Low temperature heat capacity of Fe_{1-x}Ga_{x} alloys with large magneostriction

The low temperature heat capacity C_{p} of Fe_{1-x}Ga_{x} alloys with large magnetostriction has been investigated. The data were analyzed in the standard way using electron ($\gamma T$) and phonon ($\beta T^{3}$) contributions. The Debye temperature $\Theta_{D}$ decreases approximately linearly with increasing Ga concentration, consistent with previous resonant ultrasound measurements and measured phonon dispersion curves. Calculations of $\Theta_{D}$ from lattice dynamical models and from measured elastic constants C_{11}, C_{12} and C_{44} are in agreement with the measured data. The linear coefficient of electronic specific heat $\gamma$ remains relatively constant as the Ga concentration increases, despite the fact that the magnetoelastic coupling increases. Band structure calculations show that this is due to the compensation of majority and minority spin states at the Fermi level.Comment: 14 pages, 6 figure

Electron transport through multilevel quantum dot

Quantum transport properties through some multilevel quantum dots sandwiched between two metallic contacts are investigated by the use of Green's function technique. Here we do parametric calculations, based on the tight-binding model, to study the transport properties through such bridge systems. The electron transport properties are significantly influenced by (a) number of quantized energy levels in the dots, (b) dot-to-electrode coupling strength, (c) location of the equilibrium Fermi energy $E_F$ and (d) surface disorder. In the limit of weak-coupling, the conductance ($g$) shows sharp resonant peaks associated with the quantized energy levels in the dots, while, they get substantial broadening in the strong-coupling limit. The behavior of the electron transfer through these systems becomes much more clearly visible from our study of current-voltage ($I$-$V$) characteristics. In this context we also describe the noise power of current fluctuations ($S$) and determine the Fano factor ($F$) which provides an important information about the electron correlation among the charge carriers. Finally, we explore a novel transport phenomenon by studying the surface disorder effect in which the current amplitude increases with the increase of the surface disorder strength in the strong disorder regime, while, the amplitude decreases in the limit of weak disorder. Such an anomalous behavior is completely opposite to that of bulk disordered system where the current amplitude always decreases with the disorder strength. It is also observed that the current amplitude strongly depends on the system size which reveals the finite quantum size effect.Comment: 12 pages, 7 figure

Physical Conditions in Orion's Veil

Orion's veil consists of several layers of largely neutral gas lying between us and the main ionizing stars of the Orion nebula. It is visible in 21cm H I absorption and in optical and UV absorption lines of H I and other species. Toward the Trapezium, the veil has two remarkable properties, high magnetic field (~100 microGauss) and a surprising lack of molecular hydrogen given its total hydrogen column density. Here we compute photoionization models of the veil to establish its gas density and its distance from the Trapezium. We use a greatly improved model of the hydrogen molecule that determines level populations in ~1e5 rotational/vibrational levels and provides improved estimates of molecular hydrogen destruction via the Lyman-Werner bands. Our best fit photoionization models place the veil 1-3 pc in front of the star at a density of 1e3-1e4 cubic centimeters. Magnetic energy dominates the energy of non-thermal motions in at least one of the 21cm H I velocity components. Therefore, the veil is the first interstellar environment where magnetic dominance appears to exist. We find that the low ratio of molecular to atomic hydrogen (< 1e-4) is a consequence of high UV flux incident upon the veil due to its proximity to the Trapezium stars and the absence of small grains in the region.Comment: 45 pages, 20 figures, accepted for publication in Ap

Atomic Diagnostics of X-ray Irradiated Protoplanetary Disks

We study atomic line diagnostics of the inner regions of protoplanetary disks with our model of X-ray irradiated disk atmospheres which was previously used to predict observable levels of the NeII and NeIII fine-structure transitions at 12.81 and 15.55mum. We extend the X-ray ionization theory to sulfur and calculate the fraction of sulfur in S, S+, S2+ and sulfur molecules. For the D'Alessio generic T Tauri star disk, we find that the SI fine-structure line at 25.55mum is below the detection level of the Spitzer Infrared Spectrometer (IRS), in large part due to X-ray ionization of atomic S at the top of the atmosphere and to its incorporation into molecules close to the mid-plane. We predict that observable fluxes of the SII 6718/6732AA forbidden transitions are produced in the upper atmosphere at somewhat shallower depths and smaller radii than the neon fine-structure lines. This and other forbidden line transitions, such as the OI 6300/6363AA and the CI 9826/9852AA lines, serve as complementary diagnostics of X-ray irradiated disk atmospheres. We have also analyzed the potential role of the low-excitation fine-structure lines of CI, CII, and OI, which should be observable by SOFIA and Herschel.Comment: Accepted by Ap

The Conserved nhaAR Operon Is Drastically Divergent between B2 and Non-B2 Escherichia coli and Is Involved in Extra-Intestinal Virulence

The Escherichia coli species is divided in phylogenetic groups that differ in their virulence and commensal distribution. Strains belonging to the B2 group are involved in extra-intestinal pathologies but also appear to be more prevalent as commensals among human occidental populations. To investigate the genetic specificities of B2 sub-group, we used 128 sequenced genomes and identified genes of the core genome that showed marked difference between B2 and non-B2 genomes. We focused on the gene and its surrounding region with the strongest divergence between B2 and non-B2, the antiporter gene nhaA. This gene is part of the nhaAR operon, which is in the core genome but flanked by mobile regions, and is involved in growth at high pH and high sodium concentrations. Consistently, we found that a panel of non-B2 strains grew faster than B2 at high pH and high sodium concentrations. However, we could not identify differences in expression of the nhaAR operon using fluorescence reporter plasmids. Furthermore, the operon deletion had no differential impact between B2 and non-B2 strains, and did not result in a fitness modification in a murine model of gut colonization. Nevertheless, sequence analysis and experiments in a murine model of septicemia revealed that recombination in nhaA among B2 strains was observed in strains with low virulence. Finally, nhaA and nhaAR operon deletions drastically decreased virulence in one B2 strain. This effect of nhaAR deletion appeared to be stronger than deletion of all pathogenicity islands. Thus, a population genetic approach allowed us to identify an operon in the core genome without strong effect in commensalism but with an important role in extra-intestinal virulence, a landmark of the B2 strains

Monitoring the Variable Interstellar Absorption toward HD 219188 with HST/STIS

We discuss the results of continued spectroscopic monitoring of the variable intermediate-velocity (IV) absorption at v = -38 km/s toward HD 219188. After reaching maxima in mid-2000, the column densities of both Na I and Ca II in that IV component declined by factors >= 2 by the end of 2006. Comparisons between HST/STIS echelle spectra obtained in 2001, 2003, and 2004 and HST/GHRS echelle spectra obtained in 1994--1995 indicate the following: (1) The absorption from the dominant species S II, O I, Si II, and Fe II is roughly constant in all four sets of spectra -- suggesting that the total N(H) and the (mild) depletions have not changed significantly over a period of nearly ten years. (2) The column densities of the trace species C I (both ground and excited fine-structure states) and of the excited state C II* all increased by factors of 2--5 between 1995 and 2001 -- implying increases in the hydrogen density n_H (from about 20 cm^{-3} to about 45 cm^{-3}) and in the electron density n_e (by a factor >= 3) over that 6-year period. (3) The column densities of C I and C II* -- and the corresponding inferred n_H and n_e -- then decreased slightly between 2001 and 2004. (4) The changes in C I and C II* are very similar to those seen for Na I and Ca II. The relatively low total N(H) and the modest n_H suggest that the -38 km/s cloud toward HD 219188 is not a very dense knot or filament. Partial ionization of hydrogen appears to be responsible for the enhanced abundances of Na I, C I, Ca II, and C II*. In this case, the variations in those species appear to reflect differences in density and ionization [and not N(H)] over scales of tens of AU.Comment: 33 pages, 6 figures, aastex, accepted to Ap

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

International audienceBACKGROUND: In structural genomics, an important goal is the detection and classification of protein-protein interactions, given the structures of the interacting partners. We have developed empirical energy functions to identify native structures of protein-protein complexes among sets of decoy structures. To understand the role of amino acid diversity, we parameterized a series of functions, using a hierarchy of amino acid alphabets of increasing complexity, with 2, 3, 4, 6, and 20 amino acid groups. Compared to previous work, we used the simplest possible functional form, with residue-residue interactions and a stepwise distance-dependence. We used increased computational resources, however, constructing 290,000 decoys for 219 protein-protein complexes, with a realistic docking protocol where the protein partners are flexible and interact through a molecular mechanics energy function. The energy parameters were optimized to correctly assign as many native complexes as possible. To resolve the multiple minimum problem in parameter space, over 64000 starting parameter guesses were tried for each energy function. The optimized functions were tested by cross validation on subsets of our native and decoy structures, by blind tests on series of native and decoy structures available on the Web, and on models for 13 complexes submitted to the CAPRI structure prediction experiment. RESULTS: Performance is similar to several other statistical potentials of the same complexity. For example, the CAPRI target structure is correctly ranked ahead of 90% of its decoys in 6 cases out of 13. The hierarchy of amino acid alphabets leads to a coherent hierarchy of energy functions, with qualitatively similar parameters for similar amino acid types at all levels. Most remarkably, the performance with six amino acid classes is equivalent to that of the most detailed, 20-class energy function. CONCLUSION: This suggests that six carefully chosen amino acid classes are sufficient to encode specificity in protein-protein interactions, and provide a starting point to develop more complicated energy functions

Physical Conditoins in Orion's Veil II: A Multi-Component Study of the Line of Sight Toward the Trapezium

Orion's Veil is an absorbing screen that lies along the line of sight to the Orion H II region. It consists of two or more layers of gas that must lie within a few parsecs of the Trapezium cluster. Our previous work considered the Veil as a whole and found that the magnetic field dominates the energetics of the gas in at least one component. Here we use high-resolution STIS UV spectra that resolve the two velocity components in absorption and determine the conditions in each. We derive a volume hydrogen density, 21 cm spin temperature, turbulent velocity, and kinetic temperature, for each. We combine these estimates with magnetic field measurements to find that magnetic energy significantly dominates turbulent and thermal energies in one component, while the other component is close to equipartition between turbulent and magnetic energies. We observe molecular hydrogen absorption for highly excited v, J levels that are photoexcited by the stellar continuum, and detect blueshifted S III and P III. These ions must arise from ionized gas between the mostly neutral portions of the Veil and the Trapezium and shields the Veil from ionizing radiation. We find that this layer of ionized gas is also responsible for He I absorption in the Veil, which resolves a 40-year-old debate on the origin of He I absorption towards the Trapezium. Finally, we determine that the ionized and mostly atomic layers of the Veil will collide in less than 85,000 years.Comment: 43 pages, 15 figures, to be published in Ap