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At least 613 records · Page 34

2024 Workshop - Remote Sensing and Fluxes Upscaling for Real-world Impact - Tutorial v1

The software-tutorial was developed within the 2024 Remote Sensing and Fluxes Upscaling for Real-world Impact workshop as part of the hands-on session. The workshop was supported by AmeriFlux, National Ecological Observatory Network (NEON) and CarbonDew. The software provides basic tools to perform the following tasks: - gather remote sensing images using Google Earth Engine API; - gather flux data; - perform basic functions, such as plotting time-series, perform QA of the data, compute vegetation indices; - perform correlation analysis between flux data and remote sensing data; - perform flux predictions based on remote sensing data integrated in different modalities.

Falco, Nicola [Lawrence Berkeley National Laborato↗

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING↗

Analysis and Grading of the Test Performance of PS Modules for the CMS Phase-II Outer Tracker Upgrade

The Outer Tracker detector of the Compact Muon Solenoid (CMS) experiment provides information about the trajectory of charged particles produced in proton-proton collisions at the Large Hadron Collider (LHC). During the High Luminosity LHC upgrade, scheduled for the late 2020s, the Outer Tracker will be replaced with new modules capable of transmitting data to the L1 Trigger. These modules are being assembled at several facilities around the world, including Fermilab, necessitating coordinated standards of module quality. Here I discuss the development of POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a C++ software which provides a standardized procedure for analyzing and grading test results of the Outer Tracker modules. The particular focus of this paper is on the analysis and grading of the PS (pixel-strip) modules in POTATO.

43 PARTICLE ACCELERATORS↗

Data from: "Warming and the dependence of limber pine (Pinus flexilis) establishment on summer soil moisture within and above its current elevation range"

This data package contains data that were used for analysis in “Warming and the dependence of limber pine (Pinus flexilis) establishment on summer soil moisture within and above its current elevation range”, by Moyes et al. 2013. All data collection and field research were completed on Niwot Ridge, Colorado, USA.This data package contains nine comma-separated-values (.csv) files, one text (.txt) file, and two zipped seedling folders that were used for leaf area analysis. One zipped folder contains 468 .jpg photographs of seedlings, and the second contains 468 corresponding Image J-processed .jpg images that include silhouette leaf area values. .csv and .txt files can be opened using any compatible simple text-editor software such as TextEdit (Mac) and Notepad (Windows); .csv’s can also be opened using R and Microsoft Excel. Image files can be opened using Preview (Mac) and Photos (Windows). In addition, there are a total of 31 Microsoft Excel files: three .xlsx files, and 28 raw Li-Cor output .xls files. This data user’s guide is available in .pdf format, and can be opened using Adobe Acrobat Reader, or any other compatible file viewing software. Geospatial data showing field site locations are also included in the archive for use and reference. There are two geospatial formats in this archive: ESRI shapefiles (.shp) and keyhole markup-language (.kml) files. Both file types contain bounding box information, with the former being polygons, and the latter containing corner coordinates for each site. ESRI shapefiles can be opened using any geospatial software compatible with the file type (such as ESRI’s ArcGIS suite and QGIS), and .kml files are compatible with Google Earth and Google Maps.--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Continued changes in climate are projected to alter the geographic distributions of plant species, in part by affecting where individuals can establish from seed. We tested the hypothesis that warming promotes uphill redistribution of subalpine tree populations by reducing cold limitation at high elevation and enhancing drought stress at low elevation. We seeded limber pine (Pinus flexilis) into plots with combinations of infrared heating and water addition treatments, at sites positioned in lower subalpine forest, the treeline ecotone, and alpine tundra. In 2010, first-year seedlings were assessed for physiological performance and survival over the snow-free growing season. Seedlings emerged in midsummer, about 5–8 weeks after snowmelt. Low temperature was not observed to limit seedling photosynthesis or respiration between emergence and October, and thus experimental warming did not appear to reduce cold limitation at high elevation. Instead, gas exchange and water potential from all sites indicated a prevailing effect of summer moisture stress on photosynthesis and carbon balance. Infrared heaters raised soil growing degree days (base 5 °C, p < 0.001) and August–September mean soil temperature (p < 0.001). Despite marked differences in vegetation cover and meteorological conditions across sites, volumetric soil moisture content (θ) at 5–10 cm below 0.16 and 0.08 m^3 m^(−3) consistently corresponded with moderate and severe indications of drought stress in midday stem water potential, stomatal conductance, photosynthesis, and respiration. Seedling survival was greater in watered plots than in heated plots (p = 0.01), and negatively related to soil growing degree days and duration of exposure to θ < 0.08 m^3 m^(−3) in a stepwise linear regression model (p < 0.0001). We concluded that seasonal moisture stress and high soil surface temperature imposed a strong limitation to limber pine seedling establishment across a broad elevation gradient, including at treeline, and that these limitations are likely to be enhanced by further climate warming.--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Maintenance log:Amended file name error in Data User's Guide May 19 2022

54 ENVIRONMENTAL SCIENCES↗

Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices

Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation, and gene location. Performance and scalability of protein similarity search have proven to be a bottleneck in many bioinformatics pipelines due to increase in cheap and abundant sequencing data. This work presents a new distributed-memory software PASTIS. PASTIS relies on sparse matrix computations for efficient identification of possibly similar proteins. We use distributed sparse matrices for scalability and show that the sparse matrix infrastructure is a great fit for protein similarity search when coupled with a fully-distributed dictionary of sequences that allow remote sequence requests to be fulfilled. Our algorithm incorporates the unique bias in amino acid sequence substitution in search without altering basic sparse matrix model, and in turn, achieves ideal scaling up to millions of protein sequences.

97 MATHEMATICS AND COMPUTING↗

The Neurodata Without Borders ecosystem for neurophysiological data science

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB’s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

59 BASIC BIOLOGICAL SCIENCES↗

BISON TRISO Modeling Advancements and Validation to AGR-1 Data

BISON is a finite element-based nuclear fuel performance code. Among its unique characteristics are its ability to model 1D, 2D, and 3D geometries and its applicability to a wide variety of nuclear fuels. For the last eight years, BISON has included a beginning capability to model tri-structural isotropic (TRISO) fuel. Recently, interest in TRISO fuel has grown, and a significant effort has been made to improve BISON’s capabilities in this area. Capability development has occurred for each material present in TRISO fuel particles: the buffer, inner pyrolytic carbon, silicon carbide, and outer pyrolytic carbon layers, as well as the fuel kernel. New elastic, creep, swelling, thermal expansion, thermal conductivity, and fission gas release (FGR) models are available. New models for the graphite matrix are also now available. Another important addition is the ability to perform statistical failure analysis of large samples of fuel particles. This new capability, which continues to grow, enables evaluation of failure due to pressure or crack formation by analyzing many thousands of particles. This enables realistic calculations of fission product release from the many particles in a TRISO-fueled reactor. These capabilities were checked via regression and verification tests. A large number of code benchmarking problems were also run, showing that BISON’s results closely match those of other software tools. Finally, a significant validation effort was completed in which fission product release, measured as part of the AGR-1 capsule experiments, was compared to BISON outputs. BISON outputs compared very well to the experimental data and to PARFUME results. Interest in BISON’s TRISO capabilities is growing, with the U.S. Nuclear Regulatory Commission (NRC) and Westinghouse Electric Company receiving training during the past year. Multiple other entities have expressed interest in or are actively using BISON. Kairos Power, LLC, has a strong partnership with Idaho National Laboratory (INL) regarding the use of BISON for TRISO analysis. While its capabilities still continue to grow, BISON has already become a powerful tool for TRISO analysis.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Double-differential Measurements of Mesonless Charged-current Muon Neutrino Interactions on Argon with Final-State Protons using the MicroBooNE Detector

This note reports the first double-differential measurements of charged-current $ν_µ$ scattering on argon leading to final states containing zero mesons and one or more protons. This event topology (hereafter abbreviated as CC0$πNp$) is the most common at the neutrino energies typically produced by the Fermilab Booster Neutrino Beam. A detailed understanding of neutrino-argon scattering in the CC0$πNp$ channel is therefore crucial for the success of the precision neutrino oscillation analyses planned for the Short-Baseline Neutrino (SBN) program. This remains true for the upcoming Deep Underground Neutrino Experiment (DUNE), but the higher mean neutrino energy used there will ensure that more inelastic reaction modes, such as single pion production, will also play a major role. The analysis described in this note builds on a previous MicroBooNE study of the CC0$πNp$ channel which obtained the first single-differential cross-section measurements on an argon target. Since that foundational work, significant improvements have been made to MicroBooNE’s simulation software, event reconstruction algorithms, and procedure for calculating systematic uncertainties. When combined with a larger dataset (corresponding to a beam exposure of 6.79 × 10 20 protons-on-target versus 1.60 × 10 20 in Ref. [3]), these enhancements allow the important CC0$πNp$ channel to be studied in more detail. This note begins with a description of the data and simulation samples used as input to the analysis. Section 3 then defines the CC0$πNp$ signal event topology, and Section 4 describes a set of selection criteria designed to identify these events in MicroBooNE data. Binning schemes are then defined in Section 5 for two double-differential measurements of event rates. The first of these considers the momentum and scattering cosine of the outgoing muon, while the second reports the same observables for the leading proton, i.e., the final-state proton with the largest momentum. After a discussion of systematic uncertainties in Section 6, the note concludes by comparing the predictions of MicroBooNE Monte Carlo (MC) simulations to the measured double-differential distributions. These results will form the basis for a future extraction of flux-averaged double-differential CC0$πNp$ cross sections that will be immediately comparable to the theoretical predictions of multiple neutrino event generators. The selection described herein may also be used to study various other observables in CC0$πNp$ events, including those which are sensitive to correlations between leptonic and hadronic kinematics in the final state.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Methodology for Thermodynamic Analysis Coupled with Computational Fluid Dynamics Modeling for Casting a Novel Aluminum–Cerium Alloy

In this paper, we present the results of computational fluid dynamics (CFD) analysis to assess castability, porosity, molten metal fluidity and other technological properties of a new Al-Ce alloy. A thermodynamic analysis of a new Al-Ce alloy is done to obtain the physical properties as a function of temperature across both solid and liquid phases. These properties are then used to build the CFD of model the full casting process from initial pouring through to final solidification of the part, here an example of a heavy duty mor mount is used. While several excellent commercial CFD codes exists this process shows that CFD can be used to assess the capability of the alloy to properly fill the mold, as well as give predictions where scattered porosity or large-scale defects may occur in the casting. Further, unlike the commercially available software (e.g., ProCAST, SOLIDCast , MAGMASOFT®) the complex 3D-analysis of the stress / strain fields in cast parts is not performed at this time. However, the availability of free software for assessing the required thermodynamic / thermo-physical properties of new alloys (OpenCALPHAD) and CFD codes such as OpenFOAM® makes the developed option attractive and economical, especially for the analysis of new Al-Ce alloys, for which the available data does not exist.

36 MATERIALS SCIENCE↗

Accelerating End-to-End Deep Learning for Particle Reconstruction using CMS open data

Machine learning algorithms are gaining ground in high energy physics for applications in particle and event identification, physics analysis, detector reconstruction, simulation and trigger. Currently, most data-analysis tasks at LHC experiments benefit from the use of machine learning. Incorporating these computational tools in the experimental framework presents new challenges. This paper reports on the implementation of the end-to-end deep learning with the CMS software framework and the scaling of the end-to-end deep learning with multiple GPUs. The end-to-end deep learning technique combines deep learning algorithms and low-level detector representation for particle and event identification. We demonstrate the end-to-end implementation on a top quark benchmark and perform studies with various hardware architectures including single and multiple GPUs and Google TPU.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Accurate estimation of angular power spectra for maps with correlated masks

A common procedure when analyzing maps of the cosmic microwave background (CMB) or other cosmological signals is the need to remove ("mask") regions of the maps that are heavily contaminated, e.g., by non-cosmological foreground emission. After applying such a mask, one must account for its effect when inferring statistical properties of interest, such as the angular power spectrum of the field in the original map. A widely used approach to correct for such mask-induced effects was presented by Hivon et al. (2002), now widely known as the "MASTER" formalism. However, it is often the case that the map and mask are correlated in some way, such as point source masks used in CMB analyses, which have nonzero correlation with CMB secondary anisotropy fields and other mm-wave sky signals. In such situations, the MASTER approach gives biased results, as it assumes that the unmasked map and mask have zero correlation. While such effects have been discussed before with regard to specific physical models, here we derive a completely general formalism for any case where the map and mask are correlated. We show that our result ("reMASTERed") reconstructs ensemble-averaged angular power spectra to effectively exact precision, with significant improvements over traditional estimators for cases where the map and mask are correlated. An important consequence of our result is that for maps with correlated masks, it is no longer possible to invert a simple equation to obtain the true power spectrum from the observed (masked) power spectrum. Instead, our result necessitates the use of forward modeling from theory space into the observable domain of the masked power spectrum. We publicly release our software implementation of these results.

79 ASTRONOMY AND ASTROPHYSICS↗

Sensor Anomaly Detection for Nuclear Reactor Systems Utilizing Linear Regression and K-Means Unsupervised Machine Learning

Nuclear reactors and related systems are becoming increasingly complex due to advancing technologies in next-generation power reactors. This increased complexity necessitates enhanced automation and data management capabilities. To successfully realize autonomous systems, methods must be developed to handle vast volumes of data and effectively distinguish anomalous data from noise and expected data. While impressive models utilizing digital twins and similar approaches are under development, here we propose a simplified model for analyzing fundamental methods and techniques. Initially, we created a general dataset by using initial data from PCTRAN in order to represent ideal steady-state conditions. We then inserted anomalies based on prevalent sensor anomaly types (e.g., point anomalies, linear drift, and downward deviations), along with unusual anomalies such as exponential drift and upward deviations. To detect anomalies, we developed a program that employs data partitioning and linear regression to preprocess and filter the anomalous data. A K-Means machine learning (ML) method was then applied to separate and count the data within the anomalous partition. The results from all datasets—apart from exponential growth—demonstrated positive outcomes, with each returning multiple instances of greaterthan-95% accuracy. We conducted further investigations using Idaho National Laboratory’s RAVEN software to perform a sensitivity analysis on the input variables (R 2 Tolerance, Slope Tolerance, and Window Size) and found that the output variables (Accuracy and Time) were most sensitive to the Window Size. Despite the promising results published, further development is required to effectively apply these methods to nuclear systems. Nevertheless, the strengths of this approach are evident and hold promise for future applications in the field.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 3c Raw Data

XPS after 0hr of chronoampometry. Surface chemical composition and valence band structure of GaN were obtained by X-ray photoemission spectroscopy (XPS) on a Kratos Axis Ultra DLD system at a takeoff angle of 0° relative to the surface normal. An Al Kα source (hν = 1486.6 eV) was used to excite the core level electrons. Pass energy of 20 eV was used for the narrow scan of core levels and valence band spectra, and step size of 0.05 eV and 0.025 eV, respectively. The Spectral fitting was conducted using CasaXPS analysis software. The binding energy scales of all core levels were corrected to the N 1s of Ga – N bond at 397.8 eV. XPS O1s core level spectra from as-received Si/GaN sample, and deconvolution shows O - Ga bond and OH - H2O bond.

photocathode↗

Matilda v1.0: An R package for probabilistic climate projections using a reduced complexity climate model

A primary advantage to using reduced complexity climate models (RCMs) has been their ability to quickly conduct probabilistic climate projections, a key component of uncertainty quantification in many impact studies and multisector systems. Providing frameworks for such analyses has been a target of several RCMs used in studies of the future co-evolution of the human and Earth systems. In this paper, we present Matilda, an open-science R software package that facilitates probabilistic climate projection analysis, implemented here using the Hector simple climate model in a seamless and easily applied framework. The primary goal of Matilda is to provide the user with a turn-key method to build parameter sets from literature-based prior distributions, run Hector iteratively to produce perturbed parameter ensembles (PPEs), weight ensembles for realism against observed historical climate data, and compute probabilistic projections for different climate variables. This workflow gives the user the ability to explore viable parameter space and propagate uncertainty to model ensembles with just a few lines of code. The package provides significant freedom to select different scoring criteria and algorithms to weight ensemble members, as well as the flexibility to implement custom criteria. Additionally, the architecture of the package simplifies the process of building and analyzing PPEs without requiring significant programming expertise, to accommodate diverse use cases. We present a case study that provides illustrative results of a probabilistic analysis of mean global surface temperature as an example of the software application.

54 ENVIRONMENTAL SCIENCES↗

DER Digital Supply Chain Gap Analysis

Solar photovoltaic (PV) cybersecurity is a growing field of research. As deployments of solar PV have increased, cyber risk has also increased. Utility solar PV installations, however, are not required to comply with the North American Electric Reliability Corporation (NERC) Critical Infrastructure Protection (CIP) plan unless they meet a minimum generation threshold of 75 MW. Individual residential-scale solar PV deployments will not meet that generation threshold and are therefore excluded from the NERC CIP requirements. With most solar installations less than 75 MW, solar PV has been deployed with minimal oversight and highly variable cybersecurity maturity. The resources that comprise the digital supply chain can include software, code, data, and other digital components. But as clean energy technologies advance, cybersecurity threats and vulnerabilities continue to evolve and grow in sophistication. Supply chain cybersecurity represents a critical area for ensuring safe operations as the U.S. moves toward a clean energy future.

cybersecurity↗

Denoising Seismograms in the Time Domain Using a Deep Learning Model

Deep learning has emerged as a transformative tool for enhancing the extraction of reliable information from seismograms, addressing the increasing demand for precise and efficient seismic data analysis. We introduce an innovative encoder–decoder deep learning model, named WaveDenoiser, designed for noise reduction in the time domain, thereby eliminating the need for spectrogram computations that have been used for existing deep learning tools and significantly improving processing speed. Utilizing the benchmark dataset that is Stanford Earthquake Dataset, we developed three models of varying sizes: base, medium, and large. Notably, the large (referred to as WaveDenoiser) model demonstrated superior performance, achieving a median signal‐to‐noise ratio improvement of 8.8 dB on in‐distribution unseen data (in the same geographic region) and 7.7 dB on out‐distribution unseen data (in a new geographic region), outpacing both the base and medium models. Further evaluation of the WaveDenoiser model revealed a reduction in median arrival‐time errors by 0.02 s for P waves and 0.01 s for S waves when processing waveforms prior to phase picking using PhaseNet on in‐distribution unseen data. When tested on out‐distribution unseen data, the model also effectively reduced the P‐wave median arrival‐time error by 0.02 and 0.01 s in median arrival‐time error for S waves. Importantly, the application of WaveDenoiser resulted in a significant reduction of phase picking outliers by 1.1% to 3.6% for both P and S waves. In addition, we achieved over five times acceleration in processing speed compared with the seisBench implementation of DeepDenoiser. Our findings underscore the potential of WaveDenoiser as a powerful tool for improving seismic data analysis and processing efficiency.

P-waves↗

MemFriend: Understanding Memory Performance with Spatial-Temporal Affinity

In HPC applications, memory access behavior is one of the main factors affecting performance. Improving an application’s memory access behavior involves optimizing data layout and/or restructuring code, and requires studying spatial-temporal data locality. Existing data locality analyses focus on single-location metrics and are restricted to evaluating temporal locality. We introduce spatial-temporal affinity metrics that quantify temporal access proximity, forward access correlation, and nearby access correlation between pairs of memory locations. We describe methods for distinguishing between potential vs. realized affinity and for reasoning about affinity at multiple resolutions (3D, 2D, 1D). Finally, we construct spatial-temporal affinity signatures that classify memory behavior and that be used to reason about changes in software (data relayout, code refactoring) or hardware (caching, prefetching). We describe methods for signature visualization, interpretation, and quantitative comparison of signatures. We evaluate our methodology using applications with variants that contrast data structures, data layouts and algorithms. We show that spatial-temporal affinity analysis provides novel insights and enables predictive reasoning about application performance when contrasted with reuse distance analysis.

Suriyakumar, Yasodhadevi↗

PVcircuit [SWR-22-26]

The software contains objects that are building blocks for PV modeling and interactive data fitting based on: Optoelectronic models for tandem/multijunction solar cells including resistive and luminescent coupling; simulation of modules composed of 2T, 3T, and 4T tandem solar cells; and energy yield analysis of PV systems composed of tandem solar cells.

Geisz, John↗