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At least 487 records · Page 27

Constructing Space-Time Views from Fixed Size Statistical Data: Getting the Best of Both Worlds

Many performance monitoring tools are currently available to the super-computing community. The performance data gathered and analyzed by these tools fall under two categories: statistics and event traces. Statistical data is much more compact but lacks the probative power event traces offer. Event traces, on the other hand, can easily fill up the entire file system during execution such that the instrumented execution may have to be terminated half way through. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. The user can trade-off tracing overhead, trace data size vs. data quality incrementally. In other words, the user will be able to limit the amount of trace collected and, at the same time, carry out some of the analysis event traces offer using spacetime views for the entire execution. Two basic ideas are employed: the use of averages to replace recording data for each instance and "formulae" to represent sequences associated with communication and control flow. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected vs. event traces. We found that the trace files thus obtained are, in deed, small, bounded and predictable before program execution and that the quality of the space time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture 100% of all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at run-time to learn longer sequences.

Schmidt, Melisa↗

CRITICA: coding region identification tool invoking comparative analysis

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

Non-NASA Center↗

Constructing Space-Time Views from Fixed Size Statistical Data: Getting the Best of both Worlds

Many performance monitoring tools are currently available to the super-computing community. The performance data gathered and analyzed by these tools fall under two categories: statistics and event traces. Statistical data is much more compact but lacks the probative power event traces offer. Event traces, on the other hand, can easily fill up the entire file system during execution such that the instrumented execution may have to be terminated half way through. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. The user can trade-off tracing overhead, trace data size vs. data quality incrementally. In other words, the user will be able to limit the amount of trace collected and, at the same time, carry out some of the analysis event traces offer using space-time views for the entire execution. Two basic ideas arc employed: the use of averages to replace recording data for each instance and formulae to represent sequences associated with communication and control flow. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected vs. event traces. We found that the trace files thus obtained are, in deed, small, bounded and predictable before program execution and that the quality of the space time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture 100% of all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at run-time to learn longer sequences.

Schmidt, Melisa↗

Apatite geochemistry as a tool for understanding the petrogenesis of layered mafic-ultramafic rocks in the Bushveld Complex, South Africa

The sources of the magmas that formed the Rustenburg Layered Suite of the Bushveld Complex in South Africa remain debated, despite decades of research. Vertical and lateral variation in bulk rock and mineral separate Sr-Nd isotopic compositions, which generally indicate enriched sources, demonstrate that the layered sequence was formed by the emplacement of multiple batches of magma, crucially resulting in episodes of PGE-Cr-V mineralisation. The Lu-Hf isotope compositions of zircon are, however, at odds with the bulk rock Sr-Nd isotopic heterogeneity as they show near homogeneous compositions throughout the layered sequence (εHf (2.06 Ga) =−8). This lack of variation in Hf isotope composition has been attributed to deep, continental lithospheric mantle-related and/or crustal contamination of plume-derived Bushveld magmas. In this study, we analysed the major, trace element and Sr-Nd isotope geochemistry of apatite in the Rustenburg Layered Suite. Apatite occurs as an intercumulus mineral in the lowermost regions and a cumulus mineral in the uppermost regions of the layered sequence and can therefore be used to test existing models for the isotopic disequilibrium between bulk rock Sr-Nd and zircon Hf isotopic compositions. Apatite is largely chlorapatite in the lowermost regions and fluorapatite in the uppermost regions of the layered sequence. The Merensky Reef is unusual in that it comprises both chlorapatite and fluorapatite. Apatite throughout the layered sequence is generally unzoned and shows no evidence of late-stage alteration. Trace element data show that apatite is enriched in L/HREE, with common negative Eu-Sr anomalies. These trace element signatures are consistent with a magmatic origin for the apatite grains, with prior, or concurrent, plagioclase crystallization from the same melt. Variability in in situ Sr and Nd isotope compositions of apatite is recorded throughout the layered sequence with εNd (2.06 Ga) compositions varying between −2.5 and − 10.2 and initial 87 Sr/ 86 Sr compositions varying between 0.7079 and 0.7103 (for the Marikana dikes only). The variability in Sr-Nd isotope compositions of apatite is consistent with the bulk rock (and mineral separate) variation in Sr-Nd isotope compositions, suggesting apatite preserves primary magmatic compositions in the Rustenburg Layered Suite.

Apatite↗

Pilot Testing of a Highly Efficient Pre-combustion Sorbent-based Carbon Capture System

TDA developed and demonstrated a highly efficient pre-combustion carbon capture system. The overall objective of this work was to develop a new sorbent-based pre-combustion carbon capture technology for Integrated Gasification Combined Cycle (IGCC) power plants. In this project our goal was to demonstrate the techno-economic viability of the new technology by 1) demonstrating it in large-scale slipstream tests, and 2) carrying out a high fidelity engineering and cost analysis. TDA’s process used an advanced physical adsorbent that selectively removes CO 2 from coal-derived synthesis gas above the dew point of the gas at temperatures as high as 300°C. The sorbent consists of a mesoporous carbon whose surface was grafted with functional groups that remove CO 2 via a well-known acid-base interaction. As documented in bench-scale experiments and field tests with actual coal gas, the sorbent achieved a very high capacity for CO 2 at temperatures as high as 300°C. The sorbent bound CO 2 more strongly than common physical adsorbents, providing the chemical potential needed for the high temperature operation. However, because CO 2 does not form a true covalent bond with the surface sites (as is the case with chemical absorbents), the sorbent regeneration could be carried out with only a very small energy input. The heat input to regenerate our sorbent was only 4.9 kcal per mol of CO 2 , which is much lower than that for chemical absorbents (e.g., 29.9 kcal/mol CO 2 for sodium carbonate) and was similar to the requirements of physical solvents (e.g., 4 kcal/mol CO 2 for Selexol TM ). Because the sorbent operates above the dew point of the synthesis gas (unlike the Selexol TM process), a higher power cycle efficiency can be achieved. With previous DOE/NETL funding (Contract No. DE-FE-0000469), we demonstrated the techno-economic viability of the technology in bench-scale tests and slipstream demonstrations at the National Carbon Capture Center (NCCC), Wilsonville, Alabama and Wabash River IGCC plant in Terra Haute, Indiana. We demonstrated a stable working CO 2 capacity for over 11,650 cycles with simulated synthesis gas. We also evaluated its performance with actual synthesis gas in two test campaigns at the Wabash River IGCC Plant, Terre Haute, IN and the National Carbon Capture Center (NCCC), Wilsonville, AL. The slipstream tests clearly showed that the actual coal gas constituents and potential contaminants (e.g. trace metals, halides, tars) had no effect on the sorbent’s ability to remove CO 2 (the same sorbent beds were used in both field tests with no sign of deactivation for 2,000 cycles with over 26,750 SCF of gas treated). As expected, due to the high temperature CO 2 removal capability and low energy needed to regenerate the sorbent, the power cycle efficiency with our process was greater than 34% on a higher heating value (HHV) basis; in comparison, the same IGCC plant equipped with the Selexol TM solvent for carbon capture can only achieve 31.4% HHV efficiency. The capital cost for an IGCC system with TDA’s process is estimated as $2,417/kW e , which is 12% lower than that of the IGCC/ Selexol TM process. The levelized cost for electricity including the transport, storage and monitoring (TS&M) cost for CO 2 was calculated as $\$ $92.9/MWh (lowest reported to our knowledge), which is much better than the $105.2/MWh estimated for the IGCC/ Selexol TM process. In this project (DE-FE0013105), TDA Research, in collaboration with our partners Gas Technology Institute (GTI), Illinois Clean Coal Institute (ICCI), University of California, Irvine (UCI), University of Alberta (UOA), Siemens, NCCC and Sinopec advanced the technical maturity of the technology; scaling it up by a factor of 100. We optimized the reactor design using computational fluid dynamics (CFD); using adsorption modeling we improved the pressure swing adsorption (PSA) cycle sequence. We carried out two field test campaigns with a fully-equipped 0.1 MW e prototype unit (for a total of 844 hours) using actual synthesis gas to prove the viability of the new technology. A successful 30 day (707 hrs) evaluation was completed at NCCC under air blown gasification conditions. We demonstrated 97.3% carbon capture at 1,500 SLPM, 93% carbon capture at 1,800 SLPM, and 90% carbon capture at 2,100 SLPM in the NCCC tests. We also demonstrated the system for 137 hours at a Sinopec petrochemical plant under oxygen blown gasification, demonstrating 86% carbon capture at 2,660 SLPM. In collaboration with University of California, Irvine (UCI), we completed a techno-economic analysis (TEA) for TDA’s warm gas cleanup technology integrated to IGCC power plant. The net plant efficiencies (on a coal HHV basis) for the warm gas cleanup cases were estimated to be 34.0% for E-GasTM gasifier, 34.4% for GE gasifier, 33.4 for the Shell gasifier and 34.2 for the TRIG TM gasifier (Cases 2, 4, 6 and 8 in this study) with a catalytic combustor for CO 2 purification, which are significantly higher than those for the Cold Gas Case, or an increase of as much as 12% in the heat rate for Case 2, 6% for Case 4, 9% for Case 6, and 9% for Case 8. The 1st year cost of electricity with the transport, storage and monitoring (TS&M) costs for the CO 2 included was $\$ $129.2/MWh for the E-GasTM gasifier Warm Gas Cleanup Case, $\$ $131.9/MWh for the GE gasifier Warm Gas Cleanup Case, $\$ $146.8/MWh for the Shell Gasifier Warm Gas Cleanup Case, and $\$ $129.9/MWh for the TRIG TM gasifier Warm Gas Cleanup Case. For comparison, the costs for the baseline Cold Gas CO 2 removal with Selexol for the different gasifiers were: $\$ $146.6/MWh for the E-Gas TM gasifier, $\$ $142.2/MWh for the GE gasifier, $\$ $159.0/MWh for the Shell gasifier and $\$ $144.3/MWh for the TRIG TM gasifier. In summary, the costs for our system were 7 to 12% lower than the corresponding Cold Gas Cleanup cases. The results of this techno-economic analysis suggested that TDA’s high temperature PSA-based Warm Gas Clean-up Technology can make a substantial improvement in the IGCC plant thermal performance for achieving near zero CO 2 emissions for E-Gas TM , GE, Shell and TRIG TM gasifier based IGCC power plants. The capital expenses were estimated to be lower than that of Selexol’s™. Taken together, the higher net plant efficiency and lower capital and operating costs resulted in substantial reduction in the cost of carbon capture for the IGCC plant equipped with TDA’s high temperature PSA-based carbon capture system. Finally, in collaboration with Gas Technology Institute (GTI) we completed the environmental health and safety assessment for TDA’s warm gas carbon capture technology.

01 COAL, LIGNITE, AND PEAT↗

Determination of load sequence effects on the degradation and failure of composite materials

A theoretical model was established to predict the fatigue behavior of composite materials, with emphasis placed on predictions of the degradation of residual strength and residual stiffness during fatigue cycling. The model parameters were evaluated from three test series including static strength fatigue life and residual strength tests. The tests were applied to two graphite/epoxy laminates. Load sequence effects were emphasized for both laminates and the predicted results agreed quite well with subsequent verification tests. Dynamic as well as static stiffness reduction data were collected by use of a PDP11-03 computer, which performed quite satisfactorily and permitted the recording of a substantial amount of dynamic stiffness reduction data.

Yang, J. N.↗

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295 T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved p CO 2 , and requires exogenous vitamin B 12 . In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (~5.6 µM) O 2 concentrations. The abundance of a potentially more efficient CO 2 -fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb 3 -type terminal oxidase increased under O 2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O 2 -sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O 2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.

59 BASIC BIOLOGICAL SCIENCES↗

The engineered single guide RNA structure as a biomarker for gene-editing reagent exposure

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a prevalent adaptive immune system in bacteria and archaea. These systems defend against exogenous parasitic mobile genetic elements. The adaption of single effector CRISPR-Cas systems has massively facilitated gene-editing due to the reprogrammable guide RNA. The guide RNA affords little priming space for conventional PCR-based nucleic acid tests without foreknowledge of the spacer sequence. Further impeding detection of gene-editor exposure, these systems are derived from human microflora and pathogens ( Staphylococcus pyogenes , Streptococcus aureus , etc.) that contaminate human patient samples. The single guide RNA—formed from the CRISPR RNA (crRNA) and transactivating RNA (tracrRNA)—harbors a variable tetraloop sequence between the two RNA segments, complicating PCR assays. Identical single effector Cas proteins are used for gene-editing and naturally by bacteria. Antibodies raised against these Cas proteins are unable to distinguish CRISPR-Cas gene-editors from bacterial contaminant. To overcome the high potential for false positives, we have developed a DNA displacement assay to specifically detect gene-editors. We leveraged the single guide RNA structure as an engineered moiety for gene-editor exposure that does not cross-react with bacterial CRISPRs. Our assay has been validated for five common CRISPR systems and functions in complex sample matrices.

59 BASIC BIOLOGICAL SCIENCES↗

Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions

Marburg virus (MARV) disease is lethal, with fatality rates up to 90%. Neutralizing antibodies (Abs) are promising drug candidates to prevent or treat the disease. Current efforts are focused in part on vaccine development to induce such MARV-neutralizing Abs. We analyzed the antibody repertoire from healthy unexposed and previously MARV-infected individuals to assess if naïve repertoires contain suitable precursor antibodies that could become neutralizing with a limited set of somatic mutations. Here, we computationally searched the human Ab variable gene repertoire for predicted structural homologs of the neutralizing Ab MR78 that is specific to the receptor binding site (RBS) of MARV glycoprotein (GP). Eight Ab heavy-chain complementarity determining region 3 (HCDR3) loops from MARV-naïve individuals and one from a previously MARV-infected individual were selected for testing as HCDR3 loop chimeras on the MR78 Ab framework. Three of these chimerized antibodies bound to MARV GP. We then tested a full-length native Ab heavy chain encoding the same 17-residue-long HCDR3 loop that bound to the MARV GP the best among the chimeric Abs tested. Despite only 57% amino acid sequence identity, the Ab from a MARV-naïve donor recognized MARV GP and possessed neutralizing activity against the virus. Crystallization of both chimeric and full-length native heavy chain-containing Abs provided structural insights into the mechanism of binding for these types of Abs. Our work suggests that the MARV GP RBS is a promising candidate for epitope-focused vaccine design to induce neutralizing Abs against MARV.

59 BASIC BIOLOGICAL SCIENCES↗

Impact-Driven Sampling Strategies for Hybrid Attack Graphs

Cyber-Physical Systems (CPSs) have a large input space, with discrete and continuous elements across multiple layers. Hybrid Attack Graph (HAG) provide a flexible and efficient approach to generate attack sequences for a CPS. Analysis and testing of large-scale HAGs are prohibitively costly. We propose a dimension reduction via property-preserving multi-layer graph sampling algorithms. Existing property-preserving graph sampling approaches generate a representative subgraph of an original large-sized graph while preserving the key properties, such as node and edge distribution, clustering coefficients, and betweenness. On the other hand, we propose impact-driven sampling strategies to transform the input data to a lower-dimensional representation while retaining key properties of the data.

Subasi, Omer↗

Basic failure mechanisms in advanced composites

Fundamental failure mechanisms in carbon-epoxy composites were studied for more reliable prediction of the performance of these materials. Single and multiple fiber specimens were tested under tensile loads, and the sequence of failure events was observed. Parameters such as resin crack sensitivity, fiber surface treatment and variations in fibers from batch to batch are being evaluated. The analysis of bulk composite fracture processes using acoustic emission techniques is being studied in order to correlate microscopic observations with bulk composite behavior. Control of the fracture process through matrix and interface modification is being attempted, and study of failure processes in composite/metal specimens is being conducted. Most of the studies involved DEN 438 epoxy novolac as the matrix, but some experiments are now underway using the higher temperature resin ERLA 4617.

Mullin, J. V.↗

The synergistic effects of slip ring-brush design and materials

The design, fabrication, and testing of four power slip rings for synchronous orbit application are considered. Environmental and instrumentation systems necessary for monitoring electrical noise, friction, and brush wear in air and at less than 5 X 10 to the minus 8th power torr were developed. Composite brushes consisting of silver-molybdenum disulfide-graphite and silver-niobium diselenide-graphite were employed on rings of coin silver and rhodium plate. These four contact combinations were tested during ambient condition run-in at 150 and a humidity sequence at 0.1. The first nine months of a two year vacuum test performed at 0.1 rpm were completed.

Lewis, N. E.↗

An uncoupled viscoplastic constitutive model for metals at elevated temperature

An uncoupled constitutive model for predicting the transient response of thermal and rate dependent, inelastic material behavior is presented. The uncoupled model assumes that there is a temperature below which the total strain consists essentially of elastic and rate insensitive inelastic strains only. Above this temperature, the rate dependent inelastic strain (creep) dominates. The rate insensitive inelastic strain component is modeled in an incremental form with a yield function, flow rule and hardening law. Revisions to the hardening rule permit the model to predict temperature-dependent kinematic-isotropic hardening behavior, cyclic saturation, asymmetric stress-strain response upon stress reversal, and variable Bauschinger effect. The rate dependent inelastic strain component is modeled using a rate equation in terms of back stress, drag stress and exponent n as functions of temperature and strain. A sequence of hysteresis loops and relaxation tests are utilized to define the rate dependent inelastic strain rate. Evaluation of the model is performed by comparison with experiments involving various thermal and mechanical load histories on 5086 aluminum alloy, 304 stainless steel and Hastelloy-X.

Haisler, W. E.↗

Estimating the temperature and height of overshooting thunderstorm tops from geostationary satellite infrared data

Information is presented on the extent to which the brightness temperature is overestimated. A revised version of the technique proposed by Adler and Markus (1982) for overcoming this problem is discussed, together with aspects of its application. GOES IR thunderstorm top observations are compared with high-resolution data. The technique described here to estimate the small-scale cloud top temperature from the GOES data corrects for most of the field-of-view effect but requires additional analysis and testing. When applied to a time sequence of a growing thunderstorm, the calculated cloud top temperature time profile is found to agree very well with a similar profile derived from stereo measurements.

Adler, R. F.↗

Flat-plate solar array progress and plans

The emphasis of the Flat-plate Solar Array Project has been shifted from price goals and commercial development toward longer-term, higher risk, higher-potential-payoff opportunities. The revised objectives, status, and plans of the project are presented and technical progress is noted in the areas of: large-area sheet formation; silicon feedstock refinement; flat-plate module process sequence development; and engineering and environmental testing.

Callaghan, W. T.↗

Flat-plate solar array progress and plans

The results of research into the technology of flat-plate solar arrays undertaken in the Flat-Plate Solar Array Project under the sponsorship of the U.S. Department of Energy are surveyed. Topics examined include Si refinement, ribbon-sheet substrate formation, module process sequences, environmental isolation, module engineering and testing, and photovoltaic-array economics.

Callaghan, W. T.↗

Development of constitutive models for cyclic plasticity and creep behavior of super alloys at high temperature

An uncoupled constitutive model for predicting the transient response of thermal and rate dependent, inelastic material behavior was developed. The uncoupled model assumes that there is a temperature below which the total strain consists essentially of elastic and rate insensitive inelastic strains only. Above this temperature, the rate dependent inelastic strain (creep) dominates. The rate insensitive inelastic strain component is modelled in an incremental form with a yield function, blow rule and hardening law. Revisions to the hardening rule permit the model to predict temperature-dependent kinematic-isotropic hardening behavior, cyclic saturation, asymmetric stress-strain response upon stress reversal, and variable Bauschinger effect. The rate dependent inelastic strain component is modelled using a rate equation in terms of back stress, drag stress and exponent n as functions of temperature and strain. A sequence of hysteresis loops and relaxation tests are utilized to define the rate dependent inelastic strain rate. Evaluation of the model has been performed by comparison with experiments involving various thermal and mechanical load histories on 5086 aluminum alloy, 304 stainless steel and Hastelloy X.

Haisler, W. E.↗

Space Station Freedom - Technical and management challenges

The development of the Space Station is reviewed, focusing on the technical and managerial aspects of the program. The optimization of the Space Station configuration, utilization impacts on design, technical aspects of the distribution systems, and the problems of designing for a lifetime of 30 years or more are discussed. In addition, cost reduction studies, testing and verification, determining the assembly sequence, and operational communications and support systems are examined. Managerial aspects of the program include organization, program control, management tools and processes, and the integration of elements from the international partners.

Moser, Thomas L.↗