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

Computing spectral sequences

In this paper, a set of programs enhancing the Kenzo system is presented. Kenzo is a Common Lisp program designed for computing in Algebraic Topology, in particular it allows the user to calculate homology and homotopy groups of complicated spaces. The new programs presented here entirely compute Serre and Eilenberg-Moore spectral sequences, in particular the groups and differential maps for arbitrary r. They also determine when the spectral sequence has converged and describe the filtration of the target homology groups induced by the spectral sequence

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

Renormalisation group determination of the order of the DNA denaturation transition

We report on the nature of the thermal denaturation transition of homogeneous DNA as determined from a renormalisation group analysis of the Peyrard-Bishop-Dauxois model. Our approach is based on an analogy with the phenomenon of critical wetting that goes further than previous qualitative comparisons, and shows that the transition is continuous for the average base-pair separation. However, since the range of universal critical behaviour appears to be very narrow, numerically observed denaturation transitions may look first-order, as it has been reported in the literature.Comment: 6 pages; no figures; to appear in Europhysics Letter