Modeling columnar thin films as platforms for surface-plasmonic-polaritonic optical sensing

Via exploitation of surface plasmon polaritons (SPPs), columnar thin films (CTFs) are attractive potential platforms for optical sensing as their relative permittivity dyadic and porosity can be tailored to order. Nanoscale model parameters of a CTF were determined from its measured relative permittivity dyadic, after inverting the Bruggeman homogenization formalism. These model parameters were then used to determine the relative permittivity dyadic of a fluid-infiltrated CTF. Two boundary-value problems were next solved: the first relating to SPP-wave propagation guided by the planar interface of a semi-infinitely thick metal and a semi-infinitely thick CTF, and the second to the plane-wave response of the planar interface of a finitely thick metallic layer and a CTF in a modified Kretschmann configuration. Numerical studies revealed that SPP waves propagate at a lower phase speed and with a shorter propagation length, if the fluid has a larger refractive index. Furthermore, the angle of incidence required to excite an SPP wave in a modified Kretschmann configuration increases as the refractive index of the fluid increases

Cellular Levels and Binding of c-di-GMP Control Subcellular Localization and Activity of the Vibrio cholerae Transcriptional Regulator VpsT

The second messenger, cyclic diguanylate (c-di-GMP), regulates diverse cellular processes in bacteria. C-di-GMP is produced by diguanylate cyclases (DGCs), degraded by phosphodiesterases (PDEs), and receptors couple c-di-GMP production to cellular responses. In many bacteria, including Vibrio cholerae, multiple DGCs and PDEs contribute to c-di-GMP signaling, and it is currently unclear whether the compartmentalization of c-di-GMP signaling components is required to mediate c-di-GMP signal transduction. In this study we show that the transcriptional regulator, VpsT, requires c-di-GMP binding for subcellular localization and activity. Only the additive deletion of five DGCs markedly decreases the localization of VpsT, while single deletions of each DGC do not impact VpsT localization. Moreover, mutations in residues required for c-di-GMP binding, c-di-GMP-stabilized dimerization and DNA binding of VpsT abrogate wild type localization and activity. VpsT does not co-localize or interact with DGCs suggesting that c-di-GMP from these DGCs diffuses to VpsT, supporting a model in which c-di-GMP acts at a distance. Furthermore, VpsT localization in a heterologous host, Escherichia coli, requires a catalytically active DGC and is enhanced by the presence of VpsT-target sequences. Our data show that c-di-GMP signaling can be executed through an additive cellular c-di-GMP level from multiple DGCs affecting the localization and activity of a c-di-GMP receptor and furthers our understanding of the mechanisms of second messenger signaling

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment—some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20°C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere—anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles

Small-angle X-ray scattering study of the microstructure of highly porous silicon

Small-Angle X-ray Scattering is well suited to the study of porous silicon microstructure since the pore radii range (2-10 nm) corresponds to the small-angle scattering range (1-100 nm). In all the studies realized till now, the porous silicon layers were always supported by the substrate. Recently, it has been possible to detach the porous silicon layer from the substrate. We performed small-angle X-ray scattering measurements, on such P-type samples, at a synchrotron radiation source. Close to the origin, the scattering pattern shows an anisotropic behaviour when titling the sample surface with respect to the X-ray beam. This anisotropy is different from the one observed previously in the case of P+ samples

REACTION KINETICS OF MoSi2 SILICIDE OBTAINED BY cw LASER ANNEALING OF Si (a) AND Sipoly/Mo BILAYERS

La cinétique de croissance du siliciure de molybdène MoSi2 a été étudiée par recuit laser en balayage de films de molybdène déposés sur du silicium amorphe ou polycristallin. Les cinétiques mesurées sont diffusionnelles dans certains cas, contrôlées par les réactions à l'interface dans d'autres cas. Le siliciure est obtenu facilement à partir du silicium amorphe. Nous avons comparé la rapidité de formation du siliciure par réaction du métal avec le silicium amorphe ou monocristallin.The growth kinetics of molybdenum silicide MoSi2 by cw scanned laser annealing of molybdenum films deposited on amorphous and polycrystalline silicon are studied. Silicide formation kinetics exhibits time dependence behaviour of interface controlled reaction in some cases and diffusion controlled reaction in others. Silicide formation with amorphous silicon occurs quite easily. Growth rates of silicide from metal reaction with monocrystalline and amorphous silicon are compared