Interaction of moving breathers with an impurity

We analyze the influence of an impurity in the evolution of moving discrete breathers in a Klein--Gordon chain with non-weak nonlinearity. Three different behaviours can be observed when moving breathers interact with the impurity: they pass through the impurity continuing their direction of movement; they are reflected by the impurity; they are trapped by the impurity, giving rise to chaotic breathers. Resonance with a breather centred at the impurity site is conjectured to be a necessary condition for the appearance of the trapping phenomenon.Comment: 4 pages, 2 figures, Proceedings of the Third Conference, San Lorenzo De El Escorial, Spain 17-21 June 200

Nonlinear charge transport mechanism in periodic and disordered DNA

We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two different kind of modes representing fluctuating twist motions of the base pairs and H-bond distortions within the double helix structure of $\lambda-$DNA. Localized stationary states are constructed with the help of a nonlinear map approach for a periodic double helix and in the presence of intrinsic static parametrical and/or structural disorder reflecting the impact of ambient solvent coordinates. It is demonstrated that charge transport is mediated by moving polarons respectively breather compounds carrying not only the charge but causing also local temporal deformations of the helix structure through the traveling torsion and bond breather components illustrating the interplay of structure and function in biomolecules.Comment: 23 pages, 13 figure

Charge transport in a nonlinear, three--dimensional DNA model with disorder

We study the transport of charge due to polarons in a model of DNA which takes in account its 3D structure and the coupling of the electron wave function with the H--bond distortions and the twist motions of the base pairs. Perturbations of the ground states lead to moving polarons which travel long distances. The influence of parametric and structural disorder, due to the impact of the ambient, is considered, showing that the moving polarons survive to a certain degree of disorder. Comparison of the linear and tail analysis and the numerical results makes possible to obtain further information on the moving polaron properties.Comment: 9 pages, 2 figures. Proceedings of the conference on "Localization and energy transfer in nonlinear systems", June 17-21, 2002, San Lorenzo de El Escorial, Madrid, Spain. To be publishe

Modeling the thermal evolution of enzyme-created bubbles in DNA

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 are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that in fact from certain local structural distortions there originate oscillating localized patterns, that is radial and torsional breathers, which are associated with localized H-bond deformations, being reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim the underlying nonlinear oscillator network of the DNA duplex is brought in contact with a heat bath using the Nos$\rm{\acute{e}}$-Hoover-method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers, sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for nonzero temperature the H-bond breathers move coherently along the double chain whereas at T=0 standing radial and torsional breathers result.Comment: 19 pages, 7 figure

Charge transport in poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity the breather mobility in the latter case is comparatively restrained inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)-poly(dC) DNA molecules acts as a semiconducting nanowire and exhibits better conductance than poly(dA)-poly(dT) ones.Comment: 11 pages, 5 figure

Breathers in FPU systems, near and far from the phonon band

There exists a recent mathematical proof on the existence of small amplitude breathers in FPU systems near the phonon band, which includes a prediction of their amplitude and width. In this work we obtain numerically these breathers, and calculate the range of validity of the predictions, which extends relatively far from the phonon band. There exist also large amplitude breathers with the same frequency, with the consequence that there is an energy gap for breather creation in these systems.Comment: 3 pages, 2 figures, proceeding of the conference on Localization and to and Energy Transfer in Nonlinear Systems, June 17-21, 2002, San Lorenzo de El Escorial, Madrid, Spain. To be published by World Scientifi

Bright and dark breathers in Fermi-Pasta-Ulam lattices

In this paper we study the existence and linear stability of bright and dark breathers in one-dimensional FPU lattices. On the one hand, we test the range of validity of a recent breathers existence proof [G. James, {\em C. R. Acad. Sci. Paris}, 332, Ser. 1, pp. 581 (2001)] using numerical computations. Approximate analytical expressions for small amplitude bright and dark breathers are found to fit very well exact numerical solutions even far from the top of the phonon band. On the other hand, we study numerically large amplitude breathers non predicted in the above cited reference. In particular, for a class of asymmetric FPU potentials we find an energy threshold for the existence of exact discrete breathers, which is a relatively unexplored phenomenon in one-dimensional lattices. Bright and dark breathers superposed on a uniformly stressed static configuration are also investigated.Comment: 11 pages, 16 figure

Influence of moving breathers on vacancies migration

A vacancy defect is described by a Frenkel--Kontorova model with a discommensuration. This vacancy can migrate when interacts with a moving breather. We establish that the width of the interaction potential must be larger than a threshold value in order that the vacancy can move forward. This value is related to the existence of a breather centred at the particles adjacent to the vacancy.Comment: 11 pages, 10 figure

Discrete breathers for understanding reconstructive mineral processes at low temperatures

Reconstructive transformations in layered silicates need a high tem- perature in order to be observed. However, very recently, some systems have been found where transformation can be studied at temperatures 600 C below the lowest experimental results previously reported, including sol-gel methods. We explore the possible relation with the existence of intrinsic localized modes, known as discrete breathers. We construct a model for nonlinear vibrations within the cation layer, obtain their parameters and calculate them numerically, obtaining their energies. Their statistics shows that although there are far less breathers than phonons, there are much more above the activation energy, being therefore a good candidate to explain the reconstructive transformations at low temperature.Comment: 27 pages, 11 figure