Breathers in a system with helicity and dipole interaction

Recent papers that have studied variants of the Peyrard-Bishop model for DNA, have taken into account the long range interaction due to the dipole moments of the hydrogen bonds between base pairs. In these models the helicity of the double strand is not considered. In this particular paper we have performed an analysis of the influence of the helicity on the properties of static and moving breathers in a Klein--Gordon chain with dipole-dipole interaction. It has been found that the helicity enlarges the range of existence and stability of static breathers, although this effect is small for a typical helical structure of DNA. However the effect of the orientation of the dipole moments is considerably higher with transcendental consequences for the existence of mobile breathers.Comment: 4pages, 5 eps figure

Pattern Formation by Traveling Localized Modes in Two-Dimensional Dissipative Media with Lattice Potentials

We analyze pattern-formation scenarios in the two-dimensional (2D) complex Ginzburg-Landau (GL) equation with the cubic-quintic nonlinearity and a cellular potential. The equation models laser cavities with built-in gratings, which stabilize 2D patterns. The pattern-building process is initiated by kicking a compound mode, in the form of a dipole, quadrupole, or vortex which is composed of four local peaks. The hopping motion of the kicked mode through the cellular structure leads to the generation of various extended patterns pinned by the structure. In the ring-shaped system, the persisting freely moving dipole hits the stationary pattern from the opposite side, giving rise to several dynamical regimes, including periodic elastic collisions, i.e., persistent cycles of elastic collisions between the moving and quiescent dissipative solitons, and transient regimes featuring several collisions which end up by absorption of one soliton by the other. Another noteworthy result is transformation of a strongly kicked unstable vortex into a stably moving four-peaked cluster

Long range annealing of defects in germanium by low energy plasma ions

Ions arriving at a semiconductor surface with very low energy (2–8 eV) are interacting with defects deep inside the semiconductor. Several different defects were removed or modified in Sb-doped germanium, of which the EE-center has the highest concentration. The low fluence and low energy of the plasma ions imply that the energy has to be able to travel in a localized way to be able to interact with defects up to a few microns below the semiconductor surface. After eliminating other possibilities (electric field, light, heat) we now conclude that moving intrinsic localized modes (ILMs), as a mechanism of long-distance energy transport, are the most likely cause. This would be striking evidence of the importance of ILMs in crystals and opens the way to further experiments to probe ILM properties both in semiconductors and in the metals used for contacts. Although most of the measurements have been performed on germanium, similar effects have been found in silicon.MICINN, project FIS2008-04848; the South African National Research Foundation and the European Regional Development Fund, project 3.2.0101.11-0029, Centre of Excellence Mesosystems: Theory and Applications.http://www.elsevier.com/locate/physdhj201

Moving breathers in a bent DNA-related model

We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We show that the movement of a breather is hindered by the bending of the chain as a particle in a potential barrier. We have also found that the behaviour of moving breathers in an homogeneous bent chain and in a straight chain with a small impurity is qualitatively equivalent.Comment: 13 pages, 8 figure

Moving excitations In cation lattices

We consider a model made out of identical particles that repel each other with the Coulomb interaction. We study numerically and analytically the existence and properties of supersonic kinks, showing that they are very easy to be produced and propagate long distances. They have a wide range of velocities and energies. We are motivated by a special characteristic of the muscovite mica mineral. Tracks from particles such as muons can be distinguished in a complex decoration, but the only explanation to most of the tracks is localized excitations called quodons. They move in the cation lattice, sandwiched between the silicate layers, along the lattice directions. Quodons have also been observed experimentally [EPL 78 (2007) 1005]Archilla, J.; Kosevich ., Y.; Jimenez, N.; Sánchez Morcillo, VJ.; García-Raffi, LM. (2013). Moving excitations In cation lattices. Ukrainian Journal of Physics. 58(7):646-656. http://hdl.handle.net/10251/58347S64665658

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.Comment: 6 pages, 12 figures. Submitted to Physical Review E, Oct. 13, 200

Discrete moving breather collisions in a Klein-Gordon chain of oscillators

We study collision processes of moving breathers with the same frequency, traveling with opposite directions within a Klein-Gordon chain of oscillators. Two types of collisions have been analyzed: symmetric and non-symmetric, head-on collisions. For low enough frequency the outcome is strongly dependent of the dynamical states of the two colliding breathers just before the collision. For symmetric collisions, several results can be observed: breather generation, with the formation of a trapped breather and two new moving breathers; breather reflection; generation of two new moving breathers; and breather fusion bringing about a trapped breather. For non-symmetric collisions the possible results are: breather generation, with the formation of three new moving breathers; breather fusion, originating a new moving breather; breather trapping with also breather reflection; generation of two new moving breathers; and two new moving breathers traveling as a ligand state. Breather annihilation has never been observed.Comment: 19 pages, 12 figure

Stretching and relaxation dynamics in double stranded DNA

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening-closing dynamics of double-stranded DNA molecules which are forced into non-equilibrium conformations. Mechanical stress imposed at one terminal end of the DNA molecule brings it into a partially opened configuration. We examine the subsequent relaxation dynamics connected with energy exchange processes between the various degrees of freedom and structural rearrangements leading to complete recombination to the double-stranded conformation. The similarities and differences between the relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are discussed in detail. In this way we show that the attainment of a quasi-equilibrium regime proceeds faster in the case of the twisted DNA form than for its thus less flexible ladder counterpart. Furthermore we find that the velocity of the complete recombination of the DNA molecule is lower than the velocity imposed by the forcing unit which is in compliance with the experimental observations for the opening-closing cycle of DNA molecules.Comment: 21 pages, 9 figure

Theory of a quodon gas. With application to precipitation kinetics in solids under irradiation

Rate theory of the radiation-induced precipitation in solids is modified with account of non-equilibrium fluctuations driven by the gas of lattice solitons (a.k.a. quodons) produced by irradiation. According to quantitative estimations, a steady-state density of the quodon gas under sufficiently intense irradiation can be as high as the density of phonon gas. The quodon gas may be a powerful driver of the chemical reaction rates under irradiation, the strength of which exponentially increases with irradiation flux and may be comparable with strength of the phonon gas that exponentially increases with temperature. The modified rate theory is applied to modelling of copper precipitation in FeCu binary alloys under electron irradiation. In contrast to the classical rate theory, which disagrees strongly with experimental data on all precipitation parameters, the modified rate theory describes quite well both the evolution of precipitates and the matrix concentration of copper measured by different methodsComment: V. Dubinko, R. Shapovalov, Theory of a quodon gas. With application to precipitation kinetics in solids under irradiation. (Springer International Publishing, Switzerland, 2014

Asymptotic stability of breathers in some Hamiltonian networks of weakly coupled oscillators

We consider a Hamiltonian chain of weakly coupled anharmonic oscillators. It is well known that if the coupling is weak enough then the system admits families of periodic solutions exponentially localized in space (breathers). In this paper we prove asymptotic stability in energy space of such solutions. The proof is based on two steps: first we use canonical perturbation theory to put the system in a suitable normal form in a neighborhood of the breather, second we use dispersion in order to prove asymptotic stability. The main limitation of the result rests in the fact that the nonlinear part of the on site potential is required to have a zero of order 8 at the origin. From a technical point of view the theory differs from that developed for Hamiltonian PDEs due to the fact that the breather is not a relative equilibrium of the system