We have started upgrading the control room programs for the injector at the Advanced Light Source (ALS). We chose to program in C* exclusively on the .NET Framework to create EPICS client programs on Windows Vista PCs. This paper reports the status of this upgrade project.

We report the demonstration of a reflection microscope that operates at 13.2-nm wavelength with a spatial resolution of 55 {+-} 3 nm. The microscope uses illumination from a table-top EUV laser to acquire aerial images of photolithography masks with a 20 second exposure time. The modulation transfer function of the optical system was characterized.

The slowing pace of commodity microprocessor performance improvements combined with ever-increasing chip power demands has become of utmost concern to computational scientists. As a result, the high performance computing community is examining alternative architectures that address the limitations of modern cache-based designs. In this work, we examine the potential of the using the forth coming STI Cell processor as a building block for future high-end computing systems. Our work contains several novel contributions. We are the first to present quantitative Cell performance data on scientific kernels and show direct comparisons against leading superscalar (AMD Opteron), VLIW (IntelItanium2), and vector (Cray X1) architectures. Since neither Cell hardware nor cycle-accurate simulators are currently publicly available, we develop both analytical models and simulators to predict kernel performance. Our work also explores the complexity of mapping several important scientific algorithms onto the Cells unique architecture. Additionally, we propose modest microarchitectural modifications that could significantly increase the efficiency of double-precision calculations. Overall results demonstrate the tremendous potential of the Cell architecture for scientific computations in terms of both raw performance and power efficiency.

The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 {angstrom} resolution, respectively. These structures reveal a core fold that is comprised of an {alpha}-helix lying diagonally across a five-stranded, mixed {beta}-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the {beta}-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

Chromosomal mosaicism in human preimplantation embryos is a common cause ofspontaneous abortions, however, our knowledge of its etiology is limited. We used multicolor fluorescence in situ hybridization (FISH) painting to investigate whether paternally-transmitted chromosomal aberrations result in mosaicism in mouse 2-cell embryos. Paternal exposure to acrylamide, an important industrial chemical also found in tobacco smoke and generated during the cooking process of starchy foods, produced significant increases in chromosomally defective 2-cell embryos, however, the effects were transient primarily affecting the postmeiotic stages of spermatogenesis. Comparisons with our previous study of zygotes demonstrated similar frequencies of chromosomally abnormal zygotes and 2-cell embryos suggesting that there was no apparent selection against numerical or structural chromosomal aberrations. However, the majority of affected 2-cell embryos were mosaics showing different chromosomal abnormalities in the two blastomeric metaphases. Analyses of chromosomal aberrations in zygotes and 2-cell embryos showed a tendency for loss of acentric fragments during the first mitotic division ofembryogenesis, while both dicentrics and translocations apparently underwent propersegregation. These results suggest that embryonic development can proceed up to the end of the second cell cycle of development in the presence of abnormal paternal chromosomes and that even dicentrics can persist through cell division. The high …

We report the scaling behavior of Barkhausen avalanches for every small field step along the hysteresis loop in CoCrPt alloy film having perpendicular magnetic anisotropy. Individual Barkhausen avalanche is directly observed utilizing a high-resolution soft X-ray microscopy that provides real space images with a spatial resolution of 15 nm. Barkhausen avalanches are found to exhibit power-law scaling behavior at all field steps along the hysteresis loop, despite their different patterns for each field step. Surprisingly, the scaling exponent of the power-law distribution of Barkhausen avalanches is abruptly altered from 1 {+-} 0.04 to 1.47 {+-} 0.03 as the field step is close to the coercive field. The contribution of coupling among adjacent domains to Barkhausen avalanche process affects the sudden change of the scaling behavior observed at the coercivity-field region on the hysteresis loop of CoCrPt alloy film.

The authors measured labradorite (Ca{sub 0.6}Na{sub 0.4}Al{sub 1.6}Si{sub 2.4}O{sub 8}) dissolution rates using a mixed flow reactor from 30 to 130 C as a function of CO{sub 2} (3 x 10{sup -3} and 0.6 M), and aluminum (10{sup -6} to 10{sup -3}M) at pH 3.2. Over these conditions, labradorite dissolution can be described with a single rate expression that accounts for observed increases in dissolution rate with temperature and decreases in dissolution rate with dissolved aluminum: Rate{sub Si} (mol Labradorite cm{sup -2} s{sup -1}) = k{double_prime} x 10{sup -Ea/2.303RT} [(a{sub H{sup +}}{sup 3n}/a{sub Al{sup 3+}}{sup n})K{sub T}/(1+K{sub T} (a{sub H{sup +}}{sup 3n}/a{sub Al{sup 3+}}{sup n}))] where the apparent dissolution rate constant, k{double_prime} = 10{sup -5.69} (mol Labradorite cm{sup -2}s{sup -1}); the net activation energy, E{sub a} = 10.06 (kcal mol{sup -1}); H{sup +}-Al{sup 3+} exchange coefficient, n = 0.31; and silica rich surface complex formation constant K{sub T} = 4.5 to 5.6 from 30 to 130 C. The effect of CO{sub 2}(aq) on mineral dissolution is accounted for by changes in solution pH. At temperatures below 60 C, labradorite dissolves incongruently with preferential dissolution of Na, Ca and Al over Si.

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The process of interest in this study is the solidification of a molten metal subjected to rapid pressurization. Most details about solidification occurring when the liquid-solid coexistence line is suddenly transversed along the pressure axis remain unknown. We present preliminary results from an ongoing study of this process for both simple models of metals (Cu) and more sophisticated material models (MGPT potentials for Ta). Atomistic (molecular dynamics) simulations are used to extract details such as the time and length scales that govern these processes. Starting with relatively simple potential models, we demonstrate how molecular dynamics can be used to study solidification. Local and global order parameters that aid in characterizing the phase have been identified, and the dependence of the solidification time on the phase space distance between the final (P,T) state and the coexistence line has been characterized.

We have developed a compact, 14.7 nm, sub-5 ps x-ray laser source at LLNL together with a Mach-Zehnder type Diffraction Grating Interferometer built at Colorado State University for probing dense, high intensity laser-produced plasmas. The short wavelength and pulse length of the probe reduces refraction and absorption effects within the plasma and minimizes plasma motion blurring. This unique diagnostic capability gives precise 2-D density profile snapshots and is generating new data for rapidly evolving laser-heated plasmas. A review of the results from dense, mm-scale line focus plasma experiments will be described with detailed comparisons to hydrodynamic simulations.

That tumor cells for all practical purposes are unstable and plastic could be expected. However, the astonishing ability of the nuclei from cells of normal adult tissues to be reprogrammed - given the right embryonic context - found its final truth even for mammals in the experiments that allowed engineering Dolly (1). The landmark experiments showed that nuclei originating from cells of frozen mammary tissues were capable of being reprogrammed by the embryonic cytoplasm and its microenvironment to produce a normal sheep. The rest is history. However, whether microenvironments other than those of the embryos can also reprogram adult cells of different tissue origins still containing their cytoplasm is of obvious interest. In this issue of PNAS, the laboratory of Gilbert Smith (2) reports on how the mammary gland microenvironment can reprogram both embryonic and adult stem neuronal cells. The work is a follow-up to their previous report on testis stem cells that were reprogrammed by the mammary microenvironment (3). They demonstrated that cells isolated from the seminiferous tubules of the mature testis, mixed with normal mammary epithelial cells, contributed a sizable number of epithelial progeny to normal mammary outgrowths in transplanted mammary fat pads. However, in those experiments they …

An extended structure zone diagram is proposed that includes energetic deposition, characterized by a large flux of ions typical for deposition by filtered cathodic arcs and high power impulse magnetron sputtering. The axes are comprised of a generalized homologous temperature, the normalized kinetic energy flux, and the net film thickness, which can be negative due to ion etching. It is stressed that the number of primary physical parameters affecting growth by far exceeds the number of available axes in such a diagram and therefore it can only provide an approximate and simplified illustration of the growth condition?structure relationships.

We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

Partitioned Global Address Space languages like Unified Parallel C (UPC) are typically valued for their expressiveness, especially for computations with fine-grained random accesses. In this paper we show that the one-sided communication model used in these languages also has a significant performance advantage for bandwidth-limited applications. We demonstrate this benefit through communication microbenchmarks and a case-study that compares UPC and MPI implementations of the NAS Fourier Transform (FT) benchmark. Our optimizations rely on aggressively overlapping communication with computation but spreading communication events throughout the course of the local computation. This alleviates the potential communication bottleneck that occurs when the communication is packed into a single phase (e.g., the large all-to-all in a multidimensional FFT). Even though the new algorithms require more messages for the same total volume of data, the resulting overlap leads to speedups of over 1.75x and 1.9x for the two-sided and one-sided implementations, respectively, when compared to the default NAS Fortran/MPI release. Our best one-sided implementations show an average improvement of 15 percent over our best two-sided implementations. We attribute this difference to the lower software overhead of one-sided communication, which is partly fundamental to the semantic difference between one-sided and two-sided communication. Our UPC results use …

The Department of Energy (DOE) operates many nuclear facilities on large complexes across the United States in support of national defense. The operation of these many and varied facilities and processes require meteorological support for many purposes, including: for routine operations, to respond to severe weather events, such as lightning, tornadoes and hurricanes, to support the emergency response functions in the event of a release of materials to the environment, for engineering baseline and safety documentation, as well as hazards assessments etc. This paper describes a program of meteorological support to the Savannah River Site, a DOE complex located in South Carolina.

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A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the concept of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user.

Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access …

Laboratory facilities present a unique challenge for energy efficient and sustainable design, with their inherent complexity of systems, health and safety requirements, long-term flexibility and adaptability needs, energy use intensity, and environmental impacts. The typical laboratory is about three to five times as energy intensive as a typical office building and costs about three times as much per unit area. In order to help laboratory stakeholders assess the environmental performance of their laboratories, the Labs21 program, sponsored by the US Environmental Protection Agency and the US Department of Energy, is developing the Environmental Performance Criteria (EPC), a point-based rating system that builds on the LEED(TM) rating system. Currently, LEED(TM) is the primary tool used to rate the sustainability of commercial buildings. However, it lacks some attributes essential to encouraging the application of sustainable design principles to laboratory buildings. Accordingly, the EPC has additions and modifications to the prerequisites and credits in each of the six sections of LEED(TM). It is being developed in a consensus-based approach by a diverse group of architects, engineers, consulting experts, health & safety personnel and facilities personnel. This report describes the EPC version 2.0, highlighting the underlying technical issues, and describes implications for the development …

The observation of the top (t) quark served as one of the major confirmations of the validity of the standard model (SM) of particle interactions. Through radiative corrections of the SM, the mass of the top quark, along with that of the W boson, provide the best indication for the value of the mass of the hypothesized Higgs boson. The mass of the W is known to a precision of < 0.1%, while the uncertainty on the mass of the top quark is at the 4% level. Improvements in both measurements are required to limit the range of mass that the Higgs boson can assume in the SM, and, of course, to check whether that agrees with expectation. It is therefore important to develop techniques for extracting the mass of the top quark that can provide the sharpest values possible.

Energy conversion efficiencies of better than 23% have been demonstrated for small scale tests of a few thermophotovoltaic (TPV) cells using front surface, tandem filters [1, 2]. The engineering challenge is to build this level of efficiency into arrays of cells that provide useful levels of energy. Variations in cell and filter performance will degrade TPV array performance. Repeated fabrication runs of several filters each provide an initial quantification of the fabrication variation for front surface, tandem filters for TPV spectral control. For three performance statistics, within-run variation was measured to be 0.7-1.4 percent, and run-to-run variation was measured to be 0.5-3.2 percent. Fabrication runs using a mask have been shown to reduce variation across interference filters from as high as 8-10 percent to less than 1.5 percent. Finally, several system design and assembly approaches are described to further reduce variation.

Recent developments in plasma synthesis of hard materials using energetic ions are described. Metal Plasma Immersion Ion Implantation and Deposition (MePIIID) has been used to prepare several hard films: from diamondlike carbon (DLC) to carbides, from nitrides to oxides. The energy of the depositing species is controlled to maximize adhesion as well as to change the physical and chemical properties of the films. Adhesion is promoted by the creation of a graded interface between the film and the substrate. The energy of the depositing ions is also used to modify and control the intrinsic stresses and the microstructure of the films. The deposition is carried out at room temperature, which is important for temperature sensitive substrates. A correlation between intrinsic stresses and the energetics of the deposition is presented for the case of DLC films, and means to reduce stress levels are discussed.

Transition-free lattices are favored as possible realization of proton drivers. Several variants have been proposed, some of which have considerably different behavior. One of the main quantities used to characterize this behavior is the short term dynamic aperture (DA). In this note we study three different variants of such lattices, and show that the differences in DA among the lattices essentially disappear as soon as magnet multipole errors are included in the simulation. The tracking results can be understood in terms of the normal form based amplitude dependent tune shift and resonance strength coefficients.

Superconducting accelerator magnets must provide a uniform field during operation. However, the field quality significantly deteriorates due to persistent currents induced in superconducting filaments. This effect is especially large for the Nb{sub 3}Sn conductor being implemented in the next generation of accelerator magnets. A simple and inexpensive method of passive correction of the persistent current effect was developed and experimentally verified. This paper describes numerical simulations of the passive correctors and reports the test results.