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At least 37 records · Page 2

3x3 array module of 8×8×32 mm 3 position-sensitive virtual frisch-grid CdZnTe detectors for imaging and spectroscopy of cosmic gamma-rays

Here, we evaluated the performance of the 3x3 array of 32-mm long position-sensitive virtual Frisch-grid (VFG) CdZnTe (CZT) detectors read out by the IDEAS GDS-100 data acquisition system. The array is a mechanically solid module designed for integration into a large effective area gamma-ray telescope proposed for imaging and spectroscopy of cosmic gamma-rays. The array employs the bar-shaped 8x8x32 mm 3 CZT crystals which recently became available from Redlen Technologies, Inc. and Kromek-eV Group PLC at affordable costs. The waveform sampling IDE3421 application-specific integrated circuit (ASIC), developed by the University of Michigan and IDEAS for CZT pixel detectors, was adapted to capture the signals from the array's VFG detectors. We showed good spectral performance of the Redlen detectors with an energy resolution of <1% FWHM at 662 keV and slightly poorer performance of the Kromek-eV detectors with a resolution of <2% measured at a reduced temperature of 13 °C. By testing the same detectors as single devices using hybrid charge-sensitive preamplifiers, we demonstrated improved energy resolutions at a normal temperature of ~25°C: <1% and 1.3-1.7%, respectively. However, the Kromek-eV detectors did not perform as well as the Redlen ones. We explained this by the space charge formation (polarization) decreasing the electric field and the electron drift times. The polarization was likely caused by the high injections of holes from the anode contacts. The absence of polarization in Redlen detectors suggested that the quality of the contacts might have played a role in this case.

47 OTHER INSTRUMENTATION↗

X-ray wavefront sensor development at the Advanced Light Source

At Lawrence Berkeley National Laboratory's Advanced Light Source, we are developing x-ray wavefront sensors to support the creation and operation of beamlines with diffraction-limited quality. Our new approach to rapid, intermittent wavefront sensing operates in reflection at glancing incidence angles and is compatible with the high-power densities of modern beamlines. For soft x-ray applications especially, the wavefront sensor can operate upstream of the exit slit in a vertically dispersed beam. This single-shot technique supports lateral shearing interferometry and Hartmann wavefront sensing; it can be adapted to speckle-based techniques as well. The reflected beam is directed to an off-axis YAG crystal that produces scintillated visible light. A small mirror reflects the light to a microscope and camera, and the measured wavefront shape information can be used as feedback to adaptive x-ray mirror elements. A compact array of gratings enables measurement across a broad range of photon energies or wavefront curvatures. We describe recent demonstrations at soft x-ray and hard x-ray wavelengths measuring an adaptive x-ray mirror, and a toroidal focusing mirror.

Goldberg, Kenneth A↗

Viskores: Integrating Parallel Scientific Visualization Research into Applications

Viskores is a scientific visualization library that is the primary deployment of such algorithms to the parallel accelerated processors of modern DOE supercomputers. In this paper, we review the capabilities provided by Viskores and how these capabilities are leveraged by other software in the high-performance computing ecosystem. We discuss the Viskores data representation and pay particular attention to array management. Through this array management we describe how data is adapted between Viskores and other software along with strategies for converting dynamic, polymorphic objects to static representations better suited to GPU processing. We conclude with several examples of Viskores integrating with high-performance software that is used in production today.

Moreland, Ken [ORNL] (ORCID:0000000270513288)↗

A Length Adaptive Algorithm-Hardware Co-design of Transformer on FPGA Through Sparse Attention and Dynamic Pipelining

Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm–hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 × and 2.6 × speedup compared to CPU and GPU implementation, and 4 × higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.

Peng, Hongwu↗

Multi-Functional Distributed Fiber Sensors for Pipeline Monitoring and Methane Detections. Final Report

As an abundant and cheap fossil energy source, natural gas has become a significant energy supply to support the United States’ economy. However, the large-scale extraction and utilization of natural gas also impose significant challenges on methane leakage. This problem is exacerbated by aging gas utility delivery systems, including interstate high-pressure pipelines, storage, and transmission facilities. This project aims to develop a cost-effective fiber optical sensing method that can perform multi-parameter real-time measurements of natural gas pipelines across long interrogation distances up to 100 km with 1-meter spatial resolution. This sensing tool can evaluate overall pipeline efficiency and reduce methane emissions for mid-stream methane infrastructures. To accomplish this objective, research and development efforts funded by this project have resulted in the following accomplishments: This project successfully has developed new functional sensory polymer materials using Metal-Organic Frameworks (MOFs) that can be coated on optical fiber through the reel-to-reel coating process. Functional polymer-coated optical fibers can perform sensitive methane detection through evanescence wave interaction and strain-based measurements to achieve 1% detection sensitivities. The new sensors fibers support both distributed measurements and multiplexed fiber sensors array for multi-point measurements. This project developed and optimized a new multi-core optical fiber that supports simultaneous and distributed measurements of strain and temperatures with 1-meter spatial resolutions across up to 100-km interrogation distance. This new fiber, combined with sensory polymercoated fiber, could perform both distributed temperature and methane detections. This project developed a new artificial intelligence big data algorithm approach that can effectively analyze high-resolution data harnessed by distributed fiber sensors to protect natural gas pipelines against external threats and detect internal defects induced by corrosion. Working with our industry partner, this project developed new optical fibers that support fiber sensor fabrications through polymer coating after the fibers are drawn. These new fibers eliminate the need for direct sensor fabrication when the fiber is fabricated on a fiber draw tower, which drastically expands fiber sensors' applicability. This research project has significantly advanced the distributed fiber sensing technology. It will dramatically increase the applicability and adaptability of distributed fiber sensors for a wide array of applications in energy, sustainability, and environmental science, including structural health monitoring of natural gas pipelines, oil infrastructures, hydrogen facilities, and environmental monitoring of carbon storage sites, water supply systems, and others.

03 NATURAL GAS↗

A novel integrated time-resolved array avalanche photodiode detection system for nuclear resonant scattering measurements

Here, the nuclear resonant scattering (NRS) experiment requires photon-counting detectors with high time resolution, short dead time, large dynamic range, low noise, and large detection area. An 8-channel avalanche photodiode (APD) array detector system with high integrity, flexibility, and reliability has been developed to adapt to the demands of NRS experiments. The detector system mainly consists of four key parts: (i) an array-APD sensor, (ii) 8-channel integrated fast preamplifiers, (iii) the time-to-digital converter readout electronics, and (iv) a data acquisition system and EPICS support software. Remarkably, the system exhibits a time resolution of better than 500 ps and has a sufficiently low noise level, allowing for the lowest detection energy threshold of 4 keV. The performance of the new array-APD system as well as its real application in nuclear forward scattering (NFS) and nuclear resonant inelastic x-ray scattering (NRIXS) experiments was tested in two synchrotron facilities. With the new system, the NFS signal very close to the prompt electronic scattering signal can be extracted. Thanks to the customized EPICS-areaDetector-based control software, NRIXS spectra can be readily measured with time and energy information of the NRIXS signal stored in the raw data, which is promising for developing NRIXS data analysis in the time domain. The array-APD detector can be deployed for nuclear resonant scattering experiments at various synchrotron radiation facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Validation of standardized data formats and tools for ground-level particle-based gamma-ray observatories

Context. Ground-based γ-ray astronomy is still a rather young field of research, with strong historical connections to particle physics. This is why most observations are conducted by experiments with proprietary data and analysis software, as is usual in the particle physics field. However, in recent years, this paradigm has been slowly shifting toward the development and use of open-source data formats and tools, driven by upcoming observatories such as the Cherenkov Telescope Array (CTA). In this context, a community-driven, shared data format (the gamma-astro-data-format, or GADF) and analysis tools such as Gammapy and ctools have been developed. So far, these efforts have been led by the Imaging Atmospheric Cherenkov Telescope community, leaving out other types of ground-based γ-ray instruments. Aims. We aim to show that the data from ground particle arrays, such as the High-Altitude Water Cherenkov (HAWC) observatory, are also compatible with the GADF and can thus be fully analyzed using the related tools, in this case, Gammapy. Methods. We reproduced several published HAWC results using Gammapy and data products compliant with GADF standard. We also illustrate the capabilities of the shared format and tools by producing a joint fit of the Crab spectrum including data from six different γ-ray experiments. Results. We find excellent agreement with the reference results, a powerful confirmation of both the published results and the tools involved. Conclusions. The data from particle detector arrays such as the HAWC observatory can be adapted to the GADF and thus analyzed with Gammapy. A common data format and shared analysis tools allow multi-instrument joint analysis and effective data sharing. To emphasize this, a sample of Crab nebula event lists is made public with this paper. Because of the complementary nature of pointing and wide-field instruments, this synergy will be distinctly beneficial for the joint scientific exploitation of future observatories such as the Southern Wide-field Gamma-ray Observatory and CTA.

79 ASTRONOMY AND ASTROPHYSICS↗

Floating Wind Farm Layout Optimization Considering Moorings and Seabed Variations

This paper presents a method for optimizing the layout of floating wind farms that accounts for realistic seabed variations and the consequent adjustments to the mooring systems required for different turbine positions. The mooring lines of floating wind farms create large spatial constraints that are depth-dependent, since mooring designs must adapt to variations in seabed conditions over the array area. We develop a layout optimization methodology that addresses this, adjusting mooring system designs based on the local seabed characteristics as the layout changes and using steady-state models for the wake effects and mooring lines. The approach includes design algorithms that adjust the anchor positions and line length to achieve the desired mooring line profile for different water depths, and a layout optimization framework that implements spatial constraints between the turbines, mooring lines, and lease area boundaries. Demonstrating the method on several cases shows the effect of the seabed and spatial-constraint factors, as well as their interactions, on the optimal array layout. This demonstration paves the way for scaling up the method, using more powerful optimization algorithms to handle larger farm sizes and situations with more intensely varied seabed conditions.

17 WIND ENERGY↗

Dual transposon sequencing profiles the genetic interaction landscape in bacteria

Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform for assaying the fitness of a comprehensive double mutant pool in parallel. Dual Tn-seq couples random barcode transposon site sequencing with the Cre-lox system, enabling deep sampling of 73% of the 1.3 million possible double gene deletions in Streptococcus pneumoniae. The genetic interactions identified span a wide range of biochemical processes, revealing new factors in presumably well-studied pathways, exemplified by a cytidine triphosphate synthase PyrJ. Moreover, this approach should permit further investigation of growth condition–specific genetic interactions. Because dual Tn-seq does not require the construction of a large array of single mutants, it should be readily adaptable to various microorganisms.

CTP synthesis↗

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗

A Virtual Element Method for the Full MHD system

In this manuscript we present a novel discretization for the incompressible MHD system. Our approach follows the framework of the Virtual Element Method and offers two main advantages. The method can be implemented in unstructured meshes making it highly versatile and capable of handling a wide array of problems involving interfaces, free-boundaries or adaptive refinements on the mesh. The second advantage involves the divergence of the magnetic field, our approach guarantees that it remains solenoidal. We include a theoretical proof of the condition on the magnetic field as well as energy estimates and a well-posedness study. The latter sheds light as to the stability properties of the method.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗

Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina

The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.

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↗

Radio Frequency Field Programable Gate Array Implementation of Reflectometry Cable Monitoring

This document describes the development of a field programable gate array (FPGA) radio frequency system on a chip (RF SoC) adaptation and evaluation of the single-board device to perform both Frequency Domain Reflectometry (FDR) and Spread Spectrum Time Domain Reflectometry (SSTDR) for offline and online cable testing. The work builds on and leverages the work of Pacific Northwest National Laboratory (PNNL) in airport millimeter wave technology by using the same development hardware employed in that program. The work is performed under sponsorship from the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) program and the task objective is to confirm and demonstrate feasibility to adapt FPGA technology for a cost-effective multiplexed single-board electronic module to perform cable tests that are equivalent to commercial and laboratory test instruments for FDR and SSTDR cable tests. The developed 2-channel (extendable to 7 channels) system was compared to dedicated and proven test instruments and shown to produce equivalent results on a range of cables and with a range of damage types. The FPGA reflectometry test board is one of several technologies that could facilitate implementation of online monitoring of safety critical cable systems.

42 ENGINEERING↗

Reference floating wind array designs for three representative regions

This work presents the systematic development of three open-source reference floating wind array designs. The designs are tailored to representative site conditions for three regions of the United States: Humboldt Bay off the coast of California, the Gulf of Maine, and the Gulf of America. We adopted existing reference designs for the individual 15 MW turbines, semisubmersible floating platforms, substations, mooring systems, and power cables – integrating and adapting them as needed for each location. We adapted existing dynamic cable designs to use larger conductor sizes to meet the arrays' power transmission requirements, and we set up redundant mooring systems for each substation. The layout of each array is a uniform-grid design optimized to approximately minimize the levelized cost of energy (LCOE) within a square lease area while satisfying spatial constraints. These constraints ensure adequate clearances between adjacent turbines and between underwater components during the layout optimization to prevent clashing and ensure that all components reside within the lease boundaries. Substations are included to allow accounting for intra-array cable costs. They are placed within the uniform grid to maintain the navigability of the arrays. For each feasible layout considered, annual energy production and cable routing costs are calculated and updated in the LCOE objective function. After the optimization, we refined the cable routing with a mix of algorithmic and manual methods to ensure that the cables avoid mooring system components and approach the substation with adequate clearances. We confirmed the suitability of each reference array's layout by comparing the wake losses at each wind heading angle to the wind rose, observing that the optimized layouts largely avoid wake losses in the predominant wind directions. These reference arrays provide open-source baseline designs to enable future research and innovation of floating wind technology at the array scale.

17 WIND ENERGY↗

Modeling Wind in Agrivoltaics and its Impact on Eddy Covariance Flux Measurements

Silicon Ranch is conducting a research study at their 138MW Bancroft Station agrivoltaics site, the largest agrivoltaics research array in the US, in which they are using an eddy covariance flux tower to measure the carbon budget. They are interested in finding out if the presence of the panels changes the effectiveness of these measurements. To investigate this topic, NLR performed numerical simulations of wind through the agrivoltaic array to identify under what environmental conditions (wind speed, wind direction, temperatures) and panel tilt angles the mean wind speeds at the measurement heights are significantly altered by the presence of the solar panels. NLR adapted and used the PVade simulation tool [1] to model wind in Silicon Ranch's agrivoltaic array and found that at the height of the flux tower (6m), the wind speed measured is not significantly altered by the presence of solar panels. The percent difference is less than 4% and is generally greatest during daytime conditions at higher wind speeds and perpendicular wind direction. Closer to the ground, the flow is significantly altered (wind speeds are reduced) by the presence of solar panels and the percent difference increases in strong winds. The work confirmed that eddy covariance flux towers can be used within the context of a solar array field.

14 SOLAR ENERGY↗

Blue Rock CropSpanPV - Low Cost Racking for Agricultural Solar Photovoltaics

In this work, a total of four solar panel layouts, applied to Agrivoltaics, are investigated. This study presents two hypotheses: 1. Prefabrication - Lower total cost can be achieved by constructing a pre-assembled, pre-wired solar array in a factory, with automation, then rapidly deploying it in the field. 2. Tension Structures - Using tension structures in a way to suspend an overhead solar array also reduces costs when compared to conventional support methods. Designs are presented for frames to hold the panels. Configurations are advanced to connect the frames into arrays. Supports and foundations to hold the arrays in the desired layout are calculated, selected and presented. Cost models are prepared for the four layouts, which include definition of the business enterprise, the manufacturing operation, and the required facility for production at scale. Cost models include, detail material and task/labor take-offs for both manufacturing and installation. Comparisons with conventional system adapted to Agrivoltaics reveal that the two hypotheses do not hold true. A prefabricated array requires additional material that is not needed in the base system and the cost of this additional material is not outweighed by the cost savings of reduced field installation. The cost of wire rope for a tension structure does result in an economy of material, however, the cost of end connections and tensioning devices adds significantly to the cost of the overall tension structure. Foundation loads with tension structures, especially the large wind uplift seen with a fixed tilt solar array, impose significant constraints and high costs. The following conclusions are recommended for further consideration: 1. Best Case Agrivoltaic Configuration - The best value/lowest cost configuration for agrivoltaics is the installation of solar panels mounted on a single axis tracker in either a 2-in-portrait or 2-in landscape arrangement. This is useful for grazing lands and for staple crops which require high light levels. These applications represent the vast majority of the potential agrivoltaic market. Important elements in this configuration are the specific geometric layout coordinated with the various field operations and a control system linked between the farm equipment and single axis tracker. The control system is to monitor location and orientation, then actively tilt the solar panels or brake the field equipment to provide clearance and avoid collisions. 2. Long Span Applications - The use of tension structures for an overhead fixed tilt array is beneficial where long spans are a necessity, especially where the base support in the project location has consolidated rock near the surface or some other solid structure. One application is spanning wide irrigation canals. Another may be as an installation at the top deck of parking structures. 3. Direct Ground Mount Configuration – Having skids at the base of a pre-fabricated array that extend when the array is deployed, could be a successful design. This could be a useful strategy for dense, flat, ground-mount configurations like that employed by a couple of successful commercial operations (5G Maverick and Erthos). Arrays would be orientated north and south, deployed very low on prepared grade. Arrays would be aligned closely next to each other and anchored with small ground screws or simply with ballast. This same product arrangement could be very useful for rapid deployment and set-up of solar arrays for temporary deployments, disaster response and the military operations

14 SOLAR ENERGY↗