Theory of imaging a photonic crystal with transmission near-field optical microscopy

While near-field scanning optical microscopy (NSOM) can provide optical images with resolution much better than the diffraction limit, analysis and interpretation of these images is often difficult. We present a theory of imaging with transmission NSOM that includes the effects of tip field, tip/sample coupling, light propagation through the sample and light collection. We apply this theory to analyze experimental NSOM images of a nanochannel glass (NCG) array obtained in transmission mode. The NCG is a triangular array of dielectric rods in a dielectric glass matrix with a two-dimensional photonic band structure. We determine the modes for the NCG photonic crystal and simulate the observed data. The calculations show large contrast at low numerical aperture (NA) of the collection optics and detailed structure at high NA consistent with the observed images. We present calculations as a function of NA to identify how the NCG photonic modes contribute to and determine the spatial structure in these images. Calculations are presented as a function of tip/sample position, sample index contrast and geometry, and aperture size to identify the factors that determine image formation with transmission NSOM in this experiment.Comment: 28 pages of ReVTex, 14 ps figures, submitted to Phys. Rev.

Re-entrant ferroelectricity in liquid crystals

The ferroelectric (Sm C$^*$) -- antiferroelectric (Sm C$^*_A$) -- reentrant ferroelectric (re Sm C$^*$) phase temperature sequence was observed for system with competing synclinic - anticlinic interactions. The basic properties of this system are as follows (1) the Sm C$^*$ phase is metastable in temperature range of the Sm C$^*_A$ stability (2) the double inversions of the helix handedness at Sm C$^*$ -- Sm C$^*_A$ and Sm C$^*_A$% -- re-Sm C$^*$ phase transitions were found (3) the threshold electric field that is necessary to induce synclinic ordering in the Sm C$^*_A$ phase decreases near both Sm C$^*_A$ -- Sm C$^*$ and Sm C$^*_A$ -- re-Sm C$^*$ phase boundaries, and it has maximum in the middle of the Sm C$^*_A$ stability region. All these properties are properly described by simple Landau model that accounts for nearest neighboring layer steric interactions and quadrupolar ordering only.Comment: 10 pages, 5 figures, submitted to PR

Free-field propagation of high intensity noise

Research on high intensity (finite amplitude) acoustic waves shows that nonlinear distortion effects generally result in a shift of energy to higher frequencies. The higher intensities associated with supersonic jets would therefore indicate that high frequency enhancement of the spectrum should occur, resulting in the differences observed between subsonic and supersonic jets. A 10,000 acoustic watt source installed in an anechoic chamber generates sound levels such that acoustic shocks are readily observable. Dual frequency excitation of the source produces a strong parametric effect with a difference frequency comparable in level to the primary frequency. The test set up and recording equipment being used to determine the finite amplitude noise representative of an actual supersonic jet are described as well as the development of a computer program based on Burger's equation. The spectra of 1/2 octave band, 1 kHz sine wave, and dual frequency input and output are presented in graphs along with waveforms at Z = .025, 0.1, and 1.0

Weight Management Program for Fire Fighters: Feasibility Pilot

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Mesoscopic molecular ions in Bose-Einstein condensates

We study the possible formation of large (mesoscopic) molecular ions in an ultracold degenerate bosonic gas doped with charged particles (ions). We show that the polarization potentials produced by the ionic impurities are capable of capturing hundreds of atoms into loosely bound states. We describe the spontaneous formation of these hollow molecular ions via phonon emission and suggest an optical technique for coherent stimulated transitions of free atoms into a specific bound state. These results open up new interesting possibilities for manipulating tightly confined ensembles.Comment: 4 pages (two-columns), 2 figure

Kinetics of gas-phase reactions relevant to the chemical vapor deposition of indium compounds

Compounds containing indium are of interest for electronic and optical applications. These compounds include III-V semiconductors such as InP and InAs used in both electronic devices and solar cells, and indium tin oxide, which can be used for optical memory and antireflection coatings. Chemical vapor deposition (CVD) techniques can be used to deposit these materials on a variety of substrates. At the temperatures typically employed (550--900 K), gas-phase chemical reactions involving the indium-containing precursor can occur. The kinetics of trimethylindium pyrolysis are investigated in a flow reactor equipped with a molecular-beam mass-spectrometric sampling system. Data are analyzed using a new computational approach that accounts for heat and mass transport in the reactor. The measured activation energy, 46.2 kcal/mol, is in good agreement with previously reported values

Shear modulus of the hadron-quark mixed phase

Robust arguments predict that a hadron-quark mixed phase may exist in the cores of some "neutron" stars. Such a phase forms a crystalline lattice with a shear modulus higher than that of the crust due to the high density and charge separation, even allowing for the effects of charge screening. This may lead to strong continuous gravitational-wave emission from rapidly rotating neutron stars and gravitational-wave bursts associated with magnetar flares and pulsar glitches. We present the first detailed calculation of the shear modulus of the mixed phase. We describe the quark phase using the bag model plus first-order quantum chromodynamics corrections and the hadronic phase using relativistic mean-field models with parameters allowed by the most massive pulsar. Most of the calculation involves treating the "pasta phases" of the lattice via dimensional continuation, and we give a general method for computing dimensionally continued lattice sums including the Debye model of charge screening. We compute all the shear components of the elastic modulus tensor and angle average them to obtain the effective (scalar) shear modulus for the case where the mixed phase is a polycrystal. We include the contributions from changing the cell size, which are necessary for the stability of the lower-dimensional portions of the lattice. Stability also requires a minimum surface tension, generally tens of MeV/fm^2 depending on the equation of state. We find that the shear modulus can be a few times 10^33 erg/cm^3, two orders of magnitude higher than the first estimate, over a significant fraction of the maximum mass stable star for certain parameter choices.Comment: 22 pages, 12 figures, version accepted by Phys. Rev. D, with the corrections to the shear modulus computation and Table I given in the erratu

Transcription-associated breaks in Xeroderma Pigmentosum group D cells from patients with combined features of Xeroderma Pigmentosum and Cockayne Syndrome

Defects in the XPD gene can result in several clinical phenotypes, including xeroderma pigmentosum (XP), trichothiodystrophy, and, less frequently, the combined phenotype of XP and Cockayne syndrome (XP-D/CS). We previously showed that in cells from two XP-D/CS patients, breaks were introduced into cellular DNA on exposure to UV damage, but these breaks were not at the sites of the damage. In the present work, we show that three further XP-D/CS patients show the same peculiar breakage phenomenon. We show that these breaks can be visualized inside the cells by immunofluorescence using antibodies to either gamma-H2AX or poly-ADP-ribose and that they can be generated by the introduction of plasmids harboring methylation or oxidative damage as well as by UV photoproducts. Inhibition of RNA polymerase II transcription by four different inhibitors dramatically reduced the number of UV-induced breaks. Furthermore, the breaks were dependent on the nucleotide excision repair (NER) machinery. These data are consistent with our hypothesis that the NER machinery introduces the breaks at sites of transcription initiation. During transcription in UV-irradiated XP-D/CS cells, phosphorylation of the carboxy-terminal domain of RNA polymerase II occurred normally, but the elongating form of the polymerase remained blocked at lesions and was eventually degraded

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus "Candidatus Accumulibacter"

“Candidatus Accumulibacter” was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as “Candidatus Accumulibacter phosphatis,” despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer-scale differentiation into different “types” and “clades”; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with “Candidatus Accumulibacter phosphatis,” “Candidatus Accumulibacter delftensis,” and “Candidatus Accumulibacter aalborgensis.” To compare the species in situ, we designed new species-specific fluorescence in situ hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, “Ca. Accumulibacter” species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all “Ca. Accumulibacter” species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. IMPORTANCE “Candidatus Accumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of genes and pathways of interest, validated in situ by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms