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At least 325 records · Page 18

In‐depth comparative analysis of Illumina ® MiSeq run metrics: Development of a wet‐lab quality assessment tool

Abstract Whole genome sequencing of bacterial isolates has become a daily task in many laboratories, generating incredible amounts of data. However, data acquisition is not an end in itself; the goal is to acquire high‐quality data useful for understanding genetic relationships. Having a method that could rapidly determine which of the many available run metrics are the most important indicators of overall run quality and having a way to monitor these during a given sequencing run would be extremely helpful to this effect. Therefore, we compared various run metrics across 486 MiSeq runs, from five different machines. By performing a statistical analysis using principal components analysis and a K ‐means clustering algorithm of the metrics, we were able to validate metric comparisons among instruments, allowing for the development of a predictive algorithm, which permits one to observe whether a given MiSeq run has performed adequately. This algorithm is available in an Excel spreadsheet: that is, MiSeq Instrument & Run (In‐Run) Forecast. Our tool can help verify that the quantity/quality of the generated sequencing data consistently meets or exceeds recommended manufacturer expectations. Patterns of deviation from those expectations can be used to assess potential run problems and plan preventative maintenance, which can save valuable time and funding resources.

Kastanis, George John↗

Phase I (Final Report)

The focus of this proposal was the development of a new instrument capable of in-situ, spatially resolved, measurement of the energy spectra of ions in the edge of a tokamak plasma. The energy spectra of the ions determines the rates of sputtering and erosion of the plasma facing surfaces. The ion spectra in the edge is not easily determined spectroscopically and must be measured in situ since the ions are confined by the strong magnetic fields of the tokamak. Conventional energy analyzers are too large and expensive to install in multiple locations around the tokamak torus. The probes to be developed in this project are compact, low cost, and small enough to be placed inside of specially prepared wall tiles – essentially creating a “smart” plasma facing surface in a tokamak. Phase 1 of this project successfully demonstrated that two key elements of the instrument, the collimator and the energy analyzer, could be fabricated on a single silicon wafer and the combination functioned as designed when tested with an electron beam.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Development and characterization of a laser-gated, high resolution x-ray radiography platform for high energy density experiments using toroidally bent crystals

Bent crystal x-ray imagers are a well-established diagnostic tool to study high energy density (HED) objects by acquiring two-dimensional x-ray radiographs. Often, studying these HED objects requires very high spatial resolution, which is limited by astigmatism when using spherically bent crystals. By using toroidal-shaped crystals instead, astigmatism can be reduced and the overall spatial resolution of the instrument improved. Here, the development and characterization of a laser-gated x-ray radiography platform at the National Ignition Facility using a toroidal crystal is presented. This includes measurements of the spatial and temporal profile, which is determined by the x-ray source. In conclusion, to properly validate the reduced astigmatism, a new multi-plane grid approach was implemented, which, for the first time, allows a depth of field measurement, alignment verification and x-ray source size estimate in a single shot, demonstrating the current platform’s capability to provide sub-10 μm resolution over a 0.9 mm depth of field with a temporal resolution of 110 ps.

Crystal optics↗

Preparing for the Next Generation of EUV Lithography at the Center for X-ray Optics

The introduction of EUV lithography into high-volume semiconductor manufacturing this year represents a monumental milestone for EUV technology. After nearly 30 years of development, the EUV research community has overcome many of the key obstacles required to enable the long-awaited integration of EUV lithography into the lab. These obstacles have included: the development of a stable, high-powered EUV source to ensure adequate exposure tool reliability; controlling EUV mask defects and mask contamination; and the development of EUV resists with adequate sensitivity, resolution, and line width roughness to meet the tolerances required for high-volume manufacturing. As EUV moves into its second generation, there will be new challenges facing the community as it works to push EUV technology into the future. Smaller feature sizes will be achieved using higher numerical aperture optics, which are planned to have an anamorphic geometry (asymmetric magnification and numerical aperture between horizontal and vertical axes) to overcome 3D effects at the mask. This new geometry and its larger angle ranges make understanding mask absorber and multilayer effects all the more important. New methods for high-NA wavefront metrology need to be tested to ensure that these optical systems can be aligned to operate with minimal aberrations. Mask defects need to continue to be studied, and the inclusion of EUV pellicles in the roadmap requires that mask inspection and review systems adapt accordingly. Finally, new resists must be developed to support the increased resolution of feature sizes below 8 nm half pitch. The Center for X-ray Optics (CXRO) at Berkeley Lab has been a leader in EUV research for the past 25 years. Leveraging 13.5 nm EUV light from the Advanced Light Source synchrotron facility, CXRO is home to several EUV and soft X-ray (SXR) research tools that have provided important insights into EUV resists, masks, and coatings. The 0.3 NA Microfield exposure tool (MET) and Dose Calibration Tool (DCT) have played an instrumental role in the development of the current generation of high-resolution EUV resists. The Actinic Inspection Tool (AIT) and its successor, SHARP, have enabled aerial image analysis, providing key insights into mask defects, 3D mask effects, illumination, and aberrations. And the CXRO Reflectometer continues to be the industry standard in multilayer coating and EUV mask scattering metrology. To address the new challenges facing the next generation of EUV lithography, CXRO has upgraded its suite of EUV research tools. The 0.5 NA MET5 is a newly commissioned projection lithography tool that is capable of printing feature sizes down to 8 nm half pitch. A new radiation chemistry program is deploying several techniques aimed at dissecting the role of primary photoelectrons and secondary electrons in EUV resists. The SHARP microscope has been outfitted with anamorphic zone plate lenses that can emulate the geometry of next-generation EUV scanners, and the reflectometer has been applied to new scattering experiments for the purpose of understanding the 3D effects of EUV mask multilayers, as well as determining mask properties using scattering profiles. In parallel with these tools, the CXRO High-NA Wavefront Sensing Program is developing high-resolution wavefront sensors suitable for measuring aberrations at high NA. This article presents an overview of these programs and describes how they will address the primary challenges that face the EUV community as it moves to the next generation of EUV lithography.

47 OTHER INSTRUMENTATION↗

Mesoscale to Molecules: Bioimaging Science Program, Principal Investigator (PI) Meeting, February 28–March 1, 2018, Gaithersburg, Maryland

The Mesoscale to Molecules Bioimaging Science Program (Bioimaging Program), within the Department of Energy’s (DOE) Office of Biological and Environmental Research (BER), sponsors research at national laboratories and universities that addresses grand challenges for biology. These projects are centered on developing a better understanding of the spatial and temporal distributions of key metabolites and biomarkers associated with microbial and plant systems related to bioenergy and environmental systems. The Bioimaging Program is developing new and improved instruments, which are being designed and constructed from the ground up, adapted from other scientific disciplines, or upgraded with new capabilities to create a comprehensive and versatile toolbox for imaging biological dynamics and chemistry. These approaches involve (1) hypothesis-based approaches focused on solving particular problems for plant biology, biofuels, and biogeochemistry and (2) broad-based systems and design-based technologies that can lead to new discoveries. Scientists developing both approaches keep in mind that versatility, transferability, and portability will help foster widespread adoption by the larger science community for future field and laboratory studies.

09 BIOMASS FUELS↗

Design of Instrumentation for Noble Gas Transport in LSTL Needed for Model Development

Development of molten salt reactors (MSRs) requires consideration of several physical phenomena that are different from the light water reactor (LWR) experience. While small-scale tests have been performed to understand the behavior of molten salts, the scale-up to larger experiments is an important step in the development of MSR designs. These small-scale experiments have given information on the thermodynamic state of the heat transport fluid and its constituents, thermophysical properties, convective flow, and corrosion. As detailed models have been developed, using these models to simulate larger scale experiments must incorporate physics that becomes important during scale-up, temperature inhomogeneities, complex flow behavior, and two-phase flow. The purpose of the work package has been to link experimental and modeling efforts in the support of licensing development to design and evaluate technologies to mitigate radionuclide release from MSRs. There were two main activities in this work package—one investigating fission product transport into the cover gas and the other on fission gas transport in the molten salt.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Neutron detector development for high-rate neutron reflectometry at the Second Target Station of Oak Ridge National Laboratory

The Second Target Station (STS) at the Oak Ridge National Laboratory Spallation Neutron Source (SNS) is expected to produce a neutron source that is the brightest in the world, having a significantly higher peak brightness compared to the First Target Station (FTS), where the reflectometry instruments already fall short of being able to handle the highest available flux by a factor of ~100. The neutron reflectometers at the SNS FTS are not suitable for the reflectometers planned for the SNS STS because of its unprecedentedly high peak brightness and the already limited capabilities of these instruments at high count rates. Furthermore, the high rate instruments that are now under development are expected to underperform with regard to gamma sensitivity, meaning that signal-to-noise will be reduced and they will be unable to measure weaker reflectance phenomena in the presence of the significant prompt gamma flash at SNS. To address these challenges, we conducted research to advances associated instruments, techniques, and capabilities for the SNS STS reflectometers. More specifically, we investigated the development of a scalable, 2-D positive-sensitive, pixelated, scintillator-based neutron detector module based on a newly developed scintillator. The work has potential for impact on future neutron reflectometry instruments and neutron science performed at the SNS STS. In particular, the improved background rejection capability of the developed detector could extend the available experimental dynamic Q range, allowing it to measure weak reflectance phenomena.

reflectometry, radiation instrumentation, neutron ↗

Advanced Sensors and Instrumentation Issue 10

The Advanced Sensors and Instrumentation (ASI) program, on its seventh fiscal year, continues to address key technology gaps for future nuclear energy systems. ASI’s goal is to enable the advanced instrumentation and control (I&C) technologies essential to the Office of Nuclear Energy’s research and development (R&D) efforts needed to realize its mission goals. Information on our projects can be found in our ASI annual awards summaries, annual review webinars, and newsletters posted in the Office of Nuclear Energy website (energy.gov/ne). This year, we have initiated three newly awarded projects in the area of data analytics. We also initiated a project to develop and demonstrate a prototype passive wireless sensor network. This sensor will use advanced manufacturing and printing, and be tested and demonstrated at a U.S. nuclear power plant facility. In addition, we are developing a sensor database to capture advanced sensor and instrumentation technology that is applicable to nuclear power plants. Under the In-Pile Instrumentation program, we continue to develop unique in-pile sensors and instrumentation to provide real-time, accurate, and spatially resolved information regarding the performance of fuels and materials. Due to the closure of the Halden reactor, we are focusing our near-term research in providing equivalent capability for the instrumentation of irradiation experiments in the U.S. that are needed by the nuclear industry. As the ASI program continues to award projects through competitive solicitations, we encourage the I&C community to visit our website for current funding opportunity announcements, especially for the industry-focused solicitation entitled, “U.S. Industry Opportunities for Advanced Nuclear Technology Development.”

99 GENERAL AND MISCELLANEOUS↗

Development of an L-Edge X-ray Absorbance Spectrometer for Monitoring Dissolver Solutions in H-Canyon

Savannah River National Laboratory has developed a monitor to measure plutonium and uranium concentrations in solutions of dissolved nuclear fuel. The monitor will be installed in the sample aisle location for the 6.3D Dissolver in the Savannah River Site’s H-Canyon and used in support of the electrolytic dissolution such as Fast Critical Assembly fuel. The monitor is based on the atomic absorbance of x-rays. Elements are differentiated by the appearance of absorbance features at specific energies of the x-ray spectrum that correspond to L-edge transitions of inner core electrons. Hence, the technique is called L-Edge X-Ray Absorbance Spectroscopy (L-XRAS). The technique is suitable for nuclear fuel processing due to its relative insensitivity to other components of the dissolver solution, such as nitric acid, transition metals (Fe, Cr, Ni, Mn) such as those from stainless steel, particulates, and catalysts and additives. The instrumentation consists of a commercially available x-ray source and detector, a sample cell designed to interface with the airlift sampler associated with H-Canyon Tank 6.3D, and a stainless steel enclosure. SRNL wrote instrument control software and developed chemometric models to interpret x-ray intensity spectra and estimate analyte concentrations and uncertainties in real time.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The HETDEX Instrumentation: Hobby–Eberly Telescope Wide-field Upgrade and VIRUS

The Hobby–Eberly Telescope (HET) Dark Energy Experiment (HETDEX) is undertaking a blind wide-field low-resolution spectroscopic survey of 540 deg 2 of sky to identify and derive redshifts for a million Ly α -emitting galaxies in the redshift range 1.9 < z < 3.5. The ultimate goal is to measure the expansion rate of the universe at this epoch, to sharply constrain cosmological parameters and thus the nature of dark energy. A major multiyear Wide-Field Upgrade (WFU) of the HET was completed in 2016 that substantially increased the field of view to 22' diameter and the pupil to 10 m, by replacing the optical corrector, tracker, and Prime Focus Instrument Package and by developing a new telescope control system. The new, wide-field HET now feeds the Visible Integral-field Replicable Unit Spectrograph (VIRUS), a new low-resolution integral-field spectrograph (LRS2), and the Habitable Zone Planet Finder, a precision near-infrared radial velocity spectrograph. VIRUS consists of 156 identical spectrographs fed by almost 35,000 fibers in 78 integral-field units arrayed at the focus of the upgraded HET. VIRUS operates in a bandpass of 3500–5500 Å with resolving power R ≃ 800. VIRUS is the first example of large-scale replication applied to instrumentation in optical astronomy to achieve spectroscopic surveys of very large areas of sky. This paper presents technical details of the HET WFU and VIRUS, as flowed down from the HETDEX science requirements, along with experience from commissioning this major telescope upgrade and the innovative instrumentation suite for HETDEX.

79 ASTRONOMY AND ASTROPHYSICS↗

Advancing Cross-Disciplinary Understanding of Land-Atmosphere Interactions

The evolution of disciplinary silos and increasingly narrow disciplinary boundaries have together resulted in one-sided approaches to the study of land-atmosphere interactions—a field that requires a bi-directional approach to understand the complex feedbacks and interactions that occur. The integration of surface flux and atmospheric boundary layer measurements is therefore essential to advancing our understanding. The Land-Atmosphere 2021 workshop (held virtually, June 10-11, 2021) involved almost 300 participants from around the world and promoted cross-discipline collaboration by way of talks from invited speakers, moderated discussions, breakout sessions, and a virtual poster session. The workshop focused on five main theme areas: “big picture” overview, instrumentation and remote sensing, modeling, water, and aerosols and clouds. In talks and breakout groups, there were frequent calls for more AmeriFlux sites to be instrumented for boundary layer height measurements, and for the development of some “super sites” where profiling instruments would be deployed. There was further agreement on the need for the standardization of various datasets. There was also a consensus that funding agencies need to be willing to support the sorts of large projects (including associated instrumentation) which can drive interdisciplinary work. Early-career scientists, in particular, expressed enthusiasm for working across disciplinary boundaries but noted that there need to be more financial support and training opportunities so they would be better prepared for interdisciplinary work. Investment in these career development opportunities would enable today's cohort of early-career scientists to advance the frontiers of interdisciplinary work over the next couple of decades.

54 ENVIRONMENTAL SCIENCES↗

Adapting Online Fiber Optic Colorimeter Systems for Process Measurements in H Canyon

A filter-based photometric analyzer, commonly referred to as a colorimeter, is an important instrument for monitoring uranium concentrations for nuclear safety control in SRS's H-Canyon facility. These instruments are effective but technologically out of date, and the facility does not have spare instruments on hand. Newly developed spectrophotometers will replace them and be capable of more accurate and reliable performance than the current colorimeters. However, the installation of the spectrophotometers will take some time. To make sure that the H-Canyon facility can continue processing operations and reduce the risk of a colorimeter going out of service, spare colorimeters previously configured for Pu monitoring in HB-Line will be reconfigured and calibrated for uranium. These spare colorimeters are readily available and their operating procedures are already known to the H-Canyon facility. This reconfiguration is an efficient and cost-effective means to meet a facility need. Both instruments have a linear response and accurately measure U over the range of concentrations expected in the H Canyon process. The instruments are functionally identical and can be used interchangeably. Changes of acidity within the expected process range will not introduce a bias in the measurement. Higher acidity solutions result in a positive bias, but this is conservative with respect to maintaining nuclear safety.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The ARENA Test Bed – A Versatile Resource for I&C Development and Validation

The Accelerated and Real-time Experimental Nodal Assessment (ARENA) Test Bed at the Pacific Northwest National Laboratory (PNNL) is a versatile resource for development and validation of instrumentation and control (I&C) technologies. This capability was created to facilitate in-situ testing of nuclear electrical cables in various simulated operational environments. Using cable trays, a control box, and selected test components, low voltage cables can be staged to experience local adverse environments such as elevated temperature and water immersion. Cable condition can be continuously monitored over time to track the effect of local stresses using nondestructive assessment tools. A heads-up display (ARENA TV) plots key data in real-time for users. The ARENA Test Bed has recently been used to evaluate the potential for spread spectrum time domain reflectometry (SSTDR) to monitor thermal aging of a portion of live cable powering a three-phase motor. The arrangement provided the opportunity to directly compare the performance of the novel online SSTDR method with offline results from the more standard frequency domain reflectometry (FDR) method. The ability of SSTDR and FDR to identify the presence of water in immersed shielded and unshielded cables and to detect ground faults was also assessed. A digital twin is being developed to track and predict FDR signals from a thermally aging conceptual cable region to compare with measured signals from the ARENA physical counterpart. The test bed concept addresses an important need in nuclear I&C monitoring tool development. New tools and techniques can be developed in the test bed and validated versus known methods and physical measurements. Digital twins and machine learning engines can be populated with measured data in a controlled environment that would not be readily available in the actual nuclear power plant. Proposed monitoring strategies can be confirmed for effectiveness through objective evaluation. It is anticipated that the PNNL ARENA Test Bed will be a valuable resource in advancing nuclear plant instrumentation.

nuclear electrical cables, ARENA Test Bed, conditi↗

Diagnosing and Correcting Mass Accuracy and Signal Intensity Error Due to Initial Ion Position Variations in a MALDI TOFMS

Frustrated by worse than expected error for both peak area and time-of-flight (TOF) in matrix assisted laser desorption ionization (MALDI) experiments using samples prepared by electrospray deposition, it was finally determined that there was a correlation between sample location on the target plate and the measured TOF/peak area. Variations in both TOF and peak area were found to be due to small differences in the initial position of ions formed in the source region of the TOF mass spectrometer. These differences arise largely from misalignment of the instrument sample stage, with a smaller contribution arising from the non-ideal shape of the target plates used. By physically measuring the target plates used and comparing TOF data collected from three different instruments, an estimate of the magnitude and direction of the sample stage misalignment was determined for each of the instruments. A correction method was developed to correct the TOFs and peak areas obtained for a given combination of target plate and instrument. Two correction factors are determined, one by initially collecting spectra from each sample position used and another by using spectra from a single position for each set of samples on a target plate. For TOF and mass values, use of the correction factor reduced the error by a factor of 4, with the relative standard deviation (RSD) of the corrected masses being reduced to 12-24 ppm. For the peak areas, the RSD was reduced from 28% to 16% for samples deposited twice onto two target plates over two days. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Electron transport in gaseous detectors with a Python-based Monte Carlo simulation code

Understanding electron drift and diffusion in gases and gas mixtures is a topic of central importance for the development of modern particle detection instrumentation. The industry-standard MagBoltz code has become an invaluable tool during its 20 years of development, providing capability to solve for electron transport (‘swarm’) properties based on a growing encyclopedia of built-in collision cross sections. We have made a refactorization of this code from FORTRAN into Cython, and studied a range of gas mixtures of interest in high energy and nuclear physics. The results from the new open source PyBoltz package match the outputs from the original MagBoltz code, with comparable simulation speed. An extension to the capabilities of the original code is demonstrated, in implementation of a new Modified Effective Range Theory interface. We hope that the versatility afforded by the new Python code-base will encourage continued use and development of the MagBoltz tools by the particle physics community.

97 MATHEMATICS AND COMPUTING↗

Smart Contract Architectures and Templates for Blockchain-based Energy Markets (V.1.0)

Within the field of Transactive Energy Systems (TES), there is an active need for tools that can support and accelerate the development of these new grid solutions. Among the many tools available, blockchain stands out as a viable instrument that can help researchers develop decentralized, autonomous, and tamper-resistant grid applications. In this work, we explore the use of smart contracts (SCs), a subset of blockchain technology, and analyze their applicability to facilitating the implementation of TES solutions. In particular, we focus on presenting areas of opportunity and potential drawbacks, along with use cases that can benefit from this technology building upon previous research developed by Pacific Northwest National Laboratory and other research organizations. This work builds upon the fundamentals of TES and smart contract technology to develop a series of software templates that can be used by industry to build TES-oriented grid solutions. These templates are intended to be platform agnostic and take into consideration the unique properties of SCs and distributed ledger storage mechanisms to ensure actual code implementations remain aware of the limitations of the technology. The proposed templates have the potential to enable software architects to mix and match components to satisfy their application requirements, thereby reducing the number of resources required to implement blockchain-based solutions. These templates are divided into two main components—data and behavioral models. The data models are intended to help software engineers represent the underlying grid objects along with their properties in a ledger-based storage system. The behavioral models are used to describe the processes and actions that actors within a system must perform to achieve a given outcome such as registering an asset, placing a bid, and performing bid clearances. These two components are documented in a Unified Modeling Language (UML) format and are intended for use in SC-based implementations, with special behavioral considerations to account for the asynchronous properties of the underlying ledger and the typical execution model of smart contracts. Finally, future research ideas and potential extensions to this work are discussed. In particular, known limitations and potential improvements of the developed product are identified and expected to be addressed in future revisions of the template model.

24 POWER TRANSMISSION AND DISTRIBUTION↗

HEP Software Foundation Community White Paper Working Group - Data Analysis and Interpretation

At the heart of experimental high energy physics (HEP) is the development of facilities and instrumentation that provide sensitivity to new phenomena. Our understanding of nature at its most fundamental level is advanced through the analysis and interpretation of data from sophisticated detectors in HEP experiments. The goal of data analysis systems is to realize the maximum possible scientific potential of the data within the constraints of computing and human resources in the least time. To achieve this goal, future analysis systems should empower physicists to access the data with a high level of interactivity, reproducibility and throughput capability. As part of the HEP Software Foundation Community White Paper process, a working group on Data Analysis and Interpretation was formed to assess the challenges and opportunities in HEP data analysis and develop a roadmap for activities in this area over the next decade. In this report, the key findings and recommendations of the Data Analysis and Interpretation Working Group are presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Extending water vapor measurement capability of photon-limited differential absorption lidars through simultaneous denoising and inversion

Abstract. The micropulse differential absorption lidar (MPD) was developed at Montana State University (MSU) and the National Center for Atmospheric Research (NCAR) to perform range-resolved water vapor (WV) measurements using low-power lasers and photon-counting detectors. The MPD has proven to produce accurate WV measurements up to 6 km altitude. However, the MPD's ability to produce accurate higher-altitude WV measurements is impeded by the current standard differential absorption lidar (DIAL) retrieval methods. These methods are built upon a fundamental methodology that algebraically solves for the WV using the MPD forward models and noisy observations, which exacerbates any random noise in the lidar observations. The work in this paper introduces the adapted Poisson total variation (PTV) specifically for the MPD instrument. PTV was originally developed for a ground-based high spectral resolution lidar, and this paper reports on the adaptations that were required in order to apply PTV on MPD WV observations. The adapted PTV method, coined PTV-MPD, extends the maximum altitude of the MPD from 6 to 8 km and substantially increases the accuracy of the WV retrievals starting above 2 km. PTV-MPD achieves the improvement by simultaneously denoising the MPD noisy observations and inferring the WV by separating the random noise from the non-random WV. An analysis with 130 radiosonde (RS) comparisons shows that the relative root-mean-square difference (RRMSE) of WV measurements between RS and PTV-MPD exceeds 100 % between 6 and 8 km, whereas the RRMSE between RS and the standard method exceeds 100 % near 3 km. In addition, we show that by employing PTV-MPD, the MPD is able to extend its useful range of WV estimates beyond that of the ARM Southern Great Plains Raman lidar (RRMSE exceeding 100 % between 3 and 4 km); the Raman lidar has a power-aperture product 500 times greater than that of the MPD.

54 ENVIRONMENTAL SCIENCES↗