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

Discovery of a new radio galaxy within the error box of the unidentified gamma-ray source 3EG J1735-1500

We report the discovery of a new radio galaxy within the location error box of the gamma-ray source 3EG J1735-1500. The galaxy is a double-sided jet source forming a large angle with the line of sight. Optical observations reveal a V ~ 18 magnitude galaxy at the position of the radio core. Although the association with the EGRET source is not confirmed at the present stage, because there is a competing, alternative gamma-ray candidate within the location error contours which is also studied here, the case deserves further attention. The new radio galaxy can be used to test the recently proposed possibility of gamma-ray emitting radio galaxies beyond the already known case of Centaurus A.Comment: 12 pages, 3 figures. Accepted for publication in Ap

Determining the dimensionality of bipartite orbital-angular-momentum entanglement using multi-sector phase masks

The Shannon dimensionality of orbital-angular-momentum (OAM) entanglement produced in spontaneous parametric down-conversion can be probed by using multi-sector phase analysers [1]. We demonstrate a spatial light modulator-based implementation of these analysers, and use it to measure a Schmidt number of about 50

Gravitational microlensing of gamma-ray blazars

We present a detailed study of the effects of gravitational microlensing on compact and distant $\gamma$-ray blazars. These objects have $\gamma$-ray emitting regions which are small enough as to be affected by microlensing effects produced by stars lying in intermediate galaxies. We analyze the temporal evolution of the gamma-ray magnification for sources moving in a caustic pattern field, where the combined effects of thousands of stars are taken into account using a numerical technique. We propose that some of the unidentified $\gamma$-ray sources (particularly some of those lying at high galactic latitude whose gamma-ray statistical properties are very similar to detected $\gamma$-ray blazars) are indeed the result of gravitational lensing magnification of background undetected Active Galactic Nuclei (AGNs).Comment: 30 pages, 27 figures. Four figures are being submitted only as .gif files, and should be printed separately. The abstract below has been shortened from the actual version appearing in the pape

Non-Abelian Chern-Simons-Higgs vortices with a quartic potential

We have constructed numerically non-Abelian vortices in an SU(2) Chern-Simons-Higgs theory with a quartic Higgs potential. We have analyzed these solutions in detail by means of improved numerical codes and found some unexpected features we did not find when a sixth-order Higgs potential was used. The generic non-Abelian solutions have been generated by using their corresponding Abelian counterparts as initial guess. Typically, the energy of the non-Abelian solutions is lower than that of the corresponding Abelian one (except in certain regions of the parameter space). Regarding the angular momentum, the Abelian solutions possess the maximal value, although there exist non-Abelian solutions which reach that maximal value too. In order to classify the solutions it is useful to consider the non-Abelian solutions with asymptotically vanishing $A_t$ component of the gauge potential, which may be labelled by an integer number $m$. For vortex number $n=3$ and above, we have found uniqueness violation: two different non-Abelian solutions with all the global charges equal. Finally, we have investigated the limit of infinity Higgs self-coupling parameter and found a piecewise Regge-like relation between the energy and the angular momentum.Comment: 9 pages, 13 figure

Plateau insulator transition in graphene

The quantum Hall effect in a single-layer graphene sample is studied in strong magnetic fields up to 28 T. Our measurements reveal the existence of a metal- insulator transition from filling factor $\nu=-2$ to $\nu=0$. The value of the universal scaling exponent is found to be $\kappa=0.57$ in graphene and therefore in a truly two-dimensional system. This value of $\kappa$ is in agreement with the accepted universal value for the plateau-insulator transitions in standard quasi two-dimensional electron and hole gases.Comment: 10 pages, 5 figure

Single-photon optomechanics in the strong coupling regime

We give a theoretical description of a coherently driven opto-mechanical system with a single added photon. The photon source is modeled as a cavity which initially contains one photon and which is irreversibly coupled to the opto-mechanical system. We show that the probability for the additional photon to be emitted by the opto-mechanical cavity will exhibit oscillations under a Lorentzian envelope, when the driven interaction with the mechanical resonator is strong enough. Our scheme provides a feasible route towards quantum state transfer between optical photons and micromechanical resonators.Comment: 14 pages, 6 figure

Macroscopic evidence of microscopic dynamics in the Fermi-Pasta-Ulam oscillator chain from nonlinear time series analysis

The problem of detecting specific features of microscopic dynamics in the macroscopic behavior of a many-degrees-of-freedom system is investigated by analyzing the position and momentum time series of a heavy impurity embedded in a chain of nearest-neighbor anharmonic Fermi-Pasta-Ulam oscillators. Results obtained in a previous work [M. Romero-Bastida, Phys. Rev. E {\bf69}, 056204 (2004)] suggest that the impurity does not contribute significantly to the dynamics of the chain and can be considered as a probe for the dynamics of the system to which the impurity is coupled. The ($r,\tau$) entropy, which measures the amount of information generated by unit time at different scales $\tau$ of time and $r$ of the observable, is numerically computed by methods of nonlinear time-series analysis using the position and momentum signals of the heavy impurity for various values of the energy density $\epsilon$ (energy per degree of freedom) of the system and some values of the impurity mass $M$. Results obtained from these two time series are compared and discussed.Comment: 7 pages, 5 figures, RevTeX4 PRE format; to be published in Phys. Rev.