The Focusing DIRC is considered for the Barrel PID at a possible Super-B factory. To reduce sensitivity to background, it would be desirable to reduce a size of the present BaBar photon detector. One way to do it is to replace it with a focusing optics and use smaller photon detector pixels. We have simulated the focusing optics with simulation software based on a 3D calculation performed with the Mathematica program. The software does not use Optica package, instead, it uses its own 3D algorithm. The advantage of the presented method is that it is transparent, fast and that it uses a full backing of the Mathematica graphics, and it does not require expertise to run Geat4 MC software.

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ArgoNeuT is a Liquid Argon Time Projection Chamber neutrino experiment that recently completed its physics run in the NuMI beamline at Fermilab. Along with research and design for future LArTPCs, the experiments goals include performing a number of neutrino and anti-neutrino cross section measurements. Also, ArgoNeuT hopes to further the understanding of the nuclear physics involved in neutrino scattering by characterizing the low energy protons created in such interactions.

Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiome?s predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

In many situations distribution can significantly deviate from Gaussian which requires accurate treatment of IBS. Our original interest in this problem was motivated by the need to have an accurate description of beam evolution due to IBS while distribution is strongly affected by the external electron cooling force. A variety of models with various degrees of approximation were developed and implemented in BETACOOL in the past to address this topic. A more complete treatment based on the friction coefficient and full 3-D diffusion tensor was introduced in BETACOOL at the end of 2007 under the name 'local IBS model'. Such a model allowed us calculation of IBS for an arbitrary beam distribution. The numerical benchmarking of this local IBS algorithm and its comparison with other models was reported before. In this paper, after briefly describing the model and its limitations, they present its comparison with available experimental data.

We present a study of the D{sup +}{pi}{sup -}, D{sup 0}{pi}{sup +}, and D*{sup +}{pi}{sup -} systems in inclusive e{sup +}e{sup -} {yields} c{bar c} interactions in a search for new excited D meson states. We use a dataset, consisting of {approx}454 fb{sup -1}, collected at center-of-mass energies near 10.58 GeV by the BABAR detector at the SLAC PEP-II asymmetric-energy collider. We observe, for the first time, candidates for the radial excitations of the D{sup 0}, D*{sup 0}, and D*{sup +}, as well as the L = 2 excited states of the D{sup 0} and D{sup +}, where L is the orbital angular momentum of the quarks.

The status and the most important issues in neutrino physics will be summarized as well as how the current, pressing questions will be addressed by future experiments. Since the discovery of neutrino flavor transitions by the SuperKamiokande experiment in 1998, which demonstrates that neutrinos change and hence their clocks tick, i.e. they are not traveling at the speed of light and hence are not massless, the field of neutrino physics has made remarkable progress in untangling the nature of the neutrino. However, there are still many important questions to answer.

We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important to laser mitigation experiments.

We report results on lithium alumino-silicate ion source development in preparation for warmdense-matter heating experiments on the new Neutralized Drift Compression Experiment (NDCXII). The practical limit to the current density for a lithium alumino-silicate source is determined by the maximum operating temperature that the ion source can withstand before running into problems of heat transfer, melting of the alumino-silicate material, and emission lifetime. Using small prototype emitters, at a temperature of ~;;1275 oC, a space-charge-limited Li+ beam current density of J ~;;1 mA/cm2 was obtained. The lifetime of the ion source was ~;;50 hours while pulsing at a rate of 0.033 Hz with a pulse duration of 5-6 mu s.

We present a first look at the new code for self-consistent, 2D simulations of beam dynamics affected by the coherent synchrotron radiation. The code is of the particle-in-cell variety: the beam bunch is sampled by point-charge particles, which are deposited on the grid; the corresponding forces on the grid are then computed using retarded potentials according to causality, and interpolated so as to advance the particles in time. The retarded potentials are evaluated by integrating over the 2D path history of the bunch, with the charge and current density at the retarded time obtained from interpolation of the particle distributions recorded at discrete timesteps. The code is benchmarked against analytical results obtained for a rigid-line bunch. We also outline the features and applications which are currently being developed.

The shielding design for the NSLS-II will provide adequate protection for the full injected beam loss in two periods of the ring around the injection point, but the remainder of the ring is shielded for lower losses of {le} 10% full beam. This will require a system to insure that beam losses don't exceed these levels for a period of time that could cause excessive radiation levels outside the shield walls. This beam containment system will measure, provide a level of control and alarm indication of the beam power losses along the beam path from the source (e-gun, linac) thru the injection system and the storage ring. This system will consist of collimators that will provide limits to (and potentially to measure) the beam miss-steering and control the loss points of the charge and monitors that will measure the average beam current losses along the beam path and alarm when this beam power loss exceeds the level set by the shielding specifications. This will require some new ideas in beam loss detection capability and collimation. The initial planning and R&D program will be presented.

Production of H{sup -} beam for accelerators applications by charge exchange of high brightness hydrogen neutral beam in a sodium jet cell is experimentally studied in joint BNL-BINP experiment. In the experiment, a hydrogen-neutral beam with 3-6 keV energy, equivalent current up to 5 A and 200 microsecond pulse duration is used. The atomic beam is produced by charge exchange of a proton beam in a pulsed hydrogen target. Formation of the proton beam is performed in an ion source by four-electrode multiaperture ion-optical system. To achieve small beam emittance, the apertures in the ion-optical system have small enough size, and the extraction of ions is carried out from the surface of plasma emitter with a low transverse ion temperature of {approx}0.2 eV formed as a result of plasma jet expansion from the arc plasma generator. Developed for the BNL optically pumped polarized ion source, the sodium jet target with recirculation and aperture diameter of 2 cm is used in the experiment. At the first stage of the experiment H{sup -} beam with 36 mA current, 5 keV energy and {approx}0.15 cm {center_dot} mrad normalized emittance was obtained. To increase H{sup -} beam current ballistically focused hydrogen neutral beam will …

Recently a Resistive Magnetohydrodynamics (MHD) package has been added to the KULL code. In order to be compatible with the underlying hydrodynamics algorithm, a new sub-zonal magnetics discretization was developed that supports arbitrary polygonal and polyhedral zones. This flexibility comes at the cost of many more unknowns per zone - approximately ten times more for a hexahedral mesh. We can eliminate some (or all, depending on the dimensionality) of the extra unknowns from the global matrix during assembly by using a Schur complement approach. This trades expensive global work for cache-friendly local work, while still allowing solution for the full system. Significant improvements in the solution time are observed for several test problems.

Local thermal hot-spots in microprocessors lead to worst case provisioning of global cooling resources, especially in large-scale systems. However, efficiency of cooling solutions degrade non-linearly with supply temperature, resulting in high power consumption and cost in cooling - 50 {approx} 100% of IT power. Recent advances in active cooling techniques have shown on-chip thermoelectric coolers (TECs) to be very efficient at selectively eliminating small hot-spots, where applying current to a superlattice film deposited between silicon and the heat spreader results in a Peltier effect that spreads the heat and lowers the temperature of the hot-spot significantly to improve chip reliability. In this paper, we propose that hot-spot mitigation using thermoelectric coolers can be used as a power management mechanism to allow global coolers to be provisioned for a better worst case temperature leading to substantial savings in cooling power. In order to quantify the potential power savings from using TECs in data center servers, we present a detailed power model that integrates on-chip dynamic and leakage power sources, heat diffusion through the entire chip, TEC and global cooler efficiencies, and all their mutual interactions. Our multiscale analysis shows that, for a typical data center, TECs allow global coolers to operate …

We propose a modification to the Levenberg-Marquardt minimization algorithm for a more robust and more efficient calibration of highly parameterized, strongly nonlinear models of multiphase flow through porous media. The new method combines the advantages of truncated singular value decomposition with those of the classical Levenberg-Marquardt algorithm, thus enabling a more robust solution of underdetermined inverse problems with complex relations between the parameters to be estimated and the observable state variables used for calibration. The truncation limit separating the solution space from the calibration null space is re-evaluated during the iterative calibration process. In between these re-evaluations, fewer forward simulations are required, compared to the standard approach, to calculate the approximate sensitivity matrix. Truncated singular values are used to calculate the Levenberg-Marquardt parameter updates, ensuring that safe small steps along the steepest-descent direction are taken for highly correlated parameters of low sensitivity, whereas efficient quasi-Gauss-Newton steps are taken for independent parameters with high impact. The performance of the proposed scheme is demonstrated for a synthetic data set representing infiltration into a partially saturated, heterogeneous soil, where hydrogeological, petrophysical, and geostatistical parameters are estimated based on the joint inversion of hydrological and geophysical data.

The low-{beta} magnet systems are located in the LHC insertion regions around the four interaction points. They are the key elements in the beams focusing/defocusing process and will allow proton collisions at a luminosity of up to 10{sup 34}cm{sup -2}s{sup -1}. Large radiation dose deposited at the proximity of the beam collisions dictate stringent requirements for the design and operation of the systems. The hardware commissioning phase of the LHC was completed in the winter of 2010 and permitted to validate this system safe operation. This paper presents the analysis used to qualify and quantify the safe operation of the low-{beta} magnet systems in the Large Hadron Collider (LHC) for the first years of operation.

Human biospecimens are subjected to collection, processing, and storage that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research that uses human tissues, it is crucial that information on the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications on biospecimen-related research and to help reassure patient contributors and the advocacy community that their contributions are valued and respected.

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific …

We report the measurement of differential diphoton direct production cross sections and a study of photon + 3-jet events with double parton (DP) interactions, based on data taken with the D0 experiment at the Fermilab Tevatron proton-antiproton collider. We measure single differential cross sections as a function of the diphoton mass, the transverse momentum of the diphoton system, the azimuthal angle between the photons, and the polar scattering angle of the photons. In addition, we measure double differential cross sections considering the last three kinematic variables in three diphoton mass bins. The results are compared with different perturbative QCD predictions and event generators. We have used a sample of photon + 3-jet events collected by the D0 experiment with an integrated luminosity of about 1 fb{sup -1} to determine the fraction of events with double parton scattering (f{sub DP}) in a single p{bar p} collision at {radical}s = 1.96 TeV. The DP fraction and effective cross section ({sigma}{sub eff}), a process-independent scale parameter related to the parton density inside the nucleon, are measured in three intervals of the second (ordered in p{sub T}) jet transverse momentum p{sub T}{sup jet2} within the range 15 < p{sub T}{sup jet} < 30 GeV. …

We briefly review the development history of the Gemini Planet Imager's 4K Boston Micromachines MEMS deformable mirror. We discuss essential calibration steps and algorithms to control the MEMS with nanometer precision, including voltage-phase calibration and influence function characterization. We discuss the integration of the MEMS into GPI's Adaptive Optics system at Lawrence Livermore and present experimental results of 1.5 kHz closed-loop control. We detail mitigation strategies in the coronagraph to reduce the impact of abnormal actuators on final image contrast.

The National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory (LLNL) in Livermore, CA, is now operational. The NIF is the world's most energetic laser system capable of producing 1.8 MJ and 500 TW of ultraviolet light. By concentrating the energy from its 192 extremely energetic laser beams into a mm{sup 3}-sized target, NIF can produce temperatures above 100 million K, densities of 1,000 g/cm{sup 3}, and pressures 100 billion times atmospheric pressure - conditions that have never been created in a laboratory and emulate those in planetary interiors and stellar environments. On September 29, 2010, the first integrated ignition experiment was conducted, demonstrating the successful coordination of the laser, cryogenic target system, array of diagnostics and infrastructure required for ignition demonstration. In light of this strong progress, the U.S. and international communities are examining the implication of NIF ignition for inertial fusion energy (IFE). A laser-based IFE power plant will require a repetition rate of 10-20 Hz and a laser with 10% electrical-optical efficiency, as well as further development and advances in large-scale target fabrication, target injection, and other supporting technologies. These capabilities could lead to a prototype IFE demonstration plant in the 10- to 15-year time frame. …

Graphene grown by chemical vapor deposition and supported on SiO2 and sapphire substrates was studied following controlled introduction of defects induced by 35 keV carbon ion irradiation. Changes in Raman spectra following fluences ranging from 1012 cm-2 to 1015 cm-2 indicate that the structure of graphene evolves from a highly-ordered layer, to a patchwork of disordered domains, to an essentially amorphous film. These structural changes result in a dramatic decrease in the Hall mobility by orders of magnitude while, remarkably, the Hall concentration remains almost unchanged, suggesting that the Fermi level is pinned at a hole concentration near 1x1013 cm-2. A model for scattering by resonant scatterers is in good agreement with mobility measurements up to an ion fluence of 1x1014 cm-2.

In this paper we review the most recent results concerning B Baryons at CDF and D0, including the observation and the study of the properties of the {Omega}{sub b}{sup -}, {Xi}{sub b}{sup -} and {Sigma}{sub b}{sup {+-}(*)}, the observation of new {Lambda}{sub b}{sup 0} decay modes, and a new measurement of the lifetime of the b hadrons in decays with a J/{Psi}. The {Omega}{sub b}{sup -} baryon is observed through the decay chain {Omega}{sub b}{sup -} {yields} J/{Psi}{Omega}{sup -}, where J/{Psi} {yields} {mu}{sup +}{mu}{sup -}, {Omega}{sup -} {yields} {Lambda}K{sup -}, and {Lambda} {yields} pK{sup -}, using 4.2 fb{sup -1} of data. The {Omega}{sub b}{sup -} mass is measured to be 6054.4 {+-} 6.8(stat.) {+-} 0.9(syst.) MeV/c{sup 2}, and the lifetime 1.13{sub -0.40}{sup +0.53}(stat.) {+-} 0.02(syst.) ps. For the {Xi}{sub b}{sup -} the mass is measured 5790.9 {+-} 2.6(stat.) {+-} 0.8(syst.) MeV/c{sup 2} and the lifetime 1.56{sub -0.25}{sup +0.27}(stat.) {+-} 0.02(syst.) ps. A new accurate measurement of the properties of the resonances {Sigma}{sub b}{sup +}, {Sigma}{sub b}{sup -}, {Sigma}*{sub b}{sup +}, and {Sigma}*{sub b}{sup -} has been performed in 6 fb{sup -1} of data, and the masses have been determined, m({Sigma}{sub b}{sup +}) = 5811.2{sub -0.8}{sup +0.9}(stat.) {+-} 1.7(syst.), m({Sigma}{sub b}{sup …

Diabetes mellitus results from an absolute or relative deficiency of insulin producing pancreatic beta-cells. The adult human beta-cell's turnover rate remains unknown. We employed novel techniques to examine adult human islet beta-cell turnover and longevity in vivo. Subjects enrolled in NIH clinical trials received thymidine analogues [iododeoxyuridine (IdU) or bromodeoxyuridine (BrdU)] 8-days to 4-years prior to death. Archival autopsy samples from ten patients (aged 17-74 years) were employed to assess beta-cell turnover by scoring nuclear analog labeling within insulin staining cells. Human adult beta-cell longevity was determined by estimating the cells genomic DNA integration of atmospheric carbon-14 ({sup 14}C). DNA was purified from pancreatic islets isolated from cadaveric donors; whole islet prep DNA was obtained from a 15 year old donor, and purified beta-cell DNA was obtained from two donors (age 48 and 80 years). {sup 14}C levels were then determined using accelerator mass spectrometry (AMS). Cellular 'birth date' was determined by comparing the subject's DNA {sup 14}C content relative to a well-established {sup 14}C atmospheric prevalence curve. In the two subjects less than age 20 years, 1-2% of the beta-cell nuclei co-stained for BrdU/IdU. No beta-cell nuclei co-stained in the eight patients more than 30 years old. Consistent with …