1,565 research outputs found
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
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