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.

A. ABSTRACT The importance of lateral gene transfer (LGT) in the evolution of microbial species has become increasingly evident with each completed microbial genome sequence. Most significantly, the genome of Thermotoga maritima MSB8, a hyperthermophilic bacterium isolated by Karl Stetter and workers from Vulcano Italy in 1986, and sequenced at The Institute for Genomic Research (TIGR) in Rockville Maryland in 1999, revealed extensive LGT between % . this bacterium and members of the archaeal domain (in particular Archaeoglobus fulgidus, and Pyracoccus frcriosus species). Based on whole genome comparisons, it was estimated that 24% of the genetic information in this organism was acquired by genetic exchange with archaeal species, Independent analyses including periodicity analysis of the T. maritimu genomic DNA sequence, phylogenetic reconstruction based on genes that appear archaeal-like, and codon and amino acid usage, have provided additional evidence for LGT between T. maritima and the archaea. More recently, DiRuggiero and workers have identified a very recent LGT event between two genera of hyperthermophilic archaea, where a nearly identical DNA fragment of 16 kb in length flanked by insertion sequence (IS) elements, exists. Undoubtedly, additional examples of LGT will be identified as more microbial genomes are completed. For the present moment …

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.

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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.

In this project we developed further a twin approach to the study of regional-scale climate variability and change. The two approaches involved probabilistic network (PN) models (sometimes called dynamic Bayesian networks) and intermediate-complexity coupled ocean-atmosphere models (ICMs). We thus made progress in identifying the predictable modes of climate variability and investigating their impacts on the regional scale. In previous work sponsored by DOE’s Climate Change Prediction Program (CCPP), we had developed a family of PNs (similar to Hidden Markov Models) to simulate historical records of daily rainfall, and used them to downscale seasonal predictions of general circulation models (GCMs). Using an idealized atmospheric model, we had established a novel mechanism through which ocean-induced sea-surface temperature (SST) anomalies might influence large-scale atmospheric circulation patterns on interannual and longer time scales; similar patterns were found in a hybrid coupled ocean–atmosphere–sea-ice model. In this continuation project, we built on these ICM results and PN model development to address prediction of rainfall and temperature statistics at the local scale, associated with global climate variability and change, and to investigate the impact of the latter on coupled ocean–atmosphere modes. Our main project results consist of extensive further development of the hidden Markov models for rainfall …

The authors calculate properties of A = 6 system using the accurate charge-dependent nucleon-nucleon (NN) potential at fourth order of chiral perturbation theory. By application of the ab initio no-core shell model (NCSM) and a variational calculation in the harmonic oscillator basis with basis size up to 16 {h_bar}{Omega} they obtain the {sup 6}Li binding energy of 28.5(5) MeV and a converged excitation spectrum. Also, they calculate properties of {sup 10}B using the same NN potential in a basis space of up to 8 {h_bar}{Omega}. The results are consistent with results obtained by standard accurate NN potentials and demonstrate a deficiency of Hamiltonians consisting of only two-body terms. At this order of chiral perturbation theory three-body terms appear. It is expected that inclusion of such terms in the Hamiltonian will improve agreement with experiment.

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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.

The overall objective of this collaborative project is to integrate an existing general equilibrium energy-economic growth model with a biogeochemical cycles and biophysical models in order to more fully explore the potential contribution of land use-related activities to future emissions scenarios. Land cover and land use change activities, including deforestation, afforestation, and agriculture management, are important source of not only CO2, but also non-CO2 GHGs. Therefore, contribution of land-use emissions to total emissions of GHGs is important, and consequently their future trends are relevant to the estimation of climate change and its mitigation. This final report covers the full project period of the award, beginning May 2006, which includes a sub-contract to Brown University later transferred to the National Center for Atmospheric Research (NCAR) when Co-PI Brian O'Neill changed institutional affiliations.

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 …

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This report documents the results of a project undertaken to develop an ultra-high-accuracy measurement capability, which is necessary to address a rising trend toward miniaturized mechanical products exhibiting dramatically reduced product tolerances. A significant improvement in measurement capability is therefore required to insure that a 4:1 ratio can be maintained between product tolerances and measurement uncertainty.

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.

This report is the final update on ARM research conducted at DRI through May of 2006. A relatively minor amount of work was done after May, and last month (November), two journal papers partially funded by this project were published. The other investigator on this project, Dr. Bob d'Entremont, will be submitting his report in February 2007 when his no-cost extension expires. The main developments for this period, which concludes most of the DRI research on this project, are as follows: (1) Further development of a retrieval method for cirrus cloud ice particle effective diameter (De) and ice water path (IWP) using terrestrial radiances measured from satellites; (2) Revision and publication of the journal article 'Testing and Comparing the Modified Anomalous Diffraction Approximation'; and (3) Revision and publication of our radar retrieval method for IWC and snowfall rate.

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 …

Information or data fusion of data from different sources are ubiquitous in many applications, from epidemiology, medical, biological, political, and intelligence to military applications. Data fusion involves integration of spectral, imaging, text, and many other sensor data. For example, in epidemiology, information is often obtained based on many studies conducted by different researchers at different regions with different protocols. In the medical field, the diagnosis of a disease is often based on imaging (MRI, X-Ray, CT), clinical examination, and lab results. In the biological field, information is obtained based on studies conducted on many different species. In military field, information is obtained based on data from radar sensors, text messages, chemical biological sensor, acoustic sensor, optical warning and many other sources. Many methodologies are used in the data integration process, from classical, Bayesian, to evidence based expert systems. The implementation of the data integration ranges from pure software design to a mixture of software and hardware. In this review we summarize the methodologies and implementations of data fusion process, and illustrate in more detail the methodologies involved in three examples. We propose a unified multi-stage and multi-path mapping approach to the data fusion process, and point out future prospects and …

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.