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At least 595 records · Page 33

A RESTful API for accessing microbial community data for MG-RAST

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http:// kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase’s microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.

59 BASIC BIOLOGICAL SCIENCES↗

The GREET Model Expansion for Well-to-Wheels Analysis of Heavy-Duty Vehicles

Heavy-duty vehicles (HDVs) account for a significant portion of the U.S. transportation sector’s fuel consumption, greenhouse gas (GHG) emissions, and air pollutant emissions. In our most recent efforts, we expanded the Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREETTM) model to include life-cycle analysis of HDVs. In particular, the GREET expansion includes the fuel consumption, GHG emissions, and air pollutant emissions of a variety of conventional (i.e., diesel and/or gasoline) HDV types, including Class 8b combination long-haul freight trucks, Class 8b combination short-haul freight trucks, Class 8b dump trucks, Class 8a refuse trucks, Class 8a transit buses, Class 8a intercity buses, Class 6 school buses, Class 6 single-unit delivery trucks, Class 4 single-unit delivery trucks, and Class 2b heavy-duty pickup trucks and vans. These vehicle types were selected to represent the diversity in the U.S. HDV market, and specific weight classes and body types were chosen on the basis of their fuel consumption using the 2002 Vehicle Inventory and Use Survey (VIUS) database. VIUS was also used to estimate the fuel consumption and payload carried for most of the HDV types. In addition, fuel economy projections from the U.S. Energy Information Administration, transit databases, and the literature were examined. The U.S. Environmental Protection Agency’s latest Motor Vehicle Emission Simulator was employed to generate tailpipe air pollutant emissions of diesel and gasoline HDV types.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Pellet-clad mechanical interaction screening using VERA applied to Watts Bar Unit 1, Cycles 1–3

The Consortium for Advanced Simulation of Light Water Reactors (CASL) aims to provide high-fidelity multiphysics simulations of light water nuclear reactors. To accomplish this, CASL is developing the Virtual Environment for Reactor Applications (VERA), which is a suite of code packages for thermal hydraulics, neutron transport, fuel performance, and coolant chemistry. As VERA continues to grow and expand, there has been an increased focus on incorporating fuel performance analysis methods. One of the primary goals of CASL is to estimate local cladding failure probability through pellet-clad interaction, which consists of both pellet-clad mechanical interaction (PCMI) and stress corrosion cracking. Estimating clad failure is important to preventing release of fission products to the primary system and accurate estimates could prove useful in establishing less conservative power ramp rates or when considering load-follow operations.While this capability is being pursued through several different approaches, the procedure presented in this article focuses on running independent fuel performance calculations with BISON using a file-based one-way coupling based on multicycle output data from high fidelity, pin-resolved coupled neutron transport–thermal hydraulics simulations. This type of approach is consistent with traditional fuel performance analysis methods, which are typically separate from core simulation analyses. A more tightly coupled approach is currently being developed, which is the ultimate target application in CASL.Recent work simulating 12 cycles of Watts Bar Unit 1 with VERA core simulator are capitalized upon, and quarter-core BISON results for parameters of interest to PCMI (maximum centerline fuel temperature, maximum clad hoop stress, and minimum gap size) are presented for Cycles 1–3. In conclusion, based on these results, this capability demonstrates its value and how it could be used as a screening tool for gathering insight into PCMI, singling out limiting rods for further, more detailed analysis.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A Unified Analytical Method Greenness Score ( uAMGS ) Quantifies How Microscopic Imaging Is Greener Than Conventional Liquid Chromatography

Green chemistry is a set of principles for assessing, developing, and implementing methods that are safer, more efficient, and less detrimental to the environment. The analytical method greenness score (AMGS) is one of many metrics that attempt to evaluate traditional liquid chromatography (LC) based on the energy consumption of the instrument and the safety, health risks, and environmental impact of the solvents employed. Unfortunately, in practice, the AMGS is primarily focused on traditional separation methods in the pharmaceutical industry and is not amenable to cutting-edge separation science, including miniaturization. To broaden this scope, the unified Analytical Method Greenness Score (uAMGS) is presented here, which clarifies and expands on the underlying mathematics and incorporates both dimensional and uncertainty analysis, enabling its application to a broader range of analytical techniques. The uAMGS is used to compare the greenness of two distinct methods: single-molecule microscopy (SMM) and high-performance liquid chromatography (HPLC), which were used to collect equivalent data. uAMGS determines that SMM is significantly greener than HPLC due primarily to decreased solvent consumption. Overall, the uAMGS should allow chemists ranging from undergraduates to industrial PhDs to assess the greenness of a wide range of separations.

chemical separations↗

Linking the Spin Transition of Ferric Iron in δ‐(Al,Fe)OOH to Water Storage in the Lower Mantle

As the most massive geochemical reservoir, the lower mantle affects the Earth's budget of volatile elements, including hydrogen or H 2 O. The properties of minerals in the lower mantle are further affected by changes in the electronic configurations of iron cations, that is, by spin transitions. The feedback between spin transitions and potential storage of H 2 O in solid hydrous phases in the lower mantle, however, remains unexplored. By combining high‐pressure nuclear resonant inelastic X‐ray scattering and high‐pressure high‐temperature X‐ray diffraction experiments, we constrained the thermal equation of state of δ‐(Al,Fe)OOH, a member of the phase H solid solution. Based on the derived thermal equation of state of δ‐(Al,Fe)OOH and the underlying thermodynamic model, we calculate the excess Gibbs free energy that arises from the spin transition of ferric iron in this compound and evaluate the effect on phase equilibria. The results of our analysis show that the spin transition of ferric iron in phase H may significantly reduce the thermodynamic activity and hence the concentration of H 2 O in a coexisting hydrous melt. As a consequence, nominally anhydrous minerals of the lower mantle may become dehydrated in the presence of phase H. Our analysis further suggests that, under certain conditions, the spin transition may expand the thermal stability of Fe 3+ ‐bearing phase H and create a geochemical link between the storage of H 2 O in phase H and ferric iron in the lower mantle.

Buchen, Johannes [Univ. of Bayreuth (Germany); Cal↗

A mechanistic study of mesoporous TiO 2 nanoparticle negative electrode materials with varying crystallinity for lithium ion batteries

Nanoscale oxide-based negative electrodes are of great interest for lithium ion batteries due to their high energy density, power density and enhanced safety. In this work, we conducted a case study on mesoporous TiO 2 nanoparticle negative electrodes with uniform size and varying crystallinity in order to investigate the trend in the electrochemical properties of oxide-based nanoscale negative electrodes with varying crystallinity. Furthermore, mesoporous solid spherical TiO 2 nanoparticles with a uniform particle size and varying crystallinity, i.e. , amorphous TiO 2 (A-TiO 2 ), partially crystalline TiO 2 (PC-TiO 2 ) and fully crystalline TiO 2 (FC-TiO 2 ) nanoparticles were studied. At low current rate (quasi steady-state), the specific capacity of the samples drops with the decrease of crystallinity. Ex situ synchrotron pair distribution function analysis reveals that the 1D zigzag Li ion diffusion pathway becomes expanded with the increase of crystallinity, which promotes ion mobility and charge storage. At high current rates (away from equilibrium states), however, the A-TiO 2 sample demonstrates slightly larger capacity than the FC-TiO 2 sample, both of which show larger capacities than that of the PC-TiO 2 sample. Both A-TiO 2 and FC-TiO 2 samples exhibit higher capacitive contribution to the charge storage and larger Li + diffusivity than those of the PC-TiO 2 sample, which explains their better rate capability. Moreover, the larger Li + diffusivity of the A-TiO 2 sample leads to the slightly larger specific capacity than the FC-TiO 2 sample at the highest current rate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics of implosion, bounce, and re-implosion of a shell directly driven by a time-shaped laser pulse

Gas-filled plastic spherical shells have been imploded using the 60-beam OMEGA laser. The same laser pulse was used as in a previous experiment, which demonstrated the dynamic formation of a shell by irradiating a homogeneous plastic foam sphere. In the present experiment, the shell initially implodes, bounces, and expands; a new shell then forms and undergoes a second implosion. Analysis of x-ray self-emission-streaked images and sequences of 2D x-ray self-emission framing camera images show shell evolution that is in reasonable agreement with 1D simulations. Shell integrity and symmetry are well maintained until the formation of the new shell. The final implosion, instead, is affected by substantial asymmetries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Pseudospectral particle-in-cell formulation with arbitrary charge and current-density time dependencies for the modeling of relativistic plasmas

This paper introduces a formulation of the particle-in-cell (PIC) method for the modeling of relativistic plasmas, that leverages the ability of the pseudospectral analytical time-domain solver (PSATD) to handle arbitrary time dependencies of the charge and current densities during one PIC cycle (applied to second-order polynomial dependencies here). Here, the formulation is applied to a modified set of Maxwell's equations that was proposed earlier in the context of divergence cleaning, and to recently proposed extensions of the PSATD-PIC algorithm. Detailed analysis and testings revealed that, under some condition, the formulation can expand the range of numerical parameters under which PIC simulations are stable and accurate when modeling relativistic plasmas such as, e.g., plasma-based particle accelerators.

43 PARTICLE ACCELERATORS↗

Recent highlights from GENIE v3

Abstract The release of GENIE v3.0.0 was a major milestone in the long history of the GENIE project, delivering several alternative comprehensive neutrino interaction models, improved charged-lepton scattering simulations, a range of beyond the Standard Model simulation capabilities, improved experimental interfaces, expanded core framework capabilities, and advanced new frameworks for the global analysis of neutrino scattering data and tuning of neutrino interaction models. Steady progress continued following the release of GENIE v3.0.0. New tools and a large number of new physics models, comprehensive model configurations, and tunes have been made publicly available and planned for release in v3.2.0. This article highlights some of the most recent technical and physics developments in the GENIE v3 series.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

An improved Method for Determining Transient Fuel Dilution of Oil in an Internal-Combustion Engine Using Laser-Induced Florescence and Multivariate Least Square Calibration

An optical diagnostic, based on laser-induced fluorescence (LIF), has been developed for on-engine measurements of real-time fuel dilution of engine oil or fuel in oil (FIO). Fuel dilution of oil is broadly relevant to advancing engine technology including durability, calibration, and catalyst-system management, and believed to promote destructive stochastic pre-ignition (SPI) during high-load engine operations. While standard (e.g., ASTM D3524-90) methods are not capable of real-time transient measurements, the LIF technique resolves transient dilution on the minutes time scale. We have expanded on our original FIO instrument development by introducing an improved analysis based on multivariate least square chemometrics analysis. The measurement uses a fuel dye (180–1300 parts per million, by mass) and monitors for its presence in the oil using 532 nm excitation and LIF. While the original FIO instrument utilized a two-color ratio method for analysis, the improved chemometric analysis uses the fully resolved LIF dye spectra to provide better predictive FIO accuracy (>92%) over a wide FIO range (1.5–14%) typical of engine application. We also investigate the effect of oil temperature on the LIF signal. Limited engine applications for demonstrating and validating the improved FIO instrument are shown, and the related data used to quantify practical detection limit and sensitivity. The improved analysis is insensitive to laser power fluctuation and change in detector integration time, providing an excellent FIO sensitivity (1–2%) and detection limit (0.01 %FIO) over a wide range of loads and injection timings, illustrating this updated approach to be a promising tool for advancing engine technology.

42 ENGINEERING↗

An Advanced One-Dimensional Finite Element Model for Incompressible Thermally Expandable Flow

Here, this paper provides an overview of a new one-dimensional finite element flow model for incompressible but thermally expandable flow. The flow model was developed for use in system analysis tools for whole-plant safety analysis of sodium fast reactors. Although the pressure-based formulation was implemented, the use of integral equations in the conservative form ensured the conservation laws of the fluid. A stabilization scheme based on streamline-upwind/Petrov-Galerkin and pressure-stabilizing/Petrov-Galerkin formulations is also introduced. The flow model and its implementation have been verified by many test problems, including density wave propagation, steep gradient problems, discharging between tanks, and the conjugate heat transfer in a heat exchanger.

42 ENGINEERING↗

BSSD 2019 Performance Metric Q4

The LANL SFA in Terrestrial Microbial Carbon Cycling aims to inform climate modeling and enable carbon management in terrestrial ecosystems by discovering widespread biological processes that control carbon storage and release in temperate biome soils. To achieve these goals, computational approaches are essential to analyze increasingly complex ‘omics’ data from microbial communities in environmental samples. The SFA continues to leverage advances in ‘omics' measurement technology and computation tools to decipher microbial community function in environmental samples. The computational approach is aligned with the recent shift in the SFA’s research approach. When the SFA began 10 years ago, computational approaches principally addressed “who is there” with extremely limited insight into function. Accessible ‘omics' data for complex soil communities were primarily amplicon DNA sequences of taxonomic or functional marker genes obtained by PCR, cloning, and Sanger sequencing. Computational tools for community analysis were nascent. Over the past decade, genome resources (DOE-Integrated Microbial Genomics database) and data acquisition increased 1000-fold, common computational pipelines for many analysis tasks have arisen, and the variety of ‘omics’ measurements has expanded to routinely include shotgun metagenomics, metatranscriptomics, and versions of metabolomics. The SFA is capitalizing on these advances while also developing new computational techniques to decipher how communities with different patterns of carbon cycling function from the species to ecosystem level.

54 ENVIRONMENTAL SCIENCES↗

Development of High Temperature (>700°C) Molten Salt Pump Technology for Generation 3 Solar Power Tower Systems

Bearings are required for long-shafted pumps historically used in concentrating solar thermal power applications. For molten chloride salts, bearings for such service conditions are not commercially available, nor has a design been demonstrated to work. Therefore, a project was sponsored by the Department of Energy’s Solar Energy Technologies Office for the development and demonstration of a submerged bearing for use in chloride salt pumps. This project’s tasks covered the tribological testing of candidate materials and the design, fabrication, testing, and post-test analysis of full-scale salt-compatible bearings. This work expands upon previous work. The effects of potential particulate in the salt were investigated through tribological bench testing. Through 11 tests, the MgO particulate size and concentration in a molten chloride salt were varied, and the effects on friction, wear rate, and wear characteristics were recorded. Novel journal bearings for chloride salt service were designed and fabricated based on these results. The bearings were of a relevant scale (i.e., for a 1.5 in. pump shaft) to demonstrate the technology with respect to further scale-up. The bearings were made of Haynes 244 and Yttria Partially Stabilized Zirconia. A custom bearing test rig, salt tanks, and associated infrastructure (e.g., heaters, tanks, transfer lines, gas flow control) were designed, procured, and installed. A few issues were encountered in the system fabrication process, resulting in delay of the project schedule. The system was successfully fabricated and assembled. Heating, cover gas, and pump motor systems were integrated into the control logic. This progress of the bearing test system represents a significant step forward towards demonstrating this promising technology. Nevertheless, the project ended before testing of the full-scale bearings could be performed.

14 SOLAR ENERGY↗

ESTIMATING LONG GRB JET OPENING ANGLES AND REST-FRAME ENERGETICS

We present a method to estimate the jet opening angles of long duration gamma-ray bursts (GRBs) using the prompt gamma-ray energetics and an inversion of the Ghirlanda relation, which is a correlation between the time-integrated peak energy of the GRB prompt spectrum and the collimation-corrected energy in gamma-rays. The derived jet opening angles using this method and detailed assumptions match well with the corresponding inferred jet opening angles obtained when a break in the afterglow is observed. Furthermore, using a model of the predicted long GRB redshift probability distribution observable by the Fermi Gamma-ray Burst Monitor (GBM), we estimate the probability distributions for the jet opening angle and rest-frame energetics for a large sample of GBM GRBs for which the redshifts have not been observed. Previous studies have only used a handful of GRBs to estimate these properties due to the paucity of observed afterglow jet breaks, spectroscopic redshifts, and comprehensive prompt gamma-ray observations, and we potentially expand the number of GRBs that can be used in this analysis by more than an order of magnitude. In this analysis, we also present an inferred distribution of jet breaks which indicates that a large fraction of jet breaks are not observable with current instrumentation and observing strategies. We present simple parameterizations for the jet angle, energetics, and jet break distributions so that they may be used in future studies.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantitative chemical assay of nanogram-level particulate matter using aerosol mass spectrometry: characterization of particles collected from uncrewed atmospheric measurement platforms

Abstract. Aerosol generation techniques have expanded the utility of aerosol mass spectrometry (AMS) for offline chemical analysis of airborne particles and droplets. However, standard aerosolization techniques require relatively large liquid volumes (e.g., several milliliters) and high sample masses that limit their utility. Here we report the development and characterization of a micronebulization AMS (MN-AMS) technique that requires as low as 10 µL of sample and can provide the quantification of the nanogram level of organic and inorganic substances via the usage of an isotopically labeled internal standard (34SO42-). Using standard solutions, the detection limits for this technique were determined at 0.19, 0.75, and 2.2 ng for sulfate, nitrate, and organics, respectively. The analytical recoveries for these species are 104 %, 87 %, and 94 %, respectively. This MN-AMS technique was applied successfully to analyze filter and impactor samples collected using miniature particulate matter (PM) samplers deployable on uncrewed atmospheric measurement platforms, such as uncrewed aerial systems (UASs) and tethered balloon systems (TBSs). Chemical composition of PM samples collected from a UAS field campaign conducted at the Department of Energy's (DOE) Southern Great Plains (SGP) observatory was characterized. The offline MN-AMS data compared well with the in situ PM composition measured by a co-located aerosol chemical speciation monitor (ACSM). In addition, the MN-AMS and ion chromatography (IC) agreed well for measurements of sulfate and nitrate concentrations in the PM extracts. This study demonstrates the utility of combining MN-AMS with uncrewed measurement platforms to provide quantitative measurements of ambient PM composition.

54 ENVIRONMENTAL SCIENCES↗

Space shuttle propulsion systems on-board checkout and monitoring system development study

Investigations on the fundamental space shuttle propulsion systems program are reported, with emphasis on in-depth reviews of preliminary drafts of the guidelines. The guidelines will be used to incorporate the onboard checkout and monitoring function into the basic design of the propulsion systems and associated interfacing systems. The analysis of checkout and monitoring requirements of the Titan 3 L expandable booster propulsion systems was completed, and the techniques for accomplishing the checkout and monitoring functions were determined. Updating results of the basic study of propulsion system checkout and monitoring is continuing.

Source record↗

Unsteady flow through compressor stages

The application of the nonsteady Lax-Wendroff technique to problems with asymptotically periodic solution which offers a potentially powerful method for the investigation of the interaction of rotating and stationary blade rows in turbomachinery is reported. A technique for specifying boundary conditions with phase lag was developed to accomplish this. A complete nonlinear analysis is carried out numerically to determine the entire flow field without recourse to the assumption of small disturbances of linear equations which underlie the previous acoustic theories. The result, obtained for the case of equal number of rotor and stator blades shows that transonic flow can be handled without difficulty. In addition, the program is not limited with regard to blade thickness, camber or loading. Extension of this method to incorporate viscous wakes and to analysis of fully three dimensional configuration is feasible, and would greatly expand its utility in practical applications.

Alzner, E.↗

High-altitude gas releases - Transition from collisionless flow to diffusive flow in a nonuniform atmosphere

The paper is motivated by a need for describing high-altitude gas releases from rockets or the Space Shuttle. In the tenuous upper atmosphere, the injected gases expand from a collisionless to a collision-dominated state. The analysis presented extends the efforts of Baum (1973-1974) to include the effects of a nonuniform background atmosphere and a velocity-dependent collision frequency. The unsteady expansion of gas releases is analyzed using gas kinetic theory. The Boltzmann equation with the Krook collision integral is solved numerically. At late times (after many collisions with the background atmosphere) the solution is identical to the one given by diffusion in a nonuniform atmosphere (Bernhardt, 1979). The theoretical model predicts elongation and heating of the vapor trails due to collisions.

Bernhardt, P. A.↗