In this work, we study the collision of an atomic dark-bright soliton, in a two-component Bose-Einstein condensate, with a Gaussian barrier or well. First, we present the results of an experiment, illustrating the classical particle phenomenology (transmission or reflection) in the case of an equal barrier or well in both components. Then, motivated by the experimental observations, we perform systematic simulations considering not only the case of equal heights, but also the considerably more complex setting, where the potential affects only one of the two components. We systematically classify the ensuing cases within a two-parameter diagram of barrier amplitudes in the two components, and provide intuitive explanations for the resulting observations, as well as of their variations as the size of the barrier changes.

We study deterministic escape dynamics in the framework of the discrete Klein-Gordon modelwith a repulsive quartic on-site potential. Using a combination of analytical techniques, based on differential and algebraic inequalities and selected numerical illustrations, we first derive conditions for collapse of an initially excited single-site unit, for both the Hamiltonian and the linearly damped versions of the system and showcase different potential fates of the single-site excitation, such as the possibility to be "pulled back" from outside the well or to "drive over" the barrier some of its neighbors. Next, we study the evolution of a uniform (small) segment of the chain and, in turn, consider the conditions that support its escape and collapse of the chain. Finally, our path from one to the few and finally to the many excited sites is completed by a modulational stability analysis and the exploration of its connection to the escape process for plane wave initial data. This reveals the existence of three distinct regimes, namely modulational stability, modulational instability without escape and, finally, modulational instability accompanied by escape. These are corroborated by direct numerical simulations. In each of the above cases, the variations of the relevant model parameters enable a consideration of the interplay of discreteness and nonlinearity within the observed phenomenology.

Collisions between moving localized modes (moving breathers) in non integrable lattices present a rich outcome. In this paper, some features of the interaction of moving breathers in Discrete Nonlinear Schrodinger and Klein Gordon lattices, together with some plausible explanations, are exposed.

In the present work, we numerically explore the existence and stability properties of different types of configurations of dark–bright solitons, dark–bright soliton pairs and pairs of dark–bright and dark solitons in discrete settings, starting from the anti-continuum limit. We find that while single discrete dark–bright solitons have similar stability properties to discrete dark solitons, their pairs may only be stable if the bright components are in phase and are always unstable if the bright components are out of phase. Pairs of dark–bright solitons with dark ones have similar stability properties as individual dark or dark–bright ones. Lastly, we consider collisions between dark–bright solitons and between a dark–bright one and a dark one. Especially in the latter and in the regime where the underlying lattice structure matters, we find a wide range of potential dynamical outcomes depending on the initial soliton speed.

We consider a system of two coupled nonlinear partial differential equations for describing the rotational motions of bases in both polynucleotide chains of the DNA molecule. The model was proposed by L.V. Yakushevich and it is well known that the model supports, for some operating regimes, traveling wave solutions as kink-(antikink) soliton solutions. We have tried to make some progress by performing an analysis of the classical symmetries of this model. Our study shows that the model does not have enough symmetries as to reduce the equations to ordinary differential equations. Nevertheless, the known symmetries have been useful for finding several classes of exact solutions, by imposing adequate Ansatze. Some of them are kink-(antikink) like solutions, but other ones are not traveling wave solutions. For some of the new solutions, we have carried out a qualitative study and analyzed some stability properties. We think that they could be significant for the description of the DNA molecule as well as for some other applications.

We investigate the collisions of moving breathers, with the same frequency, in three different Klein-Gordon chains of oscillators. The on-site potentials are: the asymmetric and soft Morse potential, the symmetric and soft sine-Gordon potential and the symmetric and hard φ4 potential. The simulation of a collision begins generating two identical moving breathers traveling with opposite velocities, they are obtained after perturbing two identical stationary breathers which centers are separated by a fixed number of particles. If this number is odd we obtain an on-site collision, but if this number is even we obtain an inter-site collision. Apart from this distinction, we have considered symmetric collisions, if the colliding moving breathers are vibrating in phase, and anti-symmetric collisions, if the colliding moving breathers are vibrating in anti-phase. The simulations show that the collision properties of the three chains are different. The main observed phenomena are: breather generation with trapping, with the appearance of two new moving breathers with opposite velocities, and a stationary breather trapped at the collision region; breather generation without trapping, with the appearance of new moving breathers with opposite velocities; breather trapping at the collision region, without the appearance of new moving breathers; and breather reflection. For each Klein-Gordon chain, the collision outcomes depend on the lattice parameters, the frequency of the perturbed stationary breathers, the internal structure of the moving breathers and the number of particles that initially separates the stationary breathers when they are perturbed.

We consider collisions of moving breathers (MBs) in the Peyrard-Bishop DNA model. Two identical stationary breathers, separated by a fixed number of pair-bases, are perturbed and begin to move approaching to each other with the same module of velocity. The outcome is strongly dependent of both the velocity of the MBs and the number of pair-bases that initially separates the stationary breathers. Some collisions result in the generation of a new stationary trapped breather of larger energy. Other collisions result in the generation of two new MBs. In the DNA molecule, the trapping phenomenon could be part of the complex mechanisms involved in the initiation of the transcription processes.

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard-Bishop model is augmented with a term that includes the dipole-dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard--Bishop model is augmented with a term that includes the dipole--dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.

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 discrete breather that exist at the atomic scale in a magnetic solid. Other observations of breathers refer to systems such as Josephson--junction arrays, photonic crystals and optical-switching waveguide arrays. All these observations underscore their importance in physical phenomena at all scales. The authors review some of their latest theoretical contributions in the field of classical and quantum breathers, with possible applications to these widely different physical systems and to many other such as DNA, proteins, quantum dots, quantum computing, etc.

Whereas there exists a mathematical proof for one-site breathers stability, and an unpublished one for two-site breathers, the methods for determining the stability properties of multibreathers rely on numerical computation of the Floquet multipliers or on the weak nonlinearity approximation leading to discrete nonlinear Schrödinger equations. Here we present a set of multibreather stability theorems (MST) that provides a simple method to determine multibreathers stability in Klein–Gordon systems. These theorems are based in the application of degenerate perturbation theory to Aubry's band theory. We illustrate them with several examples.

Discrete bright breathers are well known phenomena. They are localized excitations that consist of a few excited oscillators in a lattice and the rest of them having very small amplitude or none. In this paper we are interested in the opposite kind of localization, or discrete dark breathers, where most of the oscillators are excited and one or a few units of them have very small amplitude. We investigate using band analysis, Klein--Gordon lattices at frequencies not close to the linear ones. Dark breathers at low coupling are shown to be stable for Klein--Gordon chains with soft on--site potentials and repulsive dispersive interaction, and with hard on--site potentials and attractive dispersive interactions. At higher coupling dark breathers lose their stability via subharmonic, harmonic or oscillatory bifurcations, depending on the model. However, most of these bifurcations are harmless in the sense that they preserve dark localization. None of these bifurcations disappear when the system is infinite. Dark breathers in dissipative systems are found to be stable for both kinds of dispersive interaction.