252 research outputs found
Stability of Monomer-Dimer Piles
We measure how strong, localized contact adhesion between grains affects the
maximum static critical angle, theta_c, of a dry sand pile. By mixing dimer
grains, each consisting of two spheres that have been rigidly bonded together,
with simple spherical monomer grains, we create sandpiles that contain strong
localized adhesion between a given particle and at most one of its neighbors.
We find that tan(theta_c) increases from 0.45 to 1.1 and the grain packing
fraction, Phi, decreases from 0.58 to 0.52 as we increase the relative number
fraction of dimer particles in the pile, nu_d, from 0 to 1. We attribute the
increase in tan(theta_c(nu_d)) to the enhanced stability of dimers on the
surface, which reduces the density of monomers that need to be accomodated in
the most stable surface traps. A full characterization and geometrical
stability analysis of surface traps provides a good quantitative agreement
between experiment and theory over a wide range of nu_d, without any fitting
parameters.Comment: 11 pages, 12 figures consisting of 21 eps files, submitted to PR
Adaptive Mesh Refinement for Characteristic Grids
I consider techniques for Berger-Oliger adaptive mesh refinement (AMR) when
numerically solving partial differential equations with wave-like solutions,
using characteristic (double-null) grids. Such AMR algorithms are naturally
recursive, and the best-known past Berger-Oliger characteristic AMR algorithm,
that of Pretorius & Lehner (J. Comp. Phys. 198 (2004), 10), recurses on
individual "diamond" characteristic grid cells. This leads to the use of
fine-grained memory management, with individual grid cells kept in
2-dimensional linked lists at each refinement level. This complicates the
implementation and adds overhead in both space and time.
Here I describe a Berger-Oliger characteristic AMR algorithm which instead
recurses on null \emph{slices}. This algorithm is very similar to the usual
Cauchy Berger-Oliger algorithm, and uses relatively coarse-grained memory
management, allowing entire null slices to be stored in contiguous arrays in
memory. The algorithm is very efficient in both space and time.
I describe discretizations yielding both 2nd and 4th order global accuracy.
My code implementing the algorithm described here is included in the electronic
supplementary materials accompanying this paper, and is freely available to
other researchers under the terms of the GNU general public license.Comment: 37 pages, 15 figures (40 eps figure files, 8 of them color; all are
viewable ok in black-and-white), 1 mpeg movie, uses Springer-Verlag svjour3
document class, includes C++ source code. Changes from v1: revised in
response to referee comments: many references added, new figure added to
better explain the algorithm, other small changes, C++ code updated to latest
versio
The Ekpyrotic Universe: Colliding Branes and the Origin of the Hot Big Bang
We propose a cosmological scenario in which the hot big bang universe is
produced by the collision of a brane in the bulk space with a bounding orbifold
plane, beginning from an otherwise cold, vacuous, static universe. The model
addresses the cosmological horizon, flatness and monopole problems and
generates a nearly scale-invariant spectrum of density perturbations without
invoking superluminal expansion (inflation). The scenario relies, instead, on
physical phenomena that arise naturally in theories based on extra dimensions
and branes. As an example, we present our scenario predominantly within the
context of heterotic M-theory. A prediction that distinguishes this scenario
from standard inflationary cosmology is a strongly blue gravitational wave
spectrum, which has consequences for microwave background polarization
experiments and gravitational wave detectors.Comment: 67 pages, 4 figures. v2,v3: minor corrections, references adde
Coherent electron-phonon coupling and polaron-like transport in molecular wires
We present a technique to calculate the transport properties through
one-dimensional models of molecular wires. The calculations include inelastic
electron scattering due to electron-lattice interaction. The coupling between
the electron and the lattice is crucial to determine the transport properties
in one-dimensional systems subject to Peierls transition since it drives the
transition itself. The electron-phonon coupling is treated as a quantum
coherent process, in the sense that no random dephasing due to electron-phonon
interactions is introduced in the scattering wave functions. We show that
charge carrier injection, even in the tunneling regime, induces lattice
distortions localized around the tunneling electron. The transport in the
molecular wire is due to polaron-like propagation. We show typical examples of
the lattice distortions induced by charge injection into the wire. In the
tunneling regime, the electron transmission is strongly enhanced in comparison
with the case of elastic scattering through the undistorted molecular wire. We
also show that although lattice fluctuations modify the electron transmission
through the wire, the modifications are qualitatively different from those
obtained by the quantum electron-phonon inelastic scattering technique. Our
results should hold in principle for other one-dimensional atomic-scale wires
subject to Peierls transitions.Comment: 21 pages, 8 figures, accepted for publication in Phys. Rev. B (to
appear march 2001
Physics of Solar Prominences: I - Spectral Diagnostics and Non-LTE Modelling
This review paper outlines background information and covers recent advances
made via the analysis of spectra and images of prominence plasma and the
increased sophistication of non-LTE (ie when there is a departure from Local
Thermodynamic Equilibrium) radiative transfer models. We first describe the
spectral inversion techniques that have been used to infer the plasma
parameters important for the general properties of the prominence plasma in
both its cool core and the hotter prominence-corona transition region. We also
review studies devoted to the observation of bulk motions of the prominence
plasma and to the determination of prominence mass. However, a simple inversion
of spectroscopic data usually fails when the lines become optically thick at
certain wavelengths. Therefore, complex non-LTE models become necessary. We
thus present the basics of non-LTE radiative transfer theory and the associated
multi-level radiative transfer problems. The main results of one- and
two-dimensional models of the prominences and their fine-structures are
presented. We then discuss the energy balance in various prominence models.
Finally, we outline the outstanding observational and theoretical questions,
and the directions for future progress in our understanding of solar
prominences.Comment: 96 pages, 37 figures, Space Science Reviews. Some figures may have a
better resolution in the published version. New version reflects minor
changes brought after proof editin
Single Spin Asymmetry in Polarized Proton-Proton Elastic Scattering at GeV
We report a high precision measurement of the transverse single spin
asymmetry at the center of mass energy GeV in elastic
proton-proton scattering by the STAR experiment at RHIC. The was measured
in the four-momentum transfer squared range \GeVcSq, the region of a significant interference between the
electromagnetic and hadronic scattering amplitudes. The measured values of
and its -dependence are consistent with a vanishing hadronic spin-flip
amplitude, thus providing strong constraints on the ratio of the single
spin-flip to the non-flip amplitudes. Since the hadronic amplitude is dominated
by the Pomeron amplitude at this , we conclude that this measurement
addresses the question about the presence of a hadronic spin flip due to the
Pomeron exchange in polarized proton-proton elastic scattering.Comment: 12 pages, 6 figure
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Closed-Form transformation between geodetic and ellipsoidal coordinates
We present formulas for direct closed-form transformation between geodetic coordinates(Φ, λ, h) and ellipsoidal coordinates (β, λ, u) for any oblate ellipsoid of revolution.These will be useful for those dealing with ellipsoidal representations of the Earth's gravityfield or other oblate ellipsoidal figures. The numerical stability of the transformations for nearpolarand near-equatorial regions is also considered
The BRCA2 c.68-7T > A variant is not pathogenic : A model for clinical calibration of spliceogenicity
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44x10(-115). There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.Peer reviewe
Mutations in RSPH1 cause primary ciliary dyskinesia with a unique clinical and ciliary phenotype
Rationale: Primary ciliary dyskinesia (PCD) is a genetically heterogeneous recessive disorder of motile cilia, but the genetic cause is not defined for all patients with PCD. Objectives: To identify disease-causingmutations in novel genes, we performed exome sequencing, follow-up characterization, mutation scanning, and genotype-phenotype studies in patients with PCD. Methods: Whole-exome sequencing was performed using NimbleGen capture and Illumina HiSeq sequencing. Sanger-based sequencing was used for mutation scanning, validation, and segregation analysis. Measurements and Main Results: We performed exome sequencing on an affected sib-pair with normal ultrastructure in more than 85% of cilia. A homozygous splice-site mutation was detected in RSPH1 in both siblings; parents were carriers. Screening RSPH1 in 413 unrelated probands, including 325 with PCD and 88 with idiopathic bronchiectasis, revealed biallelic loss-of-function mutations in nine additional probands. Five affected siblings of probands in RSPH1 families harbored the familial mutations. The 16 individuals with RSPH1 mutations had some features of PCD; however, nasal nitric oxide levels were higher than in patients with PCD with other gene mutations (98.3 vs. 20.7 nl/min; P , 0.0003). Additionally, individuals with RSPH1 mutations had a lower prevalence (8 of 16) of neonatal respiratory distress, and later onset of daily wet cough than typical for PCD, and better lung function (FEV1), compared with 75 age- and sex-matched PCD cases (73.0 vs. 61.8, FEV1 % predicted; P = 0.043). Cilia from individuals with RSPH1 mutations had normal beat frequency (6.16Hz at 258C), but an abnormal, circular beat pattern. Conclusions: The milder clinical disease and higher nasal nitric oxide in individuals with biallelic mutations in RSPH1 provides evidence of a unique genotype-phenotype relationship in PCD, and suggests that mutations in RSPH1 may be associated with residual ciliary function
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