298 research outputs found
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish
Fermions and Kaluza-Klein vacuum decay: a toy model
We address the question of whether or not fermions with twisted periodicity
condition suppress the semiclassical decay of M^4xS^1 Kaluza--Klein vacuum. We
consider a toy (1+1)-dimensional model with twisted fermions in cigar-shaped
Euclidean background geometry and calculate the fermion determinant. We find
that contrary to expectations, the determinant is finite. We consider this as
an indication that twisted fermions do not stabilize the Kaluza--Klein vacuum.Comment: 13 pages, 2 figure
Confinement in Covariant Gauges
We examine the weak coupling limit of Euclidean SU(n) gauge theory in
covariant gauges. Following an earlier suggestion, an equivariant
BRST-construction is used to define the continuum theory on a finite torus. The
equivariant gauge fixing introduces constant ghost fields as moduli of the
model. We study the parameter- and moduli- space perturbatively. For quark flavors, the moduli flow to a non-trivial fixed point in certain
critical covariant gauges and the one-loop effective potential indicates that
the global SU(n) color symmetry of the gauge fixed model is spontaneously
broken to . Ward identities and renormalization group arguments
imply that the longitudinal gauge boson propagator at long range is dominated
by Goldstone bosons in these critical covariant gauges. In the large
limit, we derive a nonlinear integral equation for the expectation value of
large Wilson loops assuming that the exchange of Goldstone bosons dominates the
interaction at long range in critical covariant gauges. We find numerically
that the expectation value of large circular Wilson loops decreases
exponentially with the enclosed area in the absence of dynamical fermions. The
gauge invariance of this mechanism for confinement in critical covariant gauges
is discussed.Comment: 45 pages, Latex, uses psfig.sty and epsfig.sty to include
postscript-figure
Mass Spectra of Supersymmetric Yang-Mills Theories in 1+1 Dimensions
Physical mass spectra of supersymmetric Yang-Mills theories in 1+1 dimensions
are evaluated in the light-cone gauge with a compact spatial dimension. The
supercharges are constructed and the infrared regularization is unambiguously
prescribed for supercharges, instead of the light-cone Hamiltonian. This
provides a manifestly supersymmetric infrared regularization for the
discretized light-cone approach. By an exact diagonalization of the supercharge
matrix between up to several hundred color singlet bound states, we find a
rapidly increasing density of states as mass increases.Comment: LaTeX file, 32 page, 7 eps figure
On Zero Modes and the Vacuum Problem -- A Study of Scalar Adjoint Matter in Two-Dimensional Yang-Mills Theory via Light-Cone Quantisation
SU(2) Yang-Mills Theory coupled to massive adjoint scalar matter is studied
in (1+1) dimensions using Discretised Light-Cone Quantisation. This theory can
be obtained from pure Yang-Mills in 2+1 dimensions via dimensional reduction.
On the light-cone, the vacuum structure of this theory is encoded in the
dynamical zero mode of a gluon and a constrained mode of the scalar field. The
latter satisfies a linear constraint, suggesting no nontrivial vacua in the
present paradigm for symmetry breaking on the light-cone. I develop a
diagrammatic method to solve the constraint equation. In the adiabatic
approximation I compute the quantum mechanical potential governing the
dynamical gauge mode. Due to a condensation of the lowest omentum modes of the
dynamical gluons, a centrifugal barrier is generated in the adiabatic
potential. In the present theory however, the barrier height appears too small
to make any impact in this odel. Although the theory is superrenormalisable on
naive powercounting grounds, the removal of ultraviolet divergences is
nontrivial when the constrained mode is taken into account. The open aspects of
this problem are discussed in detail.Comment: LaTeX file, 26 pages. 14 postscript figure
QED and String Theory
We analyze the D9-D9bar system in type IIB string theory using Dp-brane
probes. It is shown that the world-volume theory of the probe Dp-brane contains
two-dimensional and four-dimensional QED in the cases with p=1 and p=3,
respectively, and some applications of the realization of these well-studied
quantum field theories are discussed. In particular, the two-dimensional QED
(the Schwinger model) is known to be a solvable theory and we can apply the
powerful field theoretical techniques, such as bosonization, to study the
D-brane dynamics. The tachyon field created by the D9-D9bar strings appears as
the fermion mass term in the Schwinger model and the tachyon condensation is
analyzed by using the bosonized description. In the T-dualized picture, we
obtain the potential between a D0-brane and a D8-D8bar pair using the Schwinger
model and we observe that it consists of the energy carried by fundamental
strings created by the Hanany-Witten effect and the vacuum energy due to a
cylinder diagram. The D0-brane is treated quantum mechanically as a particle
trapped in the potential, which turns out to be a system of a harmonic
oscillator.
As another application, we obtain a matrix theory description of QED using
Taylor's T-duality prescription, which is actually applicable to a wide variety
of field theories including the realistic QCD. We show that the lattice gauge
theory is naturally obtained by regularizing the matrix size to be finite.Comment: 33 pages, Latex, 4 figures, a reference adde
Tuning Fermilab Heavy Quarks in 2+1 Flavor Lattice QCD with Application to Hyperfine Splittings
We report the non-perturbative tuning of parameters--- kappa_c, kappa_b, and
kappa_crit ---that determine the heavy-quark mass in the Fermilab action. This
requires the computation of the masses of Ds^(*) and Bs^(*) mesons comprised of
a Fermilab heavy quark and a staggered light quark. Additionally, we report the
hyperfine splittings for Ds and Bs mesons as a cross-check of our simulation
and analysis methods. We find a splitting of 145 +/- 15 MeV for the Ds system
and 40 +/- 9 MeV for the Bs system. These are in good agreement with the
Particle Data Group average values of 143.9 +/- 0.4 MeV and 46.1 +/- 1.5 MeV,
respectively. The calculations are carried out with the MILC 2+1 flavor gauge
configurations at three lattice spacings approximately 0.15, 0.12, and 0.09
fm.Comment: 34 pages, 8 figures, 26 tables; some sections rearranged for clarity;
conclusions unchanged; version accepted by Phys. Rev.
Infrared Features of the Landau Gauge QCD
The infrared features of Landau gauge QCD are studied by the lattice
simulation of and . We
adopt two definitions of the gauge field; 1) linear 2) and
measured the gluon propagator and ghost propagator. Infrared singularity of the
gluon propagator is less than that of tree level result but the gluon
propagator at 0 momentum remains finite. The infrared singularity of ghost
propagator is stronger than the tree level. The QCD running coupling measured
by using the gluon propagator and the ghost propagator has a maximum
at around and decreases as approaches 0.
The data are analyzed in use of formula of the principle of minimal
sensitivity(PMS), the effective charge method and the contour-improved
perturbation method, which suggest necessity of the resummation of perturbation
series in the infrared region together with existence of the infrared fixed
point. Kugo-Ojima parameter saturates at about -0.8 in contrast to the
theoretically expected value -1.Comment: RevTex4, 9 pages, 10 eps figures, Typos corrected. To be published in
Phys. Rev. D(2004
Edge States and Entropy of 2d Black Holes
In several recent publications Carlip, as well as Balachandran, Chandar and
Momen, have proposed a statistical mechanical interpretation for black hole
entropy in terms of ``would be gauge'' degrees of freedom that become dynamical
on the boundary to spacetime. After critically discussing several routes for
deriving a boundary action, we examine their hypothesis in the context of
generic 2-D dilaton gravity. We first calculate the corresponding statistical
mechanical entropy of black holes in 1+1 deSitter gravity, which has a gauge
theory formulation as a BF-theory. Then we generalize the method to dilaton
gravity theories that do not have a (standard) gauge theory formulation. This
is facilitated greatly by the Poisson-Sigma-model formulation of these
theories. It turns out that the phase space of the boundary particles coincides
precisely with a symplectic leaf of the Poisson manifold that enters as target
space of the Sigma-model. Despite this qualitatively appealing picture, the
quantitative results are discouraging: In most of the cases the symplectic
leaves are non-compact and the number of microstates yields a meaningless
infinity. In those cases where the particle phase space is compact - such as,
e.g., in the Euclidean deSitter theory - the edge state degeneracy is finite,
but generically it is far too small to account for the semiclassical
Bekenstein-Hawking entropy.Comment: 36 pages, Late
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