Taking the C out of CVMFS

The Cern Virtual Machine File System is most well known as a distribution mechanism for the WLCG VOs@@ experiment software; as a result, almost all the existing expertise is in installing clients mount the central Cern repositories. We report the results of an initial experiment in using the cvmfs server packages to provide Glasgow-based repository aimed at software provisioning for small UK-local VOs. In general, although the documentation is sparse, server configuration is reasonably easy, with some experimentation. We discuss the advantages of local CVMFS repositories for sites, with some examples from our test VOs, vo.optics.ac.uk and neiss.org.uk

Pade Approximants, Optimal Renormalization Scales, and Momentum Flow in Feynman Diagrams

We show that the Pade Approximant (PA) approach for resummation of perturbative series in QCD provides a systematic method for approximating the flow of momentum in Feynman diagrams. In the large-$\beta_0$ limit, diagonal PA's generalize the Brodsky-Lepage-Mackenzie (BLM) scale-setting method to higher orders in a renormalization scale- and scheme-invariant manner, using multiple scales that represent Neubert's concept of the distribution of momentum flow through a virtual gluon. If the distribution is non-negative, the PA's have only real roots, and approximate the distribution function by a sum of delta-functions, whose locations and weights are identical to the optimal choice provided by the Gaussian quadrature method for numerical integration. We show how the first few coefficients in a perturbative series can set rigorous bounds on the all-order momentum distribution function, if it is positive. We illustrate the method with the vacuum polarization function and the Bjorken sum rule computed in the large-$\beta_0$ limit.Comment: 28 pages, LaTeX, including 6 figures requires epsfig.st

A logarithmic-depth quantum carry-lookahead adder

We present an efficient addition circuit, borrowing techniques from the classical carry-lookahead arithmetic circuit. Our quantum carry-lookahead (QCLA) adder accepts two n-bit numbers and adds them in O(log n) depth using O(n) ancillary qubits. We present both in-place and out-of-place versions, as well as versions that add modulo 2^n and modulo 2^n - 1. Previously, the linear-depth ripple-carry addition circuit has been the method of choice. Our work reduces the cost of addition dramatically with only a slight increase in the number of required qubits. The QCLA adder can be used within current modular multiplication circuits to reduce substantially the run-time of Shor's algorithm.Comment: 21 pages, 4 color figure

Renormalization-Scale Invariance, Minimal Sensitivity, and the Inclusive Hadronic Decays of a 115 GeV Higgs Particle

Known perturbative expressions for the decay rates of 115 GeV Higgs particle into either two gluons or a $b\bar{b}$ pair are shown to exhibit renormalization-scale-($\mu$)-dependence that is largely removed via renormalization-group/Pade-approximant estimates of these rates' next order contributions. The extrema in $\mu$ characterizing both rates, as determined from fully-known orders of perturbation theory, are very nearly equal to corresponding $\mu$-insensitive rates obtained via estimation of their next order contributions, consistent with "minimal-sensitivity" expectations.Comment: 12 pages, 3 figures, LaTe

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. RESULTS: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. CONCLUSIONS: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data

Chirped pulse Raman amplification in plasma: high gain measurements

High power short pulse lasers are usually based on chirped pulse amplification (CPA), where a frequency chirped and temporarily stretched ``seed'' pulse is amplified by a broad-bandwidth solid state medium, which is usually pumped by a monochromatic ``pump'' laser. Here, we demonstrate the feasibility of using chirped pulse Raman amplification (CPRA) as a means of amplifying short pulses in plasma. In this scheme, a short seed pulse is amplified by a stretched and chirped pump pulse through Raman backscattering in a plasma channel. Unlike conventional CPA, each spectral component of the seed is amplified at different longitudinal positions determined by the resonance of the seed, pump and plasma wave, which excites a density echelon that acts as a "chirped'" mirror and simultaneously backscatters and compresses the pump. Experimental evidence shows that it has potential as an ultra-broad bandwidth linear amplifier which dispenses with the need for large compressor gratings