family of stationary states near the impurity site, as well as examine both theoretical and numerical criteria for the transition between different localized states via a cascade of bifurcations.