SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab) DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates

Soil Fungi Alter Interactions Between the Invader Centaurea Maculosa and North American Natives

Soil microbes may affect the way exotic invasive plants interact with native neighbors. We investigated the effects of soil fungi on interactions between the invasive weed Centaurea maculosa (spotted knapweed) and six species native to the intermountain prairies of the northwestern United States. We also compared the effect of C. maculosa on the composition of the soil microbial community to that of the native species. In the field, fungicide (Benomyl) reduced AM mycorrhizal colonization of C. maculosa roots by \u3e80%. Fungicide did not significantly reduce non-AM fungi. When grown alone, the biomass of C. maculosa was not affected by the fungicide application. However, depending on the combination of native competitor and fungicide, C. maculosa biomass varied from 10-fold decreases to 1.9-fold increases. In untreated soils, C. maculosa grew larger in the presence of Festuca idahoensis or Koeleria cristata than when alone. When fungicide was applied these positive effects of Festuca and Koeleria on C. maculosa did not occur. A third native grass, Pseudoroegneria spicata, had much stronger competitive effects on C. maculosa than Festuca or Koeleria, and fungicide reduced the competitive effects of Pseudoroegneria. Fungicide increased Centaurea biomass when competing with the forb Gallardia aristata. However, fungicide did not affect the way two other forbs; Achillea millefolium and Linum lewisii, interacted with C. maculosa. Rhizosphere microbial communities in the root zones of the three native bunchgrass species differed from that of C. maculosa. However, despite the strong effects of soil fungi in field interactions and differences in microbial community composition, soil biota from different plant rhizospheres did not affect the growth of C. maculosa in the absence of native competitors in greenhouse experiments. Our results suggest that successful invasions by exotic plant species can be affected by complex and often beneficial effects of local soil microbial communities. These effects were not manifest as simple direct effects, but become apparent only when native plants, invasive plants, and soil microbial communities were interacting at the same time

Local moment formation in quantum point contacts

Spin-density-functional theory of quantum point contacts (QPCs) reveals the formation of a local moment with a net of one electron spin in the vicinity of the point contact - supporting the recent report of a Kondo effect in a QPC. The hybridization of the local moment to the leads decreases as the QPC becomes longer, while the onsite Coulomb-interaction energy remains almost constant.Comment: 10 pages, 3 figures, accepted for publication in Physical Review Letter

Quasiparticle band structure of infinite hydrogen fluoride and hydrogen chloride chains

We study the quasiparticle band structure of isolated, infinite HF and HCl bent (zigzag) chains and examine the effect of the crystal field on the energy levels of the constituent monomers. The chains are one of the simplest but realistic models of the corresponding three-dimensional crystalline solids. To describe the isolated monomers and the chains, we set out from the Hartree-Fock approximation, harnessing the advanced Green's function methods "local molecular orbital algebraic diagrammatic construction" (ADC) scheme and "local crystal orbital ADC" (CO-ADC) in a strict second order approximation, ADC(2,2) and CO-ADC(2,2), respectively, to account for electron correlations. The configuration space of the periodic correlation calculations is found to converge rapidly only requiring nearest-neighbor contributions to be regarded. Although electron correlations cause a pronounced shift of the quasiparticle band structure of the chains with respect to the Hartree-Fock result, the bandwidth essentially remains unaltered in contrast to, e.g., covalently bound compounds.Comment: 11 pages, 6 figures, 6 tables, RevTeX4, corrected typoe

Stability of the Black Hole Horizon and the Landau Ghost

The stability of the black hole horizon is demanded by both cosmic censorship and the generalized second law of thermodynamics. We test the consistency of these principles by attempting to exceed the black hole extremality condition in various process in which a U(1) charge is added to a nearly extreme Reissner--Nordstr\"om black hole charged with a {\it different\/} type of U(1) charge. For an infalling spherical charged shell the attempt is foiled by the self--Coulomb repulsion of the shell. For an infalling classical charge it fails because the required classical charge radius exceeds the size of the black hole. For a quantum charge the horizon is saved because in order to avoid the Landau ghost, the effective coupling constant cannot be large enough to accomplish the removal.Comment: 12 pages, RevTe

Kinetics of four-wave mixing for a 2D magneto-plasma in strong magnetic fields

We investigate the femtosecond kinetics of an optically excited 2D magneto-plasma at intermediate and high densities under a strong magnetic field perpendicular to the quantum well (QW). We assume an additional weak lateral confinement which lifts the degeneracy of the Landau levels partially. We calculate the femtosecond dephasing and relaxation kinetics of the laser pulse excited magneto-plasma due to bare Coulomb potential scattering, because screening is under these conditions of minor importance. In particular the time-resolved and time-integrated four-wave mixing (FWM) signals are calculated by taking into account three Landau subbands in both the valance and the conduction band assuming an electron-hole symmetry. The FWM signals exhibit quantum beats mainly with twice the cyclotron frequency. Contrary to general expectations, we find no pronounced slowing down of the dephasing with increasing magnetic field. On the contrary, one obtains a decreasing dephasing time because of the increase of the Coulomb matrix elements and the number of states in a given Landau subband. In the situation when the loss of scattering channels exceeds these increasing effects, one gets a slight increase at the dephasing time. However, details of the strongly modulated scattering kinetics depend sensitively on the detuning, the plasma density, and the spectral pulse width relative to the cyclotron frequency.Comment: 13 pages, in RevTex format, 10 figures, Phys. Rev B in pres

Generalized acceleration theorem for spatiotemporal Bloch waves

A representation is put forward for wave functions of quantum particles in periodic lattice potentials subjected to homogeneous time-periodic forcing, based on an expansion with respect to Bloch-like states which embody both the spatial and the temporal periodicity. It is shown that there exists a generalization of Bloch's famous acceleration theorem which grows out of this representation and captures the effect of a weak probe force applied in addition to a strong dressing force. Taken together, these elements point at a "dressing and probing" strategy for coherent wave-packet manipulation, which could be implemented in present experiments with optical lattices.Comment: 12 pages, 4 figure

Low thermal conductivity of the layered oxide (Na,Ca)Co_2O_4: Another example of a phonon glass and an electron crystal

The thermal conductivity of polycrystalline samples of (Na,Ca)Co_2O_4 is found to be unusually low, 20 mW/cmK at 280 K. On the assumption of the Wiedemann-Franz law, the lattice thermal conductivity is estimated to be 18 mW/cmK at 280 K, and it does not change appreciably with the substitution of Ca for Na. A quantitative analysis has revealed that the phonon mean free path is comparable with the lattice parameters, where the point-defect scattering plays an important role. Electronically the same samples show a metallic conduction down to 4.2 K, which strongly suggests that NaCo_2O_4 exhibits a glass-like poor thermal conduction together with a metal-like good electrical conduction. The present study further suggests that a strongly correlated system with layered structure can act as a material of a phonon glass and an electron crystal.Comment: 5 pages 3 figures, to be published in Phys. Rev.

Spin-Charge Separation in Two Dimensions - A Numerical Study

The question of spin-charge separation in two-dimensional lattices has been addressed by numerical simulations of the motion of one hole in a half-filled band. The calculations have been performed on finite clusters with Hubbard and t-J models. By comparing the time evolution of spin and charge polarisation currents in one and two dimensions, evidence in favor of spin-charge separation in two dimensions is presented. In contrast with this, spin-charge separation is absent in a highly doped, metallic, system.Comment: RevTeX 3.0, 10 Pages, 6 PostScript Figures (on request