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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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Magnetohydrodynamics (MHD) Aerocapture System for Enabling Faster-Larger Planetary Science & Human Exploration Missions

Since our completing the NIAC Phase I NIAC on this Advanced Aerocapture System, NASA Langley Research Center has funded or supported a number of studies and code enhancements through its Center Innovation Fund (CIF) and NASA’s NSTGRO and Internship Programs to mature the analysis capabilities and quantify the merits of the MHD Aerocapture System technology. These efforts have resulted in a plug and play analysis capability for assessing MHD aerocapture system performance for arrival at many planetary bodies of interest. Our efforts have especially focused on the potential mass savings for improving the capacity for science observations at Neptune and Triton. A re-cent Forbes article published “‘Orbital mechanics is probably going to decide for us whether we go to Uranus or Neptune because we need to flyby Jupiter,’ said Kunio Sayanagi at Hampton University, Virginia, who also worked on the Neptune Odyssey proposal…. Exactly when a mission can be sent to Uranus, or Neptune, depends on the relative position of Jupiter, which can help give a spacecraft a gravitational slingshot. That drastically shortens the cruise phase.” [1] Since shortening the cruise phase is important for these science missions, any mass savings enabled by the MHD Aerocapture System could be reallocated to increasing Thermal Protection System mass to allow faster arrival speeds and/or for onboarding additional payloads such as science instruments, batteries, or propellant for conducting more science for longer durations in the desired orbits. The analysis steps and codes for conducting trades and sizing vehicles for aerocapture are as follows: Step 1 is to conduct aeroheating analysis using LAURA of the selected entry vehicle shape to identify locations on the forebody where ionization and flow velocity are sufficient for producing Lo-rentz forces. LAURA is a multiblock structured grid finite-volume CFD solver developed at the NASA Langley Research Center. [2] LAURA has been used for aerothermal analysis support of the entry, de-scent and landing (EDL) phase of interplanetary missions over the last three decades [3-7]. Step 2 is to port the LAURA results into CFDWARP to calcu-late electrical and thermal conductivities of ionized flow for sizing MHD patch system and calculating Lorentz forces needed for controls analysis. CFDWARP is a CFD code that uses advanced nu-merical methods that enable the simulation of the full coupling between the aerodynamics, the magne-tohydrodynamics, and the non-neutral plasma sheaths. CFDWARP has the unique capability to simulate efficiently the non-neutral sheaths (near the electrodes) in coupled form with the quasi-neutral bulk MHD flow [8-11]. Step 3 is to link re-sults from LAURA and CFDWARP into POST2 for calculating entry trajectories and comparing MHD control results with other aerodynamic control strategies. The Program to Optimize Simulated Tra-jectories II (POST2) is a generalized point mass, discrete parameter targeting and optimization pro-gram. POST2 provides the capability to target and optimize point mass trajectories for multiple pow-ered or un-powered vehicles near an arbitrary rotat-ing, oblate planet [12]. Step 4: TPS sizing was per-formed using the Fully Implicit Ablation and Ther-mal-response code (FIAT) tool which computes the transient one-dimensional thermal response and surface thermochemistry of a multilayer stackup of thermal protection, bonding, and structural materi-als subject to aeroheating on one surface [13]. The sizing and margining methodology used was based on the approach documented by Mahzari and Milos [14] for the dual-layered heatshield for extreme entry environment technology (DL-HEEET) TPS concept. TPS analysis utilizes trajectory information from POST2. Using this step-wise plug and play MHD Aerocapture performance assessment process, our analysis targets a Neptune aerocapture trajectory that will place the spacecraft in an observation orbit for Triton. [15]. Magnetohydrodynamic (MHD) control of a 4.5-meter diameter MSL-style capsule resulted in TPS mass savings of nearly 2000 kg when using an MHD system mass of under 200 kg. The flight path for a vehicle using the MHD control strategy has a much lower heat rate and heat load compared to the conventional aerodynamic aerocapture strategies known as bank angle con-trolled (BAC) and direct force controlled (DFC). Both BAC and DFC have heat rates significantly greater than 1500 W/cm2 typically used as an upper limit for PICA. Thus, DL-HEEET TPS concept was required for the BAC and DFC control strategies. However, considering the more benign environ-ments for the MHD case, additional TPS concepts with improved mass efficiency were also assessed. PICA was considered for the MHD controlled strat-egy since the maximum heat rate was well within the limits (<1500 W/cm2) of PICA. TPS sizing re-sulted in a significant mass reduction. The PICA layer for this sizing case was about 7.8 cm. As a point of reference, the Mars 2020 mission, which used this same PICA concept, had a PICA thickness of 3.18 cm [16]. The trajectories used for the TPS sizing originat-ed from the POST2 simulations. The current, I, to an electromagnet configuration can be manipulated to allow for active control of the vehicle. Manipula-tion of the current, I, changes the magnetic field, B, which affects the Lorentz force and therefore the MHD drag force on the vehicle. Our analysis in-cluded both open-loop and close-loop control. Closed-loop control will enable improved overall performance when taking into account mission level uncertainties, such as interplanetary delivery errors and atmospheric modeling uncertainties. The open-loop and closed-loop MHD control cases do not dip as deep into the atmosphere as the aerodynamic cases. Three types of aerodynamic-only approach-es are investigated: bank angle modulation (BAM), director force control (DFC), and Drag Modulated. BAM and DFC make use of vehicle aerodynamic angles to steer the vehicle. Thus, changing the aer-odynamic forces acting on the vehicle for control, aerodynamic drag modulated case requires a vary-ing drag area to modulate the drag force. The MHD drag modulated case modulates MHD generated drag force that adds to the aerodynamic drag. This higher atmospheric activation of drag forces by the MHD patch results in significantly less heat flux on the vehicle. The MHD technology will enable shorter cruise times and deceleration of larger payloads for increasing the capacity for science at the Ice Giants or for returning astronauts to Earth from cislunar space or from Mars. The purpose of this presentation is to provide more details about this work and to highlight plans for further research and development including a flight demonstration.

R. W. Moses↗
DOE OSTI2018

Assessment of Quality Management for Transport Packages Not Requiring Authority Design Approval - 18194

The majority of transports of radioactive materials are carried out in packages which don't need a package design approval of a competent authority. Low active radioactive materials are transported in such kind of packages e.g. in the medical and pharmaceutical industry and in the nuclear industry as well. In Germany the decision to phase out nuclear energy leads to a strong demand for packages to transport low and middle active radioactive waste due to the dismantling and decommissioning of nuclear power plants. According to IAEA regulations the 'non-competent authority approved package types' are the excepted packages and the industrial packages of Type IP-1, IP-2 and IP-3 and of Type A. For the packages of Type IP-2, IP-3 and Type A an assessment by the German competent authority is required for the quality management for the design, manufacture, testing, documentation, use, maintenance and inspection. In general a compliance audit of the manufacturer of the packaging is required during this assessment procedure. Their regulatory level in the IAEA regulations is not comparable with the regulatory density for packages requiring competent authority design approval. The countries apply different approaches within the assessment of the quality assurance measures in the management system as well as in the quality assurance program of a special package design. To use the package or packaging in a safe manner and in compliance with the regulations a management system for each phase of the life of the package or packaging is necessary. In order to help manufactures, which measurements and documents are needed for the assessment procedure, BAM developed a guideline. The guideline BAM-GGR 016 [5] describes the needed quality management for the design, manufacture, testing, documentation, use, maintenance and inspection of a packaging and the package. The poster to be presented will explain the different requirements of the quality assurance measures and give examples. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Structural, magnetic, and Mössbauer spectroscopy of Cu substituted M-type hexaferrites

Highlights: • Single BaM hexaferrite structural phases with Cu substations were prepared. • The magnetocrystalline anisotropy decreased with Cu substitution. • The coercivity was significantly modified while the magnetization remained high. • Hexaferrites with 0.2–0.4 Cu possess properties suitable for magnetic recording. • Ionic distributions from structural refinement agreed with Mössbauer spectroscopy. - Abstract: BaFe{sub 12−x}Cu{sub x}O{sub 19} hexaferrites were prepared using ball milling and sintering at 1100 °C. Refinement of the X-ray diffraction patterns was carried out to determine the structural parameters and the ionic distribution over the crystallographic sites. The preferential site occupation and valence state of Cu was consistent with the results obtained from the analysis of Mössbauer spectra. Further, the magnetic parameters of the samples were discussed in light of the structural and Mössbauer analyses. The magnetic phase transition temperature was found to decrease with the level of Cu substitution, in accordance with the reduction of the superexchange interactions. Further, the magnetic softening of the hexaferrite and the significant reduction in magnetocrystalline anisotropy with Cu substitution was consistent with the ionic distribution in the lattice. This study clearly demonstrated the feasibility of using a simple method to fabricate hexaferrites with a modified coercivity, while maintain the saturation magnetization high enough for practical applications.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Wide range yellow emission Sr8MgLa(PO4)7: Eu2+, Mn2+, Tb3+ phosphors for near ultraviolet white LEDs

Highlights: • The wide range of the emission spectra of Sr{sub 8}MgLa(PO{sub 4}){sub 7}: Eu{sup 2+}{sub 0.03} were clarified by Van Uitert equation and the crystal field strength equation. • The Mn{sup 2+} and Tb{sup 3+} had enhanced the total PL intensity up to 30% comparing to only Eu{sup 2+} doped phosphor. • W-LEDs using Sr{sub 8}MgLa(PO{sub 4}){sub 7}: Eu{sup 2+}{sub 0.03}, Mn{sup 2+}{sub 0.06}, Tb{sup 3+}{sub 0.06} and BAM: Eu{sup 2+} resulted in an excellent CRI of 89 and CIE coordinates of (0.3463, 0.3898). - Abstract: A series of single phased phosphors Sr{sub 8}MgLa(PO{sub 4}){sub 7}: Eu{sup 2+}, Mn{sup 2+}, Tb{sup 3+} were synthesized by solid state reaction methods for applications of white light emitting diodes(w-LEDs). The broad absorption band at the near ultraviolet (NUV) region of 250–450 nm was obtained, which is ascribed to the 4f{sup 7}→ 4f{sup 6}5d{sup 1} electronic transition of the Eu{sup 2+} ions. Under NUV excitation, the broad yellow emission was obtained from tri-activated Sr{sub 8}MgLa(PO{sub 4}){sub 7} phosphors via combining three emission bands centered at 500, 550, and 600 nm contributed by Eu{sup 2+}, Tb{sup 3+} and Mn{sup 2+}, respectively. The optimized concentrations of Mn{sup 2+} and Tb{sup 3+} were 6 mol%, respectively, which enhanced the total PL intensity up to 30% comparing to only Eu{sup 2+} doped phosphor. Moreover, the quantum efficiency of Sr{sub 8}MgLa(PO{sub 4}){sub 7}: Eu{sup 2+}, Mn{sup 2+}, Tb{sup 3+} phosphor had achieved up to 52%. The combination of a NUV chip with compound of Sr{sub 8}MgLa(PO{sub 4}){sub 7}: Eu{sup 2+}, Mn{sup 2+}, Tb{sup 3+} and BaMgAl{sub 10}O{sub 17}:Eu{sup 2+} achieved tunable w-LEDs with high CRI. The results suggest that this single phased Sr{sub 8}MgLa(PO{sub 4}){sub 7}: Eu{sup 2+}, Mn{sup 2+}, Tb{sup 3+} phosphor can be a key for the phosphor converted w-LEDs for warm white light emission.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Magnetic Ground State Crossover in a Series of Glaserite Systems with Triangular Magnetic Lattices

The magnetic properties are reported for three members of the glaserite series of compounds, Na 2 BaM(VO 4 ) 2 , M = Mn, Mn 0.6 Co 0.4 , and Co. Large single crystals are grown using a high-temperature hydrothermal synthesis method. This structure type exhibits a triangular magnetic lattice in which M 2+ O 6 octahedra are interconnected with nonmagnetic (VO 4 ) 3– groups. All the structures crystallize at room temperature with rigid trigonal symmetry (space group $P\bar{3m}1$); however, at lower temperatures both Na 2 BaMn(VO 4 ) 2 and Na 2 BaMn 0.6 Co 0.4 (VO 4 ) 2 undergo a structural transition to lower symmetry (monoclinic, C2/c). The bulk magnetic measurements indicate that Mn- and Co-structures are antiferromagnetic and ferromagnetic, respectively. Na 2 BaMn 0.6 Co 0.4 (VO 4 ) 2 does not show any long-range ordering down to 0.5 K, although a broad heat capacity anomaly near 1.2 K suggests short-range magnetic order or freezing into a spin-glass-like state related to the chemical disorder and resulting competing magnetic interactions. The magnetic structures of Na 2 BaMn(VO 4 ) 2 and Na 2 BaCo(VO 4 ) 2 were determined using neutron powder diffraction. At zero magnetic field, Na 2 BaMn(VO 4 ) 2 possesses an antiferromagnetic structure with the moments ordered in a Néel-type arrangement and aligned along the C 4 axis of the octahedra. Under applied magnetic field at 0.3 K, the evolution of the magnetic structure toward a fully polarized state is observed. Na 2 BaCo(VO 4 ) 2 represents a ferromagnetic (FM) magnetic structure with Co moments aligned parallel to the c-axis direction. Finally, the relationships between these structures and magnetic properties are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Quantitative phase separation in multiferroic Bi{sub 0.88}Sm{sub 0.12}FeO{sub 3} ceramics via piezoresponse force microscopy

BiFeO{sub 3} (BFO) is a classical multiferroic material with both ferroelectric and magnetic ordering at room temperature. Doping of this material with rare-earth oxides was found to be an efficient way to enhance the otherwise low piezoelectric response of unmodified BFO ceramics. In this work, we studied two types of bulk Sm-modified BFO ceramics with compositions close to the morphotropic phase boundary (MPB) prepared by different solid-state processing methods. In both samples, coexistence of polar R3c and antipolar P{sub bam} phases was detected by conventional X-ray diffraction (XRD); the non-polar P{sub nma} or P{sub bnm} phase also has potential to be present due to the compositional proximity to the polar-to-non-polar phase boundary. Two approaches to separate the phases based on the piezoresponse force microscopy measurements have been proposed. The obtained fractions of the polar and non-polar/anti-polar phases were close to those determined by quantitative XRD analysis. The results thus reveal a useful method for quantitative determination of the phase composition in multi-phase ceramic systems, including the technologically most important MPB systems.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Blue emission of Eu{sup 2+} doped LaMgAl{sub 11}O{sub 19} phosphor prepared by combustion synthesis method

Blue-emitting phosphor LaMgAl{sub 11}O{sub 19}:Eu{sup 2+} has been synthesized successfully at 500 °C by one step combustion synthesis method. The as-synthesized materials were characterized by powder x-ray diffraction (XRD) and photoluminescence (PL) techniques. Upon 365 nm excitation, emission spectra of the LaMgAl{sub 11}O{sub 19}:Eu{sup 2+} phosphors show a blue band at 450 nm. The excitation spectra corresponding to 4f{sup 7}-4f{sup 6}5d transition of Eu{sup 2+} cover the spectral range of 280–430 nm. The concentration quenching of Eu{sup 2+} in the LaMgAl{sub 11}O{sub 19} host was determined to be 3 mol%. The CIE chromaticity of LAM: Eu{sup 2+} phosphors was compared with the commercial BAM.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Rice SNP-seek database update: new SNPs, indels, and queries

We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Webservice calls were implemented to access most data. These features enable seamless querying of SNPSeek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

International code of nomenclature of prokaryotes

Here, this volume contains the edition of the International Code of Nomenclature of Prokaryotes that was presented in draft form and available for comment at the Plenary Session of the Fourteenth International Congress of Bacteriology and Applied Microbiology (BAM), Montréal, 2014, together with updated lists of conserved and rejected bacterial names and of Opinions issued by the Judicial Commission. As in the past it brings together those changes accepted, published and documented by the ICSP and the Judicial Commission since the last revision was published. Several new appendices have been added to this edition. Appendix 11 addresses the appropriate application of the Candidatus concept, Appendix 12 contains the history of the van Niel Prize, and Appendix 13 contains the summaries of Congresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Substrate damage and incorporation of sapphire into barium hexaferrite films deposited by aerosol deposition

Barium Hexaferrite (BaM) grown on sapphire substrate by aerosol deposition is investigated in a subtractive wedge series to determine the extent of energetic substrate damage and indentation. Energy dispersive x-ray spectroscopy (EDS) mapping reveals Al 2 O 3 particulates ejected from the substrate surface during growth. The concentration of particles is higher at the substrate-film interface but persists throughout the 6 mu m thick film. An estimate of the indentation depth (similar to 600 nm) was agreed upon using two EDS techniques (line scan analysis and substrate surface reconstruction by areal integration). X-ray diffraction patterns show peak polycrystalline Al 2 O 3 intensity in 1.5 mu m thick wedges and a decrease at higher thicknesses, confirming that Al 2 O 3 particulate density decreases further from the substrate. Here, magnetic characterization showed decreased magnetic moment compared to bulk and thickness dependence consistent with the fractional increase of Al 2 O 3 content in the films. X-ray absorption at the Fe L 3 edge suggests a reduction of material close to the surface, but this reduction appears secondary in magnitude to the effect of damage from deposition.

36 MATERIALS SCIENCE↗
DOE OSTI2022

AN ESTIMATE OF SPENT NUCLEAR FUEL MECHANICAL LOADS IN THE GENERAL 30 CM PACKAGE DROP SCENARIO

The US Department of Energy Spent Fuel and Waste Science and Technology (SFWST) program is performing research to determine the mechanical loading conditions applied to spent nuclear fuel (SNF) during normal conditions of transport to inform mechanical tests of SNF and close an important knowledge gap related to the practical disposition of SNF in the US. Researchers at Pacific Northwest National Laboratory (PNNL) have completed an extensive finite element study to characterize and estimate the potential mechanical loads on SNF during a hypothetical 30 cm drop of an SNF transportation package. This modeling study is validated with test data collected by the SFWST program during a physical test campaign that included one-third scale package drop tests and full-scale single fuel assembly drop tests. The test campaign was led by Sandia National Laboratories (SNL) and included international collaboration with Equipos Nucleares S.A, S.M.E (ENSA) and Bundesanstalt für Materialforschung und -prüfung (BAM). The key contribution of the modeling study is to go beyond the limitations of the limited number of physical tests to estimate the impact response to variations in impact angle, initial gap conditions, fuel assembly design, burnup and other parameters that affect the mechanical loads. The methodology of this study included a classic parametric study to calculate the impact response of highly detailed fuel assemblies over many combinations of parameters. Models of a 17x17 pressurized water reactor fuel assembly and a generic 10x10 boiling water reactor fuel assembly were both used in this study to cover the major fuel assembly types in the US inventory. Over 2,000 impact responses were calculated. The results of the parametric study were evaluated using traditional methods and basic statistics. The results were also used to construct a damage model using multiple nonlinear regression techniques to predict the mechanical loads over the full range of all input parameters. The damage model was found to work very well for all impact angle cases where the cask came to rest on its side. It was concluded that end drop cases where the cask remained vertical (instead of tipping over onto its side) were not sufficiently characterized by the current set of parametric study cases to include in the damage model, but it was not a priority to fully investigate that range because the highest mechanical loads were observed in the broader range of side impact cases. This modeling work provides sufficient insight into the mechanical loads on SNF during a hypothetical 30 cm package drop that, when considered along with the physical test data collected by the SNL-led team, the SFSWT program can consider the knowledge gap closed.

Klymyshyn, Nicholas A.↗
DOE OSTI2025

BAMCensus (The Behavior and Advanced Mobility Census Dataset Aggregator) [SWR-25-120]

This software is a high-performance tool developed in Rust for downloading and processing large-scale geospatial datasets, specifically focusing on US Census data. It is designed to address scaling limitations found in existing tools, such as R's [tidycensus](https://walker-data.com/tidycensus/), by providing performant streaming dataset JOIN operations between various US Census datasets (like ACS and LEHD) and their corresponding geometries stored on the TIGER/Lines web server. The tool automates the process of joining these data sources, returning aggregated data to the user based on a specified census GEOID type. The tool automates the process of joining these data sources, returning aggregated data to the user based on a specified census GEOID type. Its primary motivation stems from the need for a high-performance solution to combine spatial datasets with graph traversals within the context of mobility analysis tooling being developed at NREL's Behavior and Advanced Mobility (BAM) group.

Fitzgerald, Robert [National Renewable Energy Labo↗
DOE OSTI2017

Assessing state-of-the-art capabilities for probing the atmospheric boundary layer: The XPIA field campaign

To assess current capabilities for measuring flow within the atmospheric boundary layer, including within wind farms, the U.S. Dept. of Energy sponsored the eXperimental Planetary boundary layer Instrumentation Assessment (XPIA) campaign at the Boulder Atmospheric Observatory (BAO) in spring 2015. Herein, we summarize the XPIA field experiment, highlight novel measurement approaches, and quantify uncertainties associated with these measurement methods. Line-of-sight velocities measured by scanning lidars and radars exhibit close agreement with tower measurements, despite differences in measurement volumes. Virtual towers of wind measurements, from multiple lidars or radars, also agree well with tower and profiling lidar measurements. Estimates of winds over volumes from scanning lidars and radars are in close agreement, enabling assessment of spatial variability. Strengths of the radar systems used here include high scan rates, large domain coverage, and availability during most precipitation events, but they struggle at times to provide data during periods with limited atmospheric scatterers. In contrast, for the deployment geometry tested here, the lidars have slower scan rates and less range, but provide more data during non-precipitating atmospheric conditions. Microwave radiometers provide temperature profiles with approximately the same uncertainty as Radio-Acoustic Sounding Systems (RASS). Using a motion platform, we assess motion-compensation algorithms for lidars to be mounted on offshore platforms. As a result, we highlight cases for validation of mesoscale or large-eddy simulations, providing information on accessing the archived dataset. We conclude that modern remote sensing systems provide a generational improvement in observational capabilities, enabling resolution of fine-scale processes critical to understanding inhomogeneous boundary-layer flows.

17 WIND ENERGY↗
DOE OSTI2016

A hybrid computational strategy to address WGS variant analysis in >5000 samples

Abstract Background The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. Results We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Conclusions Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark

Abstract Background XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parameter space to obtain the best possible results. Results DECA is a horizontally scalable implementation of the XHMM algorithm using the ADAM framework and Apache Spark that incorporates novel algorithmic optimizations to eliminate unneeded computation. DECA parallelizes XHMM on both multi-core shared memory computers and large shared-nothing Spark clusters. We performed CNV discovery from the read-depth matrix in 2535 exomes in 9.3 min on a 16-core workstation (35.3× speedup vs. XHMM), 12.7 min using 10 executor cores on a Spark cluster (18.8× speedup vs. XHMM), and 9.8 min using 32 executor cores on Amazon AWS’ Elastic MapReduce. We performed CNV discovery from the original BAM files in 292 min using 640 executor cores on a Spark cluster. Conclusions We describe DECA’s performance, our algorithmic and implementation enhancements to XHMM to obtain that performance, and our lessons learned porting a complex genome analysis application to ADAM and Spark. ADAM and Apache Spark are a performant and productive platform for implementing large-scale genome analyses, but efficiently utilizing large clusters can require algorithmic optimizations and careful attention to Spark’s configuration parameters.

Linderman, Michael D. (ORCID:0000000296437148)↗
DOE OSTI2016

COLLABORATIVE RESEARCH: Study of Aerosol Sources and Processing at the GVAX Pantnagar Supersite

This project was part of a collaborative campaign, including the participation of scientists from seven research groups as part of the Winter Intensive Operating Period (January-February 2012) of the Clean Air for London (ClearfLo) campaign at a rural site in Detling, UK, 45 km southeast of central London to study wintertime sources of urban particulate matter. The UW contribution by PI Thornton’s group was to make the first deployment of a chemical ionization mass spectrometer instrument (MOVI-CI-ToFMS) to measure both particle and gas phase organic acids. The new instrument ran nearly continuously during the ClearfLo WINTER IOP at the Detling site, producing a first-ever data set of molecular composition information that can be used for source apportionment and process studies. The UW group published a paper in Environmental Science and Technology and contributed to another (Bohnenstengel et al BAMS 2015) detailing a direct molecular connection between biomass/biofuel burning particles and aerosol light absorption. The ES&T paper (Mohr, et al ES&T 2013) has received 42 citations in just 3 years indicative of its significant impact on the field. These measurements of urban and rural aerosol properties will contribute to improved modeling of regional aerosol emissions, and of atmospheric aging and removal.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Improving the representation of soluble iron in climate models

Funding from this grant supported Rachel Sanza, Yan Zhang and partially Samuel Albani. Substantial progress has been made on inclusion of mineralogy, showing the quality of the simulations, and the impact on radiation in the CAM4 and CAM5 (Scanza et al., 2015). In addition, the elemental distribution has been evaluated (and partially supported by this grant) (Zhang et al., 2015), showing that using spatial distributions of mineralogy, improved resperentation of Fe, Ca and Al are possible, compared to the limited available data. A new intermediate complexity soluble iron scheme was implemented in the Bulk Aerosol Model (BAM), which was completed as part of Rachel Scanza’s PhD thesis. Currently Rachel is writing up at least two first author papers describing the general methods and comparison to observations (Scanza et al., in prep.), as well as papers describing the sensitivity to preindustrial conditions and interannual variability. This work lead to the lead PI being asked to write a commentary in Nature (Mahowald, 2013) and two review papers (Mahowald et al., 2014, Mahowald et al., submitted) and contributed to related papers (Albani et al., 2016, Albani et al., 2014, Albani et al., 2015).

54 ENVIRONMENTAL SCIENCES↗