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At least 595 records · Page 33

Computing the Properties of Matter with Leadership Computing Resources (Closeout Report for DE-SC0018121)

In order to add more capabilities to Halide, we have designed a new framework called Tiramisu and integrated this framework into Halide. Since Tiramisu enables Halide to target heterogeneous architectures, our development efforts have been refocused on Tiramisu. Most high-performance computer systems today are complex and increasingly heterogeneous; they may have CPUs, GPUs and FPGAs. Achieving best performance requires taking full advantage of all these different architectures. To address this issue, we have designed Tiramisu, an optimization framework that enables Halide (and other DSLs) to target heterogeneous architectures. Tiramisu is an optimization framework that takes as input a high level, architecture-independent representation of code and a set of scheduling and data mapping commands that guide code transformation. The input can either be generated by a domain-specific language (DSL) compiler such as Halide or directly written by a programmer. Tiramisu then applies the user-specified code and data-layout transformations and generates an architecture-specific, low-level intermediate representation (IR) that takes advantage of modern architectural features such as multicore parallelism, non-uniform memory (NUMA) hierarchies, clusters, and accelerators like GPUs and FPGAs. We integrated Tiramisu within Halide and implemented a representative set of benchmarks to evaluate this integration. Tiramisu is now open source and is available for public use (http://tiramisu-compiler.org/). A paper about Tiramisu was published, it shows that Tiramisu extends Halide with many new capabilities and that Tiramisu can generate efficient code for multicores, GPUs, FPGAs and distributed heterogeneous systems. The performance of code generated by the Tiramisu backends matches or exceeds hand optimized reference implementations. For example, the multicore backend matches the highly optimized Intel MKL library on many kernels and shows speedups reaching 4x over the original Halide. In addition to making Tiramisu more robust, we have used Tiramisu to implement a set of representative tensor operation for constructing baryon building blocks required for multi baryon contractions in LQCD. In order to implement this code, we needed to generalize Tiramisu in two ways: first we needed to support indirect array accesses, and second, we needed to add support for complex numbers to Tiramisu. The code generated by Tiramisu is 6x faster than the reference code. Our efforts towards an MPI based multi-node version of tiramisu have matured and the resulting code scales well on multiple nodes (tests up to 512 KNL nodes have been undertaken).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Design, execution, and interpretation of plant RNA-seq analyses

Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.

59 BASIC BIOLOGICAL SCIENCES↗

ForSE: A GAN-based Algorithm for Extending CMB Foreground Models to Subdegree Angular Scales

We present ForSE (Foreground Scale Extender), a novel Python package that aims to overcome the current limitations in the simulation of diffuse Galactic radiation, in the context of cosmic microwave background (CMB) experiments. ForSE exploits the ability of generative adversarial neural networks (GANs) to learn and reproduce complex features present in a set of images, with the goal of simulating realistic and non-Gaussian foreground radiation at subdegree angular scales. This is of great importance in order to estimate the foreground contamination to lensing reconstruction, delensing, and primordial B-modes for future CMB experiments. We applied this algorithm to Galactic thermal dust emission in both total intensity and polarization. Our results show how ForSE is able to generate small-scale features (at 12') having as input the large-scale ones (80'). The injected structures have statistical properties, evaluated by means of the Minkowski functionals, in good agreement with those of the real sky and which show the correct amplitude scaling as a function of the angular dimension. Furthermore, the obtained thermal dust Stokes Q and U full-sky maps as well as the ForSE package are publicly available for download.

79 ASTRONOMY AND ASTROPHYSICS↗

Tightly-coupled camera/LiDAR integration for point cloud generation from GNSS/INS-assisted UAV mapping systems

Unmanned aerial vehicles (UAVs) equipped with integrated global navigation satellite systems/inertial navigation systems (GNSS/INS) together with cameras and/or LiDAR sensors are being widely used for topographic mapping in a variety of applications such as precision agriculture, coastal monitoring, and archaeological documentation. Integration of image-based and LiDAR point clouds can provide a comprehensive 3D model of the area of interest. For such integration, ensuring a good alignment between data from the different sources is critical. Although many works have been conducted on this topic, there is still a need for a rigorous integration approach that minimizes the discrepancy between camera and LiDAR data caused by inaccurate system calibration parameters and/or trajectory artifacts. This study proposes an automated tightly-coupled camera/LiDAR integration workflow for GNSS/INS-assisted UAV systems. The proposed strategy is conducted in three main steps. First, an image-based point cloud is generated using a LiDAR/GNSS/INS-assisted structure from motion (SfM) strategy. Then, feature correspondences between image-based and LiDAR point clouds are automatically identified. Finally, an integrated-bundle adjustment procedure including image points, LiDAR raw measurements, and GNSS/INS information is conducted to minimize the discrepancy between point clouds from different sensors while estimating system calibration parameters and refining the trajectory information. The proposed SfM strategy and integration framework are evaluated using five datasets. The SfM results show that using LiDAR data can facilitate feature matching and further increase the number of reconstructed 3D points. The experimental results also illustrate that the developed automated camera/LiDAR integration strategy is capable of accurately estimating system calibration parameters to achieve good alignment among camera/LiDAR data from single/multiple systems. Finally, an absolute accuracy in the range of 3–5 cm is achieved for the image/LiDAR point clouds after the integration process.

42 ENGINEERING↗

Origin of insulating and nonferromagnetic SrRuO 3 monolayers

The electro-magnetic properties of ultrathin epitaxial ruthenate films have long been the subject of debate. Here we combine experimental with theoretical investigations of (SrTiO 3 ) 5 -(SrRuO 3 ) n -(SrTiO 3 ) 5 (STO 5 -SRO n -STO 5 ) heterostructures with n = 1 and 2 unit cells, including extensive atomic-resolution scanning-transmission-electron-microscopy imaging, electron-energy-loss-spectroscopy chemical mapping, as well as transport and magneto-transport measurements. The experimental data demonstrate that the STO 5 -SRO 2 -STO 5 heterostructure is nearly stoichiometric, metallic, and ferromagnetic with T C ~ 128 K, even though it lacks the characteristic bulk-SRO octahedral tilts and matches the cubic STO structure. In contrast, the STO 5 -SRO 1 -STO 5 heterostructure features Ru-Ti intermixing in the RuO 2 layer, also without octahedral tilts, but is accompanied by a loss of metallicity and ferromagnetism. Density-functional-theory calculations show that stoichiometric n = 1 and n = 2 heterostructures are metallic and ferromagnetic with no octahedral tilts, while non-stoichiometry in the Ru sublattice in the n = 1 case opens an energy gap and induces antiferromagnetic ordering. Furthermore, the results indicate that the observed non-stoichiometry is the cause of the observed loss of metallicity and ferromagnetism in the n = 1 case.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

IRIS-BLAS: Towards a Performance Portable and Heterogeneous BLAS Library

This paper presents IRIS-BLAS, a novel heterogeneous and performance portable BLAS library. IRIS-BLAS is built on top of the IRIS runtime and multiple vendor and open-source BLAS libraries. It can transparently use all the architectures/devices available in a heterogeneous system, using the appropriate BLAS library based on the task mapping at run time. Thus, IRIS-BLAS is portable across a broad spectrum of architectures and BLAS libraries, alleviating the worry of application developers about modifying the application source code. Even though the emphasis is on portability, IRIS-BLAS provides competitive or even better performance than other state-of-the-art references. Moreover, IRIS-BLAS offers new features such as efficiently using extremely heterogeneous systems composed of multiple GPUs from different hardware vendors.

Miniskar, Narasinga Rao↗

Planck 2018 Results - II. Low Frequency Instrument data processing

We present a final description of the data-processing pipeline for the Planck Low Frequency Instrument (LFI), implemented for the 2018 data release. Several improvements have been made with respect to the previous release, especially in the calibration process and in the correction of instrumental features such as the effects of nonlinearity in the response of the analogue-to-digital converters. We provide a brief pedagogical introduction to the complete pipeline, as well as a detailed description of the important changes implemented. Self-consistency of the pipeline is demonstrated using dedicated simulations and null tests. We present the final version of the LFI full sky maps at 30, 44, and 70 GHz, both in temperature and polarization, together with a refined estimate of the solar dipole and a final assessment of the main LFI instrumental parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

Coupling Metabolic Source Isotopic Pair Labeling and Genome Wide Association for Metabolite and Gene Annotation in Plants (Final Technical Report)

In this project, we applied our labeling pipeline to Arabidopsis and sorghum by feeding tissues with isotopically labeled versions of commercially available amino acids to identify all metabolite features that incorporate the label. In sorghum, we fed five accessions, sampled across the diversity of sorghum, to identify the precursor-of-origin for metabolites that vary between accessions as well as those that may be missing from a single reference genotype. This provided us with precursor-of-origin annotation for thousands of unknown metabolites. We then used GWA to map genes responsible for the synthesis of precursor-of-origin classified metabolites. For sorghum leaf and root ducible metabolites, we performed untargeted metabolomics on leaf and root tissues from 300 diverse genotyped sorghum inbred lines. The amino acid precursor-of-origin metabolite library were then used to identify the corresponding metabolites in the GWA data sets and to identify novel gene-metabolite associations. Finally, we utilized existing and newly generated sequenced EMS mutants of sorghum to validate the predicted gene-metabolite relationships that our labelling analysis identified. In parallel, we conducted similar feeding experiments in Arabidopsis to categorize metabolites based on precursor-of-origin, identify those that vary across our existing Arabidopsis metabolite GWA dataset, and identify genes required for the synthesis of each metabolite. To provide an independent test of gene annotation and pathway involvement, we tested the GWA gene-metabolite associations in Arabidopsis by analyzing the metabolic phenotypes of gene knockouts. Genes of particular interest from both sorghum and Arabidopsis were studied in detail by directly measuring the activity of the corresponding enzymes following heterologous expression. In summary, this work classified as-yet-unknown amino acid-derived metabolites and identified genes involved in their production generated through “omics” technologies. This information was used to validate gene function and identify new metabolism in Arabidopsis and sorghum.

09 BIOMASS FUELS↗

Non-intrusive temperature measurements in the vicinity of a thermocouple using synchrotron x-ray fluorescence

A highly spatially resolved synchrotron x-ray fluorescence (XRF) thermometry technique has been used to map temperature fields around a 125 mu m type R thermocouple immersed in a stoichiometric premixed methane flame. The high spatial resolution of the XRF technique allowed temperatures to be measured close to the thermocouple and the impact of the thermocouple on the flame to be assessed. This paper discusses some of the nontrivial challenges of these measurements including the recovery of spectral features from the krypton fluorescent agent that are overlapped by those from the thermocouple metals at locations near the bead surface. The calculated temperatures from 1D premixed flame simulations are in excellent agreement with measurements along the centerline. The results show that the 125 mu m thermocouple induces minimal disturbances to the gas flow and any catalytic effects originating from the bare wires are also inconsequential. Here, the methodology has advanced to a stage where it enables comparisons between the gas temperature in the vicinity of the thermocouple and the actual thermocouple reading.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants

A comprehensive understanding of host dependency factors for SARS-CoV-2 remains elusive. Here, we map alterations in host lipids following SARS-CoV-2 infection using nontargeted lipidomics. We find that SARS-CoV-2 rewires host lipid metabolism, significantly altering hundreds of lipid species to effectively establish infection. We correlate these changes with viral protein activity by transfecting human cells with each viral protein and performing lipidomics. We find that lipid droplet plasticity is a key feature of infection and that viral propagation can be blocked by small-molecule glycerolipid biosynthesis inhibitors. We find that this inhibition was effective against the main variants of concern (alpha, beta, gamma, and delta), indicating that glycerolipid biosynthesis is a conserved host dependency factor that supports this evolving virus.

59 BASIC BIOLOGICAL SCIENCES↗

Source Authentication of Distribution Synchrophasors for Cybersecurity of Microgrids

This letter proposes a hybrid approach combining Self-Adaptive Mathematical Morphology (SAMM) and Time-Frequency (TF) techniques to authenticate the source information of Distribution Synchrophasors (DS) within near-range locations. The SAMM can adaptively regulate the synchrophasors variations which are representatives of local environmental characteristics. Subsequently, TF mapping is employed to extract informative signatures from the regulated synchrophasors variation. Finally, Random Forest Classification (RFC) is used to correlate the extracted signatures with the source information based on the derived TF mapping. Experiment results using DS collected at multiple small geographical scales validated the proposed methodology.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Hybrid Power Plants: Status of Installed and Proposed Projects [Slides]

As battery prices fall and wind and solar generation rises, power plant developers are increasingly combining wind and solar projects with on-site batteries, creating “hybrid” power plants. But hybrid or co-located plants have been part of the U.S. electricity mix for decades, with widely ranging configurations that extend beyond pairing a generator with a battery. This new summary tracks and maps existing hybrid and co-located plants across the United States while also synthesizing data from generation interconnection queues to illustrate developer interest in the next wave of plants. The scope is inclusive of co-located hybrid plants that pair two or more generators and/or that pair generation with storage at a single point of interconnection, and also full hybrids that feature co-location and co-control. The focus is on larger, 1 MW+ systems: smaller (often behind-the-meter) projects are also increasingly common, but are not included in the data synthesis. Based in part on EIA Form 860 data, there were at least 125 co-located hybrid plants (>1 MW) already operating across the United States at the end of 2019, totaling over 14 GW of aggregate capacity. Some of the most common configurations include wind+storage (13 projects, 1,290 MW wind, 184 MW storage), PV+storage (40 projects, 882 MW PV, 169 MW storage), and fossil+storage (10 projects, 2,414 MW fossil, 91 MW storage). Data from interconnection queues demonstrates the considerable commercial interest that exists in hybrid power plants, especially solar co-located with storage. By the end of 2019, there were at least 367 GW of solar plants in the nation’s queues; 102 GW (~28%) of this capacity was proposed as a hybrid, most typically pairing PV with battery storage. For wind, 225 GW of capacity sat in the queues, with 11 GW (~5%) proposed as a hybrid, again most-often pairing wind with storage. The proposed solar+storage plants are located throughout the United States, but with California and the non-ISO West being the most prominent areas of commercial interest. Proposed wind+storage and standalone storage plants also center to a degree on these regions of the country.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Improving Nb3Sn Cavity Performance Using Centrifugal Barrel Polishing

Nb3Sn superconducting radiofrequency (SRF) cavities have been an ongoing research topic for many years motivated by the potential for higher accelerating gradients and quality factors compared to niobium SRF cavities. The highest performing Nb3Sn cavities are manufactured using tin vapor-diffusion coating, which creates a Nb3Sn film with a surface roughness of around 100-200 nm. This is thought to be one of the limiting factors for the accelerating gradient of Nb3Sn cavities due to enhancement of magnetic field near sharp surface features. To smooth Nb3Sn SRF cavities, we have developed a mechanical polishing procedure which uses centrifugal barrel polishing to smooth the surface followed by a secondary tin coating step to repair the surface. We show that the accelerating field of a Nb3Sn SRF cavity is improved by applying this procedure. We also investigate the quench mechanism of the polished cavity by utilizing temperature mapping to measure which regions of the cavity e xperience heating during RF operation. We then cut samples from these regions and analyze the film microstructure and chemical composition in 3D using EDS and EBSD measurements together with a focused ion-beam (FIB) tomography technique.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Digital Twin Empowered PV Power Prediction

The accurate prediction of photovoltaic (PV) power generation is significant to ensure the economic and safe operation of power systems. To this end, the paper proposes a new digital twin (DT) empowered PV power prediction framework that is capable of ensuring reliable data transmission and employing the DT to achieve high accuracy of power prediction. With this framework, considering potential data contamination in the collected PV data, a generative adversarial network is employed to restore the historical data set, which offers a prerequisite to ensure accurate mapping from the physical space to the digital space. Further, a new DT empowered PV power prediction method is proposed. Therein, we model a DT that encompasses a digital physical model for reflecting the physical operation mechanism and a neural network model (i.e., a parallel network of convolution and bidirectional long-short-term memory model) for capturing the hidden spatial-temporal features. The proposed method enables the use of the DT to take advantages of the digital physical model and the neural network model, resulting in enhanced prediction accuracy. Finally, a real data set is conducted to access the effectiveness of the proposed method.

14 SOLAR ENERGY↗

Next Generation System Analysis Model: Recently Added Features and Future Plans

To better enable informed decision-making regarding the back-end of the nuclear fuel cycle, the Integrated Waste Management System (IWMS) program within the U.S. Department of Energy, Office of Nuclear Energy (DOE-NE) has been sponsoring the development and application of system analysis tools capable of analyzing various system options for the management of spent nuclear fuel (SNF) and high-level radioactive waste (HLW).With these tools, IWMS architecture analyses are being conducted to support the future deployment of a comprehensive nuclear waste management system that considers all major back-end aspects of the nuclear fuel cycle (i.e., transportation, storage, and disposal). The Next Generation System Analysis Model (NGSAM) is an agent-based simulation software tool expressly designed to be capable of modeling features within various IWMS architectures. NGSAM imports data from Oak Ridge National Laboratory (ORNL)’s unified database (e.g., historic assembly information, thermal profiles for assembly heat, and at-reactor dry storage loadings) to ensure that each simulation initializes with a realistic representation of the state of commercial SNF in the U.S. Recent major enhancements implemented into NGSAM in the period since NGSAM was last presented at the WM2019 conference include: • Tracking of railroad escort car acquisition and buffer car acquisition • The addition of heavy haul truck (HHT) and barge routes for some sites, as well as support for user-defined inter-modal routes • Updates to the logic that checks the transportation cask thermal limit maps prior to package transport • An allocation method that predicts when reactor sites would pack assemblies from their spent fuel pools for dry storage, and prioritizes shipments directly from the pools of those reactor sites in the preceding periods (before the predicted loadings to dry storage), thus reducing the number of casks loaded into dry storage at reactor sites • The addition of “reactor site family” operational limits to restrict the number of loads of SNF taken from the pool and from dry storage at a given reactor site each year • Added support for multiple canister loading map options and packages with multiple compatible transportation overpacks • Updates to the handling of non-commercial SNF, including a new database that contains data to support the updates • Updates to allow analysis of hypothetical scenarios which include repackaging at reactor sites, e.g., for possible comparative analysis with other scenarios • Implementation of additional output reports, or modification of existing ones • The ability to generate and implement user edits via the NGSAM website • The ability to model loading SNF from pool storage at an interim storage facility (ISF) into dry storage at the ISF • The ability to model consolidating SNF from different existing storage containers at a DOE site into the same DOE standard canister • The ability to model transferring SNF casks from one transportation mode to another, e.g., from HHT to rail, referred to as transloading. These new features have improved NGSAM capabilities and users’ experience with the model. Preliminary NGSAM requirements for modeling advanced reactor fuels, reprocessing, treatment, and conditioning were considered, and this paper describes them at a high level. Other nuclear fuel cycle system analysis tools developed under sponsorship of DOE-NE, like the VISION code developed at Idaho National Laboratory, might be better suited for initial high-level analysis of those technologies and advanced fuel cycles. As technologies are developed and system concepts evolve, NGSAM could provide value by providing more detailed modeling of transport, storage, and disposal of spent fuel and wastes from advanced reactors and advanced fuel cycles at the fuel element and waste container level.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human brain and hiPSC-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 493 synaptic candidates supported by proteomics. We further investigate three such proteins that are associated with neurodevelopmental disorders – the CUL3 E3 ubiquitin ligase, the DDX3X and YBX1 nucleic-acid binding proteins – by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to systematically and more comprehensively resolve the synaptic architecture.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and Description of a Silicic Volcaniclastic Layer in Gale Crater, Mars, Using Active Neutron Interrogation

The Dynamic Albedo of Neutrons instrument aboard the Mars Science Laboratory rover, Curiosity, has been used to map a stratigraphically-conformable layer of high-SiO 2 material in Gale crater. Previous work has shown this material contains tridymite, a high-temperature/low-pressure felsic mineral, interpreted to have a volcanic source rock. We describe several characteristics including orientation, extent, hydration, and geochemistry, consistent with a volcaniclastic material conformably deposited within a lacustrine mudstone succession. Relationships with widely dispersed alteration features and orbital detections of hydrated SiO 2 suggest that this high-SiO 2 layer extends at least 17 km laterally. Mineralogical abundances previously reported for this high-SiO 2 material indicated that hydrous species were restricted to the amorphous (non-crystalline) fraction, which is dominated by SiO2. The low mean bulk hydration of this high-SiO 2 layer (1.85 ± 0.13 wt.% water-equivalent hydrogen) is consistent with silicic glass in addition to opal-A and opal- CT. Persistent volcanic glass and tridymite in addition to opal in an ancient sedimentary unit indicates that the conversion to more ordered forms of crystalline SiO 2 has not proceeded to completion and that this material has had only limited exposure to water since it originally erupted, despite having been transported in a uviolacustrine system. Our results, including the conformable nature, large areal extent, and presence of vol- canic glass, indicate that this high-SiO 2 material is derived from the product of evolved magma on Mars. This is the rst identi cation of a silicic volcaniclastic layer on another planet, and has important implications for magma evolution mechanisms on single-plate planets.

58 GEOSCIENCES↗

Distributed Acoustic Sensing to Estimate the Permeability

Optical fiber in a borehole can be interrogated with distributed acoustic sensors (DAS) to capture fracture displacements with the potential to map surrounding fracture networks. We designed a laboratory experiment to test the capability of DAS to determine borehole flow characteristics, and we show that for the first time DAS can be used to remotely estimate permeability. Optical fiber was wrapped around a bead filled pipe and the pressure drop and flow velocity were measured to directly calculate permeability. A machine learning model using statistical features from continuous DAS estimated the bulk permeability. Fluid interactions with the permeable material demonstrate insufficient resolution using DAS amplitude-based measurements for estimating pressure drop to infer permeability. Variations in the spectral domain relate DAS measurements to the pressure drop and provide consistent permeability estimates. Resolution with DAS is sufficient to estimate permeability and provides a reliable method to monitor at depth in borehole conditions.

58 GEOSCIENCES↗