5,411 research outputs found
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
diverges.Comment: typeset in RevTex, 13 page
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