The Cosmic Microwave Background (CMB) is a snapshot of the Universe some 400,000 years after the Big Bang. The pattern of anisotropies in the CMB carries a wealth of information about the fundamental parameters of cosmology. Extracting this information is an extremely computationally expensive endeavor, requiring massively parallel computers and software packages capable of exploiting them. One such package is the Microwave Anisotropy Dataset Computational Analysis Package (MADCAP) which has been used to analyze data from a number of CMB experiments. In this work, we compare MADCAP performance on the vector-based Earth Simulator (ES) and Cray X1 architectures and two leading superscalar systems, the IBM Power3 and Power4. Our results highlight the complex interplay between the problem size, architectural paradigm, interconnect, and vendor-supplied numerical libraries, while isolating the I/O file system as the key bottleneck across all the platforms.

Computational grids have the potential for solving large-scale scientific problems using heterogeneous and geographically distributed resources. However, a number of major technical hurdles must be overcome before this goal can be fully realized. One problem critical to the effective utilization of computational grids is efficient job scheduling. Our prior work addressed this challenge by defining a grid scheduling architecture and several job migration strategies. The focus of this study is to explore the impact of data migration under a variety of demanding grid conditions. We evaluate our grid scheduling algorithms by simulating compute servers, various groupings of servers into sites, and inter-server networks, using real workloads obtained from leading supercomputing centers. Several key performance metrics are used to compare the behavior of our algorithms against reference local and centralized scheduling schemes. Results show the tremendous benefits of grid scheduling, even in the presence of input/output data migration - while highlighting the importance of utilizing communication-aware scheduling schemes.

I'd like to welcome you to the Agent 2004 conference. As most of you are aware, this conference is the fifth in a series of meetings that began in 1999. A conference followed the next year in 2000. The 2001 conference was skipped because of some conflicts with other conferences, and the conferences have proceeded annually since then. We have the proceedings of the previous conferences available here on CDs. One CD has the proceedings from 1999, 2000, and 2002; the other contains last year's proceedings. The purpose of these conferences is to advance the state of the computational social sciences and to integrate the social sciences with the decision sciences and something that is traditionally known as the management sciences. Those of you in the operations/research area are familiar with the traditional school of modeling simulation that emerged from that scientific area. This conference will bring together a different group of people to talk about the topic of agent-based theories and simulations. This fifth agent conference is one of a group of conferences held annually around the country. Most of you are probably aware of the CASOS Conference held at Carnegie Mellon University, usually in July. UCLA holds the …

I report here a redesign of the CKM RICH velocity spectrometers for use in a 1/4 GHz unseparated beam adapted to the KTeV beam line and detector hall at Fermilab (P940). The redesigns reported here comprise modest modification to the original designs for CKM(E921) to accommodate the change in beam flux, momentum, and momentum bite of the primary beam. The ultimate performance of the velocity spectrometer systems, as quantified by the missing mass squared resolution for K{sup +} {yields} {pi}{sup +} x{sup 0}, remains largely unchanged from the original design.

With Run II of the Fermilab Tevatron well underway, many computing challenges inherent to analyzing large volumes of data produced in particle physics research need to be met. We present the computing model within CDF designed to address the physics needs of the collaboration. Particular emphasis is placed on current development of a large O(1000) processor PC cluster at Fermilab serving as the Central Analysis Farm for CDF. Future plans leading toward distributed computing and GRID within CDF are also discussed.

We have made a preliminary study of a dimuon sample corresponding to 114 pb{sup -1} of data taken in Run II at the Tevatron. From this sample we have selected 157 {+-} 20 B{sub d} {yields} J/{psi}K{sub S}{sup 0} and 133 {+-} 17 B{sub s} {yields} J/{psi}{phi} decays. In a subset of the data we have measured the B{sup {+-}} lifetime in the J/{psi}K{sup {+-}} channel to be 1.76 {+-} 0.24 ps. We have implemented a jet-charge initial-flavor tag as well as a soft-muon tag, and we have measured the respective tagging powers to be (2.4 {+-} 1.7)% and (3.3 {+-} 1.8)%. Our conclusion from these studies is that we have made good progress towards understanding all ingredients required to make CP violation measurements in the B{sub d} and B{sub s} systems.

Transparent conducting oxides were successfully prepared from mixed zinc nitrate hexahydrate and indium nitrate hydrate solutions in ethylene glycol using sol-gel technique. The In content in the film was varied (0, 2, 10, 20, 40, 75 and 100 atom %). Films were prepared by spin coating of the liquid precursors followed by thermal decomposition at 400° C after each layer. According to X-ray diffraction (XRD) measurements, the pure ZnO and pure InO films (0 and at 100 % In) were crystalline as-deposited. The crystallinity was suppressed in mixed compositions such that the films with compositions between 10 and 75 at % were amorphous. All the films were transparent with the transmission cut-off frequency near 400 nm, which is characteristic of TCO materials. All as-deposited films were conductive with 0 and 100 atom % In having the lowest resistivities. The resistivity of all compositions were improved by post-deposition reducing anneal in pure Ar at 300° C. The lowest resistivity of 0.2 Ωcm was obtained for the pure ZnO after Ar anneal. It was two-orders of magnitude higher than reported in the literature for the In-doped ZnO, which was attributed to the low processing temperature. The resistivities of as-deposited and annealed in …

The Thermochemical Process Development Unit at the National Renewable Energy Laboratory converts biomass into energy by gasification or pyrolysis. The aqueous effluent generated in these processes must be disposed of as hazardous waste according to the Resource Conservation and Recovery Act because certain components exceed the regulatory concentration limit. Gas stripping of the scrubber water was investigated as a method of reducing benzene and cresol levels. A custom-designed packed-bed column was built and a half-factorial experimental design was implemented to determine the effects of gas flow rate, liquid flow rate, and column packing height on the final benzene concentration in the liquid. The experimental results show that packing height had a significant effect on final benzene concentration; gas flow rate and liquid flow rate had little effect. The effects of each design variable on final cresol concentration were not determined. Although the current column design did significantly reduce the benzene and cresol levels in the scrubber water, it did not reduce the concentrations below the regulatory limits. A full-factorial experimental design will be implemented with an increased packing height. Other variables, including column diameter and packing type, will be investigated to determine their effects on final benzene and cresol concentrations. …

Novel aza-crown derivatives of dioctyloxy-calix[4]arene crown-6 were examined for their cesium extraction performance at different pH levels. These studies are of interest in addressing high-level waste tank remediation and the removal of 137Cs, a major contributor to heat and radiation generation. Preliminary studies were done to assess the performance of these calixarene compounds under varying conditions. Results showed an increase of cesium extraction with pH as well as expected trends in diluent effects and anion selectivity. Poor extraction performance of some aza-crown derivatives raised questions regarding the possibility of intramolecular hydrogen-bonding. A novel methylated derivative was used to address these questions. Additional experiments were conducted to determine the extraction effect on pH. Results indicate an increase in cesium extraction with pH, as shown in preliminary studies. Mono-aza derivatives were shown to exhibit better cesium extraction performance than their di-aza counterparts. The methylated derivative showed poorer extraction performance than the non-methylated derivative, indicating that completely removing the possibility of intramolecular hydrogen-bonding has negative effects on extraction performance. This suggests that the hydrogen-bonding facilitates anion co-extraction, which would lead to better overall extraction. Mono-aza derivatives were shown to cause unexpected changes in pH. This could possibly be attributed to protonation of the …

Cellular zinc homeostasis is essential to human health. Zinc transporters transport zinc ions into and out of cells to maintain cellular zinc concentrations in a narrow range. Several membrane proteins have been shown to facilitate transmembrane fluxes of zinc ions, however, structures of these zinc transporters are unknown. The purpose of this work is to express, purify and crystallize a Zinc transporter, ZitB for crystallographic studies. ZitB was over-expressed as a His-tagged membrane protein using a pET15b expression vector hosted in E. coli BL21 cells. Purification of ZitB was achieved by preparation of ZitB-containing membrane vesicles, followed by detergent extraction, and completed with Ni-NTA metal affinity and size exclusion chromatography. The molecular identity of the purified ZitB was confirmed by mass spectrometry, which showed the expected molecular weight of 35.2kDa. Crystallization trials of ZitB were conducted at 20 oC, using a series of low molecular weight PEGs as precipitants. Micro-crystals were grown in 25% PEG 1K, whereas only amorphous precipitations were observed in PEG 400 and 600. In conclusion, this work yielded highly purified ZitB protein and defined an initial crystallization condition for ZitB.

As residential areas continue to develop near military sites, possible impacts from military traffic and exercises become of greater concern. Of particular concern is the effect of particulate matter and atmospheric dust dispersion on air quality caused by such maneuvers. To aid this problem, Pacific Northwest National Laboratory proposed a plan to develop, document, and test a modeling system in support of dust dispersion reduction and management near government sites. To accomplish this task a model interface was developed that would be user friendly yet sophisticated enough to accommodate the varying needs of the client. One such need was for the modeling system to be capable of providing data for diverse locations and varying sites. To accomplish this task, the dust dispersion modeling system needed to be integrated with a geographic information system (GIS). Through use of the GIS application, data maps contained within the application could be used to create new sites. The GIS application would also allow the user to enter the point, area, or line source required to run the dispersion modeling system. Incorporating the GIS with the model would allow the user to view plume rise and expansion over actual data maps of the desired site. …

Pure and doped Ceria are known for their ability to gain or lose Oxygen, which is of interest to the Solid Oxide Fuel Cell (SOFC) and catalyst community. Current efforts are focused in SOFCs to reduce the operating temperature of the cell while maintaining ionic conduction. Ceria is known for its high ionic conductivity in the intermediate temperature region. (600-800° C) We have prepared pure and doped Ceria films by Sol-gel and magnetron sputtering methods. Enhanced grain-boundary contribution in the conductivity can be studied in the Sol-gel process due to excellent control over the synthesis conditions, which enabled us to control the average grain size. Sputtered films were grown and investigated as a prelude to possible multi-layered CeO2 structures in the near future. These films were characterized by X-ray diffraction (XRD), nuclear reaction analysis (NRA), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and Oxygen conduction measurements. We have observed greater volume diffusion in nanocrystalline Ceria compared to bulk polycrystalline films as a result of low density. Near surface diffusion properties with increasing temperature indicate a decrease in the volume diffusion as a result of grain growth. However, a linear increase in O2 content at ~600nm …

Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest …

The American Academy of Microbiology convened a colloquium November 6-7, 2003, in Key Largo, Florida, to discuss the application of genomic methods to the study of pathogenesis. Professionals in the fields of genomics, bacteriology, virology, eukaryotic microbiology, medicine, clinical diagnostics, bioinformatics, and forensics contributed their expertise to discussions on the recent advancements in the field and the outlook for future research. A number of recommendations were made for ensuring that progress in the field continues. The availability of genome sequences from pathogenic bacteria, viruses, and fungi and other eukaryotes has opened new horizons for the field of pathogenesis. The genomes of over 100 bacterial pathogens have been fully sequenced, and scientists are busy investigating the mechanisms that regulate the diversity of bacterial pathogens and their myriad abilities to evade host defenses. Close to 1,200 viral genomes have been sequenced, and virologists are now beginning to examine the genomes of those viruses that cause undetected, cryptic infections. These virus-host interactions can serve as a reservoir of viral genes that later emerge in novel pathogens with the potential to infect humans, economically important animals, or crops. A number of eukaryotic microbes, including several pathogenic fungi, have also been sequenced, revealing unimagined diversity …

The Los Alamos Crestone Project is part of the Department of Energy's (DOE) Accelerated Strategic Computing Initiative, or ASCI Program. The main goal of this software development project is to investigate the use of continuous adaptive mesh refinement (CAMR) techniques for application to problems of interest to the Laboratory. There are many code development efforts in the Crestone Project, both unclassified and classified codes. In this overview I will discuss the unclassified SAGE and the RAGE codes. The SAGE (SAIC adaptive grid Eulerian) code is a one-, two-, and three-dimensional multimaterial Eulerian massively parallel hydrodynamics code for use in solving a variety of high-deformation flow problems. The RAGE CAMR code is built from the SAGE code by adding various radiation packages, improved setup utilities and graphics packages and is used for problems in which radiation transport of energy is important. The goal of these massively-parallel versions of the codes is to run extremely large problems in a reasonable amount of calendar time. Our target is scalable performance to {approx}10,000 processors on a 1 billion CAMR computational cell problem that requires hundreds of variables per cell, multiple physics packages (e.g. radiation and hydrodynamics), and implicit matrix solves for each cycle. A …

Catalytic autothermal reforming (ATR) represents an important step of converting fossil fuel to hydrogen rich reformate for use in solid oxide fuel cell (SOFC) stacks. The state-of-the-art reforming catalyst, at present, is a Rh based material which is effective but costly. The objective of our current research is to reduce the catalyst cost by finding an efficient ATR catalyst containing no rhodium. A group of perovskite based catalysts have been synthesized and evaluated under the reforming condition of a diesel surrogate fuel. Hydrogen yield, reforming efficiency, and conversion selectivity to carbon oxides of the catalyst ATR reaction are calculated and compared with the benchmark Rh based material. Several catalyst synthesis improvements were carried out including: 1) selectively doping metals on the A-site and B-site of the perovskite structure, 2) changing the support from perovskite to alumina, 3) altering the method of metal addition, and 4) using transition metals instead of noble metals. It was found that the catalytic activity changed little with modification of the A-site metal, while it displayed considerable dependence on the B-site metal. Perovskite supports performed much better than alumina based supports.

Efforts to implement new water quality standards, increase water reuse and reclamation, and minimize the cost of waste storage motivate the development of new processes for stabilizing wastewater residuals that minimize waste volume, water content and the long-term environmental risk from related by-products. This work explores the use of an aqueous-based emulsion process to create an epoxy/rubber matrix for separating and encapsulating waste components from salt laden, arsenic contaminated, amorphous iron hydrate sludges. Such sludges are generated from conventional water purification precipitation/adsorption processes, used to convert aqueous brine streams to semi-solid waste streams, such as ion exchange/membrane separation, and from other precipitative heavy metal removal operations. In this study, epoxy and polystyrene butadiene (PSB) rubber emulsions are mixed together and then combined with a surrogate sludge. The surrogate sludge consists of amorphous iron hydrate with 1 part arsenic fixed to the surface of the hydrate per 10 parts iron mixed with sodium nitrate and chloride salts and water. The resulting emulsion is cured and dried at 80 °C to remove water. Microstructure characterization by electron microscopy confirms that the epoxy/PSB matrix surrounds and encapsulates the arsenic laden amorphous iron hydrate phase while allowing the salt to migrate to internal and …

Years of production of radioactive materials at the Hanford Site in southeastern Washington State has resulted in contamination of surface, subsurface, and surface water environments. Cleanup of the site has been aided by various tools, including computer software used to predict contaminant migration in the future and estimate subsequent impacts. The System Assessment Capability (SAC) is a total systems tool designed to simulate the movement of contaminants from all waste sites at Hanford through the vadose zone, the unconfined aquifer, and the Columbia River. Except for iodine-129, most of the contaminants modeled by SAC have acceptably matched field measurements. The two most likely reasons for the inconsistency between the measured field data and SAC modeled predictions are an underestimated inventory and an overestimated sorption value (Kd). Field data tend to be point measurements taken from near the surface of the unconfined aquifer. Thus, the depth of the iodine-129 contamination plume on the site is not well characterized. Geostatistical analyses of the measured data were conducted to determine the mass of iodine-129 for four assumed plume depths within the unconfined aquifer. Several simulations for two different Kd’s using the initial SAC inventory were run to determine the effect of an overestimated …

Quantification of special nuclear material is a necessary aspect to assuring material accountability and is often accomplished using non-destructive gamma spectrometry. For 233U, gamma rays are affected by matrix and packaging attenuation and by a strong Compton continuum from decay products of 232U (inherently found in 233U) that obscure 233U gamma photopeaks. This project, based on current work at the national repository for separated 233U located at Oak Ridge National Laboratory (ORNL), explores the effects of various parameters on the quantification of 233U– including material form and geometry. Using an attenuation correction methodology for calculating the mass of 233U from NDA analysis, a bias of almost 75% less than the actual 233U mass was identified. The source of the bias needs to be understood at a more fundamental level for further use of this quantification method. Therefore, controlled experiments using well characterized packages of 233U were conducted at the repository and are presented in this paper.

We consider the effect and correction of three types of orbit errors in SNS: quadrupole displacement errors, dipole displacement errors, and dipole field errors. Using the ORBIT beam dynamics code, we focus on orbit deflection of a standard pencil beam and on beam losses in a high intensity injection simulation. We study the correction of these orbit errors using the proposed system of 88 (44 horizontal and 44 vertical) ring beam position monitors (BPMs) and 52 (24 horizontal and 28 vertical) dipole corrector magnets. Correction is carried out numerically by adjusting the kick strengths of the dipole corrector magnets to minimize the sum of the squares of the BPM signals for the pencil beam. In addition to using the exact BPM signals as input to the correction algorithm, we also consider the effect of random BPM signal errors. For all three types of error and for perturbations of individual magnets, the correction algorithm always chooses the three-bump method to localize the orbit displacement to the region between the magnet and its adjacent correctors. The values of the BPM signals resulting from specified settings of the dipole corrector kick strengths can be used to set up the orbit response matrix, which …

Carbonation of magnesium- and calcium-silicate minerals to form their respective carbonates is one method to sequester carbon dioxide. Process development studies have identified reactor design as a key component affecting both the capital and operating costs of ex-situ mineral sequestration. Results from mineral carbonation studies conducted in a batch autoclave were utilized to design and construct a unique continuous pipe reactor with 100% recycle (flow-loop reactor). Results from the flow-loop reactor are consistent with batch autoclave tests, and are being used to derive engineering data necessary to design a bench-scale continuous pipeline reactor.

An approach proposed for removal of CO2 from flue gas cools and compresses a portion of a recirculated flue-gas stream, condensing its volatile materials for capture. Recirculating the flue gas concentrates SOx, H2O and CO2 while dramatically reducing N2 and NOx, enabling this approach, which uses readily available industrial components. A hybrid system of indirect and direct-contact heat exchange performs heat and mass transfer for pollutant removal and energy recovery. Computer modeling and experimentation combine to investigate the thermodynamics, heat and mass transfer, chemistry and engineering design of this integrated pollutant removal (IPR) system.

Coherent synchrotron radiation (CSR) is a fascinating phenomenon recently observed in electron storage rings and shows tremendous promise as a high power source of radiation at terahertz frequencies. However, because of the properties of the radiation and the electron beams needed to produce it, there are a number of interesting features of the storage ring that can be optimized for CSR. Furthermore, CSR has been observed in three distinct forms: as steady pulses from short bunches, bursts from growth of spontaneous modulations in high current bunches, and from micro modulations imposed on a bunch from laser slicing. These processes have their relative merits as sources and can be improved via the ring design. The terahertz (THz) and sub-THz region of the electromagnetic spectrum lies between the infrared and the microwave . This boundary region is beyond the normal reach of optical and electronic measurement techniques and sources associated with these better-known neighbors. Recent research has demonstrated a relatively high power source of THz radiation from electron storage rings: coherent synchrotron radiation (CSR). Besides offering high power, CSR enables broadband optical techniques to be extended to nearly the microwave region, and has inherently sub-picosecond pulses. As a result, new opportunities for …

Recent tests conducted at the Albany Research Center have addressed the possibility of in-situ storage of carbon dioxide in geological formations, particularly in deep brackish to saline non-potable aquifers, and the formation of secondary carbonate minerals over time within these aquifers. Various rock types including Columbia River Basalt Group (CRBG) drill core samples, blocks of ultra-mafic rock and sandstone were used. A solution formulated from aquifer data, a bicarbonate salt solution, and distilled water were tested. Pressure and temperature regimens were used to mimic existing in-situ conditions, higher temperatures were used to simulate longer time frames, and higher pressures were used to simulate enhanced oil recovery (EOR) pressure. Results are encouraging, indicating mineral dissolution with an increase of desirable ions (Ca, Fe2+, Mg) in solution that can form the carbonate minerals, calcite (CaCO3), siderite (FeCO3), and magnesite (MgCO3).