HepForge: A lightweight development environment for HEP software

Setting up the infrastructure to manage a software project can become a task as significant writing the software itself. A variety of useful open source tools are available, such as Web-based viewers for version control systems, "wikis" for collaborative discussions and bug-tracking systems, but their use in high-energy physics, outside large collaborations, is insubstantial. Understandably, physicists would rather do physics than configure project management tools. We introduce the CEDAR HepForge system, which provides a lightweight development environment for HEP software. Services available as part of HepForge include the above-mentioned tools as well as mailing lists, shell accounts, archiving of releases and low-maintenance Web space. HepForge also exists to promote best-practice software development methods and to provide a central repository for re-usable HEP software and phenomenology codes.Comment: 3 pages, 0 figures. To be published in proceedings of CHEP06. Refers to the HepForge facility at http://hepforge.cedar.ac.u

HepData and JetWeb: HEP data archiving and model validation

The CEDAR collaboration is extending and combining the JetWeb and HepData systems to provide a single service for tuning and validating models of high-energy physics processes. The centrepiece of this activity is the fitting by JetWeb of observables computed from Monte Carlo event generator events against their experimentally determined distributions, as stored in HepData. Caching the results of the JetWeb simulation and comparison stages provides a single cumulative database of event generator tunings, fitted against a wide range of experimental quantities. An important feature of this integration is a family of XML data formats, called HepML.Comment: 4 pages, 0 figures. To be published in proceedings of CHEP0

Consistent thermodynamics for spin echoes

Spin-echo experiments are often said to constitute an instant of anti-thermodynamic behavior in a concrete physical system that violates the second law of thermodynamics. We argue that a proper thermodynamic treatment of the effect should take into account the correlations between the spin and translational degrees of freedom of the molecules. To this end, we construct an entropy functional using Boltzmann macrostates that incorporates both spin and translational degrees of freedom. With this definition there is nothing special in the thermodynamics of spin echoes: dephasing corresponds to Hamiltonian evolution and leaves the entropy unchanged; dissipation increases the entropy. In particular, there is no phase of entropy decrease in the echo. We also discuss the definition of macrostates from the underlying quantum theory and we show that the decay of net magnetization provides a faithful measure of entropy change.Comment: 15 pages, 2 figs. Changed figures, version to appear in PR

An evaluation of genotyping by sequencing (GBS) to map the <em>Breviaristatum-e (ari-e)</em> locus in cultivated barley

ABSTRACT: We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait Loci (QTL), the first in a region encompassing the spike architecture gene Vrs1 on chromosome 2H, the second in an uncharacterised centromeric region on chromosome 3H, and the third in a region of chromosome 5H coinciding with the previously described dwarfing gene Breviaristatum-e (Ari-e). BACKGROUND: Barley cultivars in North-western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene OsSd1, or Breviaristatum-e (ari-e) on chromosome 5H. A recessive mutant allele of the latter gene, ari-e.GP, was introduced into cultivation via the cv. ‘Golden Promise’ that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today. RESULTS: Using GBS mapping data and phenotypic measurements we show that ari-e.GP maps to a small genetic interval on chromosome 5H and that alternative alleles at a region encompassing Vrs1 on 2H along with a region on chromosome 3H also influence plant height. The location of Ari-e is supported by analysis of near-isogenic lines containing different ari-e alleles. We explored use of the GBS to populate the region with sequence contigs from the recently released physically and genetically integrated barley genome sequence assembly as a step towards Ari-e gene identification. CONCLUSIONS: GBS was an effective and relatively low-cost approach to rapidly construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari-e.GP on chromosome 5H. Mapping resolution was lower than we anticipated. We found the GBS data more complex to analyse than other data types but it did directly provide linked SNP markers for subsequent higher resolution genetic analysis

Bath generated work extraction and inversion-free gain in two-level systems

The spin-boson model, often used in NMR and ESR physics, quantum optics and spintronics, is considered in a solvable limit to model a spin one-half particle interacting with a bosonic thermal bath. By applying external pulses to a non-equilibrium initial state of the spin, work can be extracted from the thermalized bath. It occurs on the timescale \T_2 inherent to transversal (`quantum') fluctuations. The work (partly) arises from heat given off by the surrounding bath, while the spin entropy remains constant during a pulse. This presents a violation of the Clausius inequality and the Thomson formulation of the second law (cycles cost work) for the two-level system. Starting from a fully disordered state, coherence can be induced by employing the bath. Due to this, a gain from a positive-temperature (inversion-free) two-level system is shown to be possible.Comment: 4 pages revte

Force balance and membrane shedding at the Red Blood Cell surface

During the aging of the red-blood cell, or under conditions of extreme echinocytosis, membrane is shed from the cell plasma membrane in the form of nano-vesicles. We propose that this process is the result of the self-adaptation of the membrane surface area to the elastic stress imposed by the spectrin cytoskeleton, via the local buckling of membrane under increasing cytoskeleton stiffness. This model introduces the concept of force balance as a regulatory process at the cell membrane, and quantitatively reproduces the rate of area loss in aging red-blood cells.Comment: 4 pages, 3 figure

Membrane shape as a reporter for applied forces

Recent advances have enabled 3-dimensional reconstructions of biological structures in vivo, ranging in size and complexity from single proteins to multicellular structures. In particular, tomography and confocal microscopy have been exploited to capture detailed 3-dimensional conformations of membranes in cellular processes ranging from viral budding and organelle maintenance to phagocytosis. Despite the wealth of membrane structures available, there is as yet no generic, quantitative method for their interpretation. We propose that by modeling these observed biomembrane shapes as fluid lipid bilayers in mechanical equilibrium, the externally applied forces as well as the pressure, tension, and spontaneous curvature can be computed directly from the shape alone. To illustrate the potential power of this technique, we apply an axial force with optical tweezers to vesicles and explicitly demonstrate that the applied force is equal to the force computed from the membrane conformation

Magnet Laboratory Research

Contains research objectives and reports on three research projects

Cauchy horizon singularity without mass inflation

A perturbed Reissner-Nordstr\"om-de Sitter solution is used to emphasize the nature of the singularity along the Cauchy horizon of a charged spherically symmetric black hole. For these solutions, conditions may prevail under which the mass function is bounded and yet the curvature scalar $R_{\alpha\beta\gamma\delta} R^{\alpha\beta\gamma\delta}$ diverges.Comment: typeset in RevTex, 13 page