Hydrogen-Related Conversion Processes of Ge-Related Point Defects in Silica Triggered by UV Laser Irradiation

The conversion processes of Ge-related point defects triggered in amorphous SiO2 by 4.7eV laser exposure were investigated. Our study has focused on the interplay between the (=Ge•-H) H(II) center and the twofold coordinated Ge defect (=Ge••). The former is generated in the post-irradiation stage, while the latter decays both during and after exposure. The post-irradiation decay kinetics of =Ge•• is isolated and found to be anti-correlated to the growth of H(II), at least at short times. From this finding it is suggested that both processes are due to trapping of radiolytic H0 at the diamagnetic defect site. Furthermore, the anti-correlated behavior is preserved also under repeated irradiation: light at 4.7eV destroys the already formed H(II) centers and restore their precursors =Ge••. This process leads to repeatability of the post-irradiation kinetics of the two species after multiple laser exposures. A comprehensive scheme of chemical reactions explaining the observed post-irradiation processes is proposed and tested against experimental data.Comment: 25 pages, 7 figures, submitted to Phys. Rev.

Symmetry Scheme for Amino Acid Codons

Group theoretical concepts are invoked in a specific model to explain how only twenty amino acids occur in nature out of a possible sixty four. The methods we use enable us to justify the occurrence of the recently discovered twenty first amino acid selenocysteine, and also enables us to predict the possible existence of two more, as yet undiscovered amino acids.Comment: 18 pages which include 4 figures & 3 table

High-order harmonic generation from polyatomic molecules including nuclear motion and a nuclear modes analysis

We present a generic approach for treating the effect of nuclear motion in the high-order harmonic generation from polyatomic molecules. Our procedure relies on a separation of nuclear and electron dynamics where we account for the electronic part using the Lewenstein model and nuclear motion enters as a nuclear correlation function. We express the nuclear correlation function in terms of Franck-Condon factors which allows us to decompose nuclear motion into modes and identify the modes that are dominant in the high-order harmonic generation process. We show results for the isotopes CH$_4$ and CD$_4$ and thereby provide direct theoretical support for a recent experiment [Baker {\it et al.}, Science {\bf 312}, 424 (2006)] that uses high-order harmonic generation to probe the ultra-fast structural nuclear rearrangement of ionized methane.Comment: 6 pages, 6 figure

Molecular Dynamics Simulation of Polymer-Metal Bonds

Molecular simulation is becoming a very powerful tool for studying dynamic phenomena in materials. The simulation yields information about interaction at length and time scales unattainable by experimental measurements and unpredictable by continuum theories. This is especially meaningful when referring to bonding between a polymer and a metal substrate. A very important characteristic of polymers is that their physical properties do not rely on the detailed chemical structure of the molecular chains but only on their flexibility, and accordingly they will be able to adopt different conformations. In this paper, a molecular simulation of the bonding between vinyl ester polymer and steel is presented. Four different polymers with increasing chain lengths have been studied. Atomic co-ordinates are adjusted in order to reduce the molecular energy. Conformational changes in the macromolecules have been followed to obtain the polymer pair correlation function. Radius of gyration and end-to-end distance distributions of the individual chains have been used as a quantitative measurement of their flexibility. There exists a correlation between flexibility of the molecular chains and the energy of adhesion between the polymer and the metal substrate. Close contacts between the two materials are established at certain points but every atom up to a certain distance from the interface contributes to the total value of the adhesion energy of the system

Graphene defect formation by extreme ultraviolet generated photoelectrons

We have studied the effect of photoelectrons on defect formation in graphene during extreme ultraviolet (EUV) irradiation. Assuming the major role of these low energy electrons, we have mimicked the process by using low energy primary electrons. Graphene is irradiated by an electron beam with energy lower than 80 eV. After e-beam irradiation, it is found that the D peak, I(D), appears in the Raman spectrum, indicating defect formation in graphene. The evolution of I(D)/I(G) follows the amorphization trajectory with increasing irradiation dose, indicating that graphene goes through a transformation from microcrystalline to nanocrystalline and then further to amorphous carbon. Further, irradiation of graphene with increased water partial pressure does not significantly change the Raman spectra, which suggests that, in the extremely low energy range, e-beam induced chemical reactions between residual water and graphene is not the dominant mechanism driving defect formation in graphene. Single layer graphene, partially suspended over holes was irradiated with EUV radiation. By comparing with the Raman results from e-beam irradiation, it is concluded that the photoelectrons, especially those from the valence band, contribute to defect formation in graphene during irradiation.Comment: appears in Journal of Applied Physics 201

Entanglement of distant optomechanical systems

We theoretically investigate the possibility to generate non-classical states of optical and mechanical modes of optical cavities, distant from each other. A setup comprised of two identical cavities, each with one fixed and one movable mirror and coupled by an optical fiber, is studied in detail. We show that with such a setup there is potential to generate entanglement between the distant cavities, involving both optical and mechanical modes. The scheme is robust with respect to dissipation, and nonlocal correlations are found to exist in the steady state at finite temperatures.Comment: 12 pages (published with minor modifications

Rotational Feshbach Resonances in Ultracold Molecular Collisions

In collisions at ultralow temperatures, molecules will possess Feshbach resonances, foreign to ultracold atoms, whose virtual excited states consist of rotations of the molecules. We estimate the mean spacing and mean widths of these resonant states, exploiting the fact the molecular collisions at low energy display chaotic motion. As examples, we consider the experimentally relevant molecules O_2, OH, and PbO. The density of s-wave resonant states for these species is quite high, implying that a large number of narrow resonant states will exist.Comment: 4 pages, 2 figure

Modelling Marek's Disease Virus (MDV) infection: parameter estimates for mortality rate and infectiousness

Background: Marek's disease virus (MDV) is an economically important oncogenic herpesvirus of poultry. Since the 1960s, increasingly virulent strains have caused continued poultry industry production losses worldwide. To understand the mechanisms of this virulence evolution and to evaluate the epidemiological consequences of putative control strategies, it is imperative to understand how virulence is defined and how this correlates with host mortality and infectiousness during MDV infection. We present a mathematical approach to quantify key epidemiological parameters. Host lifespan, virus latent periods and host viral shedding rates were estimated for unvaccinated and vaccinated birds, infected with one of three MDV strains. The strains had previously been pathotyped to assign virulence scores according to pathogenicity of strains in hosts. Results: Our analyses show that strains of higher virulence have a higher viral shedding rate, and more rapidly kill hosts. Vaccination enhances host life expectancy but does not significantly reduce the shedding rate of the virus. While the primary latent period of the virus does not vary with challenge strain nor vaccine treatment of host, the time until the maximum viral shedding rate is increased with vaccination. Conclusions: Our approach provides the tools necessary for a formal analysis of the evolution of virulence in MDV, and potentially simpler and cheaper approaches to comparing the virulence of MDV strains

Epidemiological studies of pan-azole resistant Aspergillus fumigatus populations sampled during tulip cultivation show clonal expansion with acquisition of multi-fungicide resistance as potential driver

Pan-azole resistant isolates are found in clinical and environmental Aspergillus fumigatus (Af) populations. Azole resistance can evolve in both settings, with Af directly targeted by antifungals in patients and, in the environment, Af unintendedly exposed to fungicides used for material preservation and plant disease control. Resistance to non-azole fungi-cides, including methyl benzimidazole carbamates (MBCs), quinone outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs), have recently been reported. These fungicide groups are not used in medicine but can play an important role in further spread of pan-azole resistant genotypes. We investigated the multi-fungicide resistance status and genetic diversity of Af populations sampled from tulip field soils, tulip peel waste and flower compost heaps using fungicide sensitivity testing and a range of genotyping tools, including STRAf typing and sequencing of fungicide resistant alleles. Two major clones were present in the tulip bulb population. Comparisons with clinical isolates and literature data revealed that several common clonal lineages of TR34/L98H and TR46/Y121F/T289A strains that have expanded successfully in the environment have also acquired resistance to MBC, QoI and/or SDHI fungicides. Strains carrying multiple fungicide resistant alleles have an advantage in environments where residues of multiple fungicides belonging to different modes of action are presen