Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons to available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveals 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, represent the only new genetic material in Y. pestis acquired since the divergence from Y. pseudotuberculosis. In contrast, 149 new pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive IS-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of pre-existing gene expression pathways appear to be more important than acquisition of new genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.

A damage test procedure was established for optical components that have large incident beam footprints. The procedure was applied on coated samples for a high powered 1053 nm, 3-ns pulse length laser system.

Dihadron fragmentation functions and their evolution arestudied in the process of e+e- annihilation. Under the collinearfactorization approximation and facilitated by the cut-vertex technique,the two hadron inclusive cross section at leading order (LO) is shown tofactorize into a short distance parton cross section and a long distancedihadron fragmentation function. We provide the definition of such adihadron fragmentation function in terms of parton matrix elements andderive its DGLAP evolution equation at leading log. The evolutionequation for the non-singlet quark fragmentation function is solvednumerically with a simple ansatz for the initial condition and resultsare presented for cases of physical interest.

Over half a century ago, von Neumann and Richtmyer [1] introduced the idea of adding artificial viscosity to the Euler equations in order to help stabilize shock calculations. Their ideas regarding artificial viscosity influenced Smagorinsky [2, 3] in his development of a subgrid-scale model designed to match the Kolmogorov spectrum for atmospheric turbulence (C. E. Leith, private communication). Since that time, numerous artificial viscosity formulations have been proposed for simulating both shocks and turbulence [4, 5, 6, 7, 8, 9, 10]. Over the years however, a rift has developed between shock-capturing (monotonicity-preserving) and turbulence-capturing (large-eddy simulation) methods. Artificial viscosities for shock-capturing typically depend on sound speed, which makes them unsuitable for low Mach number flows. On the other hand, subgrid-scale models, customized for incompressible turbulence, usually fail to capture shocks in a monotonic fashion. The purpose of this paper is to introduce an artificial viscosity suitable for computing shock-turbulence interactions. This is accomplished by extending the model of Cook and Cabot [10] to multi-dimensions.

The top quark is currently only observed at the Tevatron, where it is mainly produced in t{bar t} pairs. Due to the very high mass of the top quark compared to the other quarks and the gauge bosons, it is expected to play a special role in electroweak symmetry breaking. Therefore it might be especially sensitive to new physics. Measurements of various production and decay quantities of the top quark could lead to discoveries of physics beyond the standard model. Several such measurements were performed by the CDF collaboration during Run1 of the Tevatron. These measurements and first results from CDF in Run2 are presented.

Layered earth models are well justified by experience, and provide a simple means of studying fairly general behavior of the elastic and poroelastic characteristics of seismic waves in the earth. Thomsen's anisotropy parameters for weak elastic and poroelastic anisotropy are now commonly used in exploration, and can be conveniently expressed in terms of the layer averages of Backus. Since our main interest is usually in the fluids underground, it would be helpful to have a set of general equations relating the Thomsen parameters as directly as possible to the fluid properties. This end can be achieved in a rather straightforward fashion for these layered earth models, and the present paper develops and then discusses these relations. Furthermore, it is found that, although there are five effective shear moduli for any layered VTI medium, one and only one effective shear modulus for the layered system contains all the dependence of pore fluids on the elastic or poroelastic constants that can be observed in vertically polarized shear waves in VTI media. The effects of the pore fluids on this effective shear modulus can be substantial - an increase of shear wave speed on the order of 10% is shown to be possible …

Compliance can be defined as the measurement of displacement per unit of force applied e.g. nano-meters per Newton (m/N). Compliance is the reciprocal of stiffness. High stiffness means low compliance and visa versa. It is an important factor in machine tool characteristics because it reflects the ability of the machine axis to maintain a desired position as it encounters a force or torque. Static compliance is a measurement made with a constant force applied e.g. the average depth of cut. Dynamic compliance is a measurement made as a function of frequency, e.g. a fast too servo (FTS) that applies a varying cutting force or load, interrupted cuts and external disturbances such as ground vibrations or air conditioning induced forces on the machine. Compliance can be defined for both a linear and rotary axis of a machine tool. However, to properly define compliance for a rotary axis, the axis must allow a commanded angular position. Note that this excludes velocity only axes. In this paper, several factors are discussed that affect compliance but emphasis is placed on how the machine servo system plays a key role in compliance at low to mid frequency regions. The paper discusses several techniques for measuring …

VISA II is the follow-up project to the successful Visible to Infrared SASE Amplifier (VISA) experiment at the Accelerator Test Facility (ATF) in Brookhaven National Lab (BNL). This paper will report the motivation for and status of the two main experiments associated with the VISA II program. One goal of VISA II is to perform an experimental study of the physics of a chirped beam SASE FEL at the upgraded facilities of the ATF. This requires a linearization of the transport line to preserve energy chirping of the electron beam at injection. The other planned project is a strong bunch compression experiment, where the electron bunch is compressed in the chicane, and the dispersive beamline transport, allowing studies of deep saturation.

This study is to show how a model was used to enable management to better estimate production capabilities to ensure contract milestones/commitments are met, to cope with fast changing project baselines and project missions, to ensure the project will meet the negotiated throughput, and to eliminate unnecessary but costly design changes.

In this paper we will discuss several software engineering practices that have proven useful in a large multidisciplinary physics code development project at Lawrence Livermore National Laboratory. In the project discussed here, as with many large scale efforts in HPC scientific computing, we have had to balance the competing demands of being a stable ''production'' code that our user base can rely on with being a platform for research into new physics, models, and software architectures. Much of this has been learned through necessity and experience. Likewise, much of it has been learned through interactions with other similar projects and hearing of their successes, and tailoring their ideas to our own requirements. The ideas presented here are not meant to necessarily transfer to other environments with different needs. It is our belief that projects need to be given large latitude in defining their own software engineering process versus a prescribed a solution. However, the ideas presented here are hopefully high level and general enough that we hope other projects might find some inspiration and adopt similar methods if it is to their benefit, much as we have done through the years.

Motivated by many design considerations, several conceptual designs for advanced reactors have proposed that the entire reactor building and a significant portion of the steam generator building will be either partially or completely embedded below grade. For the analysis of seismic events, the soil-structure interaction (SSI) effect and passive earth pressure for these types of deeply embedded structures will have a significant influence on the predicted seismic response. Sponsored by the US Nuclear Regulatory Commission (NRC), Brookhaven National Laboratory (BNL) is carrying out a research program to assess the significance of these proposed design features for advanced reactors, and to evaluate the existing analytical methods to determine their applicability and adequacy in capturing the seismic behavior of the proposed designs. This paper summarizes a literature review performed by BNL to determine the state of knowledge and practice for seismic analyses of deeply embedded and/or buried (DEB) nuclear containment type structures. Included in the paper is BNL's review of the open literature of existing standards, tests, and practices that have been used in the design and analysis of DEB structures. The paper also provides BNL's evaluation of available codes and guidelines with respect to seismic design practice of DEB structures. Based …

Monoenergetic laser acceleration of trapped microbunches has been demonstrated for the first time. An inverse free electron laser (IFEL) is used to create microbunches, which are then accelerated by a second IFEL using a tapered undulatos. An adjustable magnetic field chicane is located between the two IFELs and is used to control the phase of the microbunches with respect to the laser field in the second IFEL. The IFELs are driven by a single lases beam from a high peak power CO{sub 2} laser. During the experiment, the trapped portion of the microbunch electrons had an energy gain of >16% with an energy width of -0.86% (full width at half-maximum).

The file-bundle caching problem arises frequently in scientific applications where jobs need to process several files simultaneously. Consider a host system in a data-grid that maintains a staging disk or disk cache for servicing jobs of file requests. In this environment, a job can only be serviced if all its file requests are present in the disk cache. Files must be admitted into the cache or replaced in sets of file-bundles, i.e. the set of files that must all be processed simultaneously. In this paper we show that traditional caching algorithms based on file popularity measures do not perform well in such caching environments since they are not sensitive to the inter-file dependencies and may hold in the cache non-relevant combinations of files. We present and analyze a new caching algorithm for maximizing the throughput of jobs and minimizing data replacement costs to such data-grid hosts. We tested the new algorithm using a disk cache simulation model under a wide range of conditions such as file request distributions, relative cache size, file size distribution, etc. In all these cases, the results show significant improvement as compared with traditional caching algorithms.

None

H-mode confinement is observed for many energy confinement times without edge localized modes (ELMs) in QH (quiescent high-confinement)-mode discharges in DIII-D. To find critical differences between ELMing and QH modes we compared electron temperature (T{sub e}), density (n{sub e}), and ion temperature (T{sub i}), in the pedestal and scrape-off layer (SOL) for a group of discharges. We also compared the electron pressures P{sub ped}, and maximum pressure gradients P{sub e,ped,max grad} because of their importance in confinement and stability. Experimental results show that the core line averaged density, median T{sub e} (pedestal), SOL T{sub e}, and T{sub e} pedestal width, and SOL T{sub i} are nearly the same in QH mode as that during ELMs. The n{sub e} (average pedestal), n{sub e} pedestal width, P{sub ped}, and P{sub e,ped,max grad} are similar to corresponding values in QH mode and at various times between ELMs. However, the pedestal T{sub i} is 1.6 times higher in QH mode than during ELMing.

Epoxy resin degradation was analyzed for NSLS X-ring magnets after two decades of 2.58-2.8 GeV continuous electron-beam operation, based on results obtained from thermoluminescent dosimeters irradiated along the NSLS ring and epoxy samples irradiated at the beamline target location. A Monte Carlo-based particle transport code, MCNP, was utilized to verify the dose from synchrotron radiation distributed along the axial- and transverse-direction in a ring model, which simulates the geometry of a ring quadrupole magnet and its central vacuum chamber downstream of the bending-magnet photon ports. The actual life expectancy of thoroughly vacuum baked-and-cured epoxy resin was estimated from radiation tests on similar polymeric materials using a radiation source developed for electrical insulation and mechanical structure studies.

In heavy-ion inertial-confinement fusion systems, intense beams of ions must be transported from the exit of the final focus magnet system through the fusion chamber to hit millimeter-sized spots on the target. Effective plasma neutralization of intense ion beams in this final transport is essential for a heavy-ion fusion power plant to be economically competitive. The physics of neutralized drift has been studied extensively with particle-in-cell simulations. To provide quantitative comparisons of theoretical predictions with experiment, the Virtual National Laboratory for Heavy Ion Fusion has completed the construction and has begun experimentation with the Neutralized Transport Experiment (NTX). The experiment consists of three main sections, each with its own physics issues. The injector is designed to generate a very high-brightness, space-charge-dominated potassium beam while still allowing variable perveance by a beam aperturing technique. The magnetic-focusing section, consisting of four pulsed magnetic quadrupoles, permits the study of beam tuning, as well as the effects of phase space dilution due to higher-order nonlinear fields. In the final section, a converging ion beam exiting the magnetic section is transported through a drift region with plasma sources for beam neutralization, and the final spot size is measured under various conditions of neutralization. In this …

In this paper we report on the results of isotope exchange experiments in the Sustained Spheromak Physics Experiment (SSPX). We have compared {approx}500 deuterium discharges with similar discharges in hydrogen. Typically, we produce plasmas with peak toroidal currents in the range of 0.6 MA, electron temperatures (T{sub e}) of {approx}200 eV and energy confinement times ({tau}{sub E}) of {approx}200 {micro}s. The D{sub 2} fueled discharges show similar results to those with H{sub 2} fueling with no obvious differences in confinement time. Electron temperatures of {approx}200 eV with similar electron densities were observed. Both the deuterium and hydrogen fueled discharges have a calculated thermal conduction below {chi}{sub e}<10 m{sup 2}/s. However, the D{sub 2} fueled discharges had a modest increase in high-Z (titanium) impurity content suggesting an increase of physical sputtering. We find no significant mass scaling effects.

The cladoceran, Ceriodaphnia dubia (C. dubia), is required by the State of South Carolina to be used in whole effluent toxicity (WET) compliance tests in order to meet limits contained within National Pollutant Discharge Elimination System (NPDES) permits. Westinghouse Savannah River Company (WSRC) experienced WET test failures for no clear reason over a long period of time. Toxicity identification examinations on effluents did not indicate the presence of toxicants; therefore, the WET test itself was brought under suspicion. Research was undertaken with an alternate cladoceran, Daphnia ambigua (D. ambigua). It was determined that this species survives better in soft water, so approval was obtained from regulating authorities to use this ''alternate'' species in WET tests. The result was better test results and elimination of non-compliances. The successful use of D. ambigua allowed WSRC to gain approval from the South Carolina Department of Health and Environmental Control (SCDHEC) to remove WET limits from the NPDES permit.

In Kitakyushu Science and Research Park, a new district energy system has been introduced. In this study, we chose this system as a case study and have carried out an analysis on the efficiency of the power generation and heat release utilization of the fuel cell and gas engine in summer by using the recorded data. The results can be summarized as follows; (1) Although the power generation efficiencies of the gas engine and fuel cell are a little bit lower than the standard designated value, they are almost running at stable condition. (2) The collected heat energy is lower than the designated value. The heat release utilization, which is used for cooling and hot water, is fairly low. Considering the efficient use of energy, it is a key to have a good use of heat release when we introduce a district energy system. (3) The discarded heat energy of the system is very big in this investigation when evaluating the system as a whole. It is fundamental to the future of energy conservation to use primary energy more efficiently.

A brief review of searches for physics beyond the Standard Model with photons using the CDF detector at the Tevatron is given here. These include searches for supersymmetry, extra dimensions, excited electrons and W/Z+{gamma} production, as well as anomalous photon production. Recent results from CDF Run II experiment are presented, but some results from Run I are also reviewed.

The edge-plasma profiles and fluxes to the divertor and walls of a divertor tokamak with a magnetic X-point are simulated by coupling a 2D transport code (UEDGE) and a 3D turbulence code (BOUT). An relaxed iterative coupling scheme is used where each code is run on its characteristic time scale, resulting in a statistical steady state. Plasma variables of density, parallel velocity, and separate ion and electron temperatures are included, together with a fluid neutral model for recycling neutrals at material surfaces. Results for the DIII-D tokamak parameters show that the turbulence is preferentially excited in the outer radial region of the edge where magnetic curvature is destabilizing and that substantial plasma particle flux is transported to the main chamber walls. These results are qualitatively consistent with some experimental observations. The coupled transport/turbulence simulation technique provides a strategy to understanding edge-plasma physics in more detailed than previously available and to significantly enhance the realism of predictions of the performance of future devices.

The edge-plasma profiles and fluxes to the divertor and walls of a divertor tokamak with a magnetic X-point are simulated by coupling a 2D transport code (UEDGE) and a 3D turbulence code (BOUT). An relaxed iterative coupling scheme is used where each code is run on its characteristic time scale, resulting in a statistical steady state. Plasma variables of density, parallel velocity, and separate ion and electron temperatures are included, together with a fluid neutral model for recycling neutrals at material surfaces. Results for the DIII-D tokamak parameters show that the turbulence is preferentially excited in the outer radial region of the edge where magnetic curvature is destabilizing and that substantial plasma particle flux is transported to the main chamber walls. These results are qualitatively consistent with some experimental observations. The coupled transport/turbulence simulation technique provides a strategy to understanding edge-plasma physics in more detailed than previously available and to significantly enhance the realism of predictions of the performance of future devices

The Image Content Engine (ICE) project at Lawrence Livermore National Laboratory (LLNL) extracts, stores and allows queries of image content on multiple levels. ICE is designed for multiple application domains. The domain explored in this work is aerial and satellite surveillance imagery. The highest level of semantic information used in ICE is graph based. After objects are detected and classified, they are grouped based in their interrelations. The graph representing a locally related set of objects is called a 'graphlet'. Graphlets are interconnected into a larger graph which covers an entire set of images. Queries based on graph properties are notoriously difficult due the inherent complexity of the graph isomorphism and sub-graph isomorphism problems. ICE exploits limitations in graph and query structure and uses a set of auxiliary data structures to quickly process a useful set of graph based queries. These queries could not be processed using semantically lower level (tile and object based) queries.