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At least 883 records · Page 49

Robust Dark Energy Constraints with the Dark Energy Spectroscopic Survey (Final Technical Report)

This project developed and applied advanced theoretical, computational, and data-analysis methodologies to extract robust and precise cosmological constraints from the Dark Energy Spectroscopic Instrument (DESI). The work focused on maximizing the scientific return of DESI through optimized survey strategy, novel higher-order clustering statistics, improved modeling of small-scale structure, and rigorous mitigation of observational systematics. Over the award period, the project made substantial contributions to DESI science planning, produced new methods for bispectrum and three-point correlation function analyses, advanced constraints on primordial non-Gaussianity, and delivered widely used software tools. The project also played a major role in training graduate students and a postdoctoral researcher who contributed directly to DESI key projects. The results have significantly enhanced the cosmological reach of DESI and provide a strong foundation for future surveys such as DESI-II and Stage-V experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

36 MATERIALS SCIENCE↗

SMATool: Strength of materials analysis toolkit

The study of the strength of materials is a cornerstone in material science and engineering, playing a critical role in shaping the progress and application of materials in diverse industrial sectors. The strength of a material is meticulously examined to understand the behavior of the material under different stress conditions and environments, thereby guiding material selection and structural design. Herein, we introduce the SMATool, a computational toolkit for the efficient calculation and analysis of material strength at both zero and finite temperatures for 3D, 2D, 1D, and tubular 2D-based nanostructures and nanotubes, as well as 1D nanoribbons. The toolkit is capable of calculating tensile, shear, ultimate, yield, and indentation (Vickers' hardness) strengths in various dimensions, as well as the energy storage capacity. We conducted several calculations both at zero and finite temperatures to validate the accuracy and reliability of the developed software. Here, the results show that the SMATool package provides accurate predictions that align with existing data on material strength. SMATool integrates seamlessly with widely used electronic structure codes like VASP and Quantum Espresso, providing a user-friendly interface catering to academic researchers and industry professionals.

36 MATERIALS SCIENCE↗

Magnetic Microcalorimeter (MMC) Gamma-Ray Detectors with Ultra-High Energy Resolution. Comprehensive Technology Readiness Assessment

Magnetic Microcalorimeter (MMC) gamma ray detectors have demonstrated very high energy resolution of 38 eV FWHM for gamma ray energies below 100 keV. This is an order or magnitude better than conventional HPGe detector and can remove most line-overlap problems in NDA by gamma spectroscopy below ~130 keV. Unlike superconducting transition edge sensors (TESs), MMCs have a reproducible and almost perfectly linear response, which greatly simplifies adding spectra from different detector pixels and reduces systematic errors in quantitative assays. The instrument is currently at TRL-5 but could advance to TRL-6 by improving the signal processing software and using the system for the quantitative analysis of a safeguards sample provided by e.g. the IAEA. Making MMC detectors commercially viable and used more widely then depends on making the technology more reliable, specifically by increasing the device uniformity and yield, and by developing commercial software. This situation is often only half-jokingly referred to as the “valley of death” and could be addressed though the SBIR program. Our collaborators at STAR Cryoelectronics LLC are well qualified to further advance MMC development, and XIA LLC is well-positioned to develop the data acquisition system and write the software for MMC readout. In addition, the advance to TRL-6 would be desirable to increase the visibility and showcase the value of MMC spectrometers, e.g. by placing one of them into the Safeguards Analytical Laboratory (SAL) at the IAEA, whose NDA experts have recently started to show interest in cryogenic detector technology. As a result of this LCP, we also now have an instrument at LLNL that we will use for various applications of MMCs in nuclear safeguards and science. We are confident that as the number of high-profile results increases, so will the interest in and commercial viability of this technology.

42 ENGINEERING↗

Magnetic Microcalorimeter (MMC) Gamma-Ray Detectors with Ultra-High Energy Resolution. Comprehensive Technology Readiness Assessment

Magnetic Microcalorimeter (MMC) gamma ray detectors have demonstrated very high energy resolution of 38 eV FWHM for gamma ray energies below 100 keV. This is an order or magnitude better than conventional HPGe detector and can remove most line-overlap problems in NDA by gamma spectroscopy below ~130 keV. Unlike superconducting transition edge sensors (TESs), MMCs have a reproducible and almost perfectly linear response, which greatly simplifies adding spectra from different detector pixels and reduces systematic errors in quantitative assays. The instrument is currently at TRL-5 but could advance to TRL-6 by improving the signal processing software and using the system for the quantitative analysis of a safeguards sample provided by e.g. the IAEA. Making MMC detectors commercially viable and used more widely then depends on making the technology more reliable, specifically by increasing the device uniformity and yield, and by developing commercial software. This situation is often only half-jokingly referred to as the “valley of death” and could be addressed though the SBIR program. Our collaborators at STAR Cryoelectronics LLC are well qualified to further advance MMC development, and XIA LLC is well-positioned to develop the data acquisition system and write the software for MMC readout. In addition, the advance to TRL-6 would be desirable to increase the visibility and showcase the value of MMC spectrometers, e.g. by placing one of them into the Safeguards Analytical Laboratory (SAL) at the IAEA, whose NDA experts have recently started to show interest in cryogenic detector technology. As a result of this LCP, we also now have an instrument at LLNL that we will use for various applications of MMCs in nuclear safeguards and science. We are confident that as the number of high-profile results increases, so will the interest in and commercial viability of this technology.

42 ENGINEERING↗

NUM-DAT File Format Specification: Used in M-9 Gun Experiment Data Archiving

The M-9 Shock and Detonation Physics group executes experiments on gun and explosive platforms with large numbers of oscilloscopes used for data acquisition. The data acquisition from these oscilloscopes was automated many years ago using a custom piece of software called RunDig . The default save format from this software is a custom structure referred to as "NUM-DAT" format. This file format includes a text ".DAT" file which is a header file used to interpret the binary ".NUM" file which contains the oscilloscope data. The data save format was originally developed by John Vorthman and has been in use by M-9 personnel for over 20 years. This data format has been used for archiving data from experiments performed by M-9 personnel at TA-40, TA-39, and the TA-55 Impact Test Facility. Numerous custom analysis and visualization programs have also been developed, and continue to be used, that utilize this data format. This document describes the NUM-DAT format and provides code examples for reading the format and converting it to other formats.

47 OTHER INSTRUMENTATION↗

Geothermal Deep Direct Use for Turbine Inlet Cooling in East Texas

The National Renewable Energy Laboratory (NREL), the Southern Methodist University Geothermal Laboratory (SMU), Eastman Chemical (Longview, TX), and TAS (Houston, TX) evaluated the feasibility of using geothermal heat to improve the performance of a natural-gas power plant in East Texas. The area of interest is the Eastman Chemical plant in Longview, Texas, which is on the northwestern margin of a geologic region known as the Sabine Uplift. The feasibility study focused on determining the potential for accessing a subsurface hot-water geothermal resource within a 10-km radius of the site to provide thermal energy for absorption chillers. Wells within a 20-km radius are included for broader geological comparison to determine the heat flow, temperature-at-depth, field porosity and permeability. The lithologies of most interest are the Lower Cretaceous Trinity Group and Upper Jurassic Cotton Valley Group. The deeper Cotton Valley formations are hotter (averaging 117 to 130°C), yet permeability and porosity are low. The shallower Trinity Group contains more variability in permeability and porosity and lower temperatures averaging about 98 to 117°C. The shallower formations are considered despite the lower temperature because of increased ability to produce larger volumes of water and extract enough heat before reinjection. The complete SMU analysis is available in the National Geothermal Data System (NGDS). Tapping such deep geothermal sources for direct heating (as opposed to power generation) is known as geothermal deep direct use (DDU). Geothermal DDU has potential across a wide swath of the United States but is underutilized due to challenging project economics associated with developing a deep geothermal resource for what are typically small-scale, variable-demand projects. This project examines the feasibility of geothermal energy integration in a natural-gas combined cycle power station in East Texas. The DDU resource is tapped to drive absorption chillers (24/7) for production of chilled water at 5-10°C (41-50°F). This chilled water is stored until needed, which allows for continuous operation with a relatively small-capacity geothermal/absorption chiller system. When conditions are favorable, the chilled water is dispatched to cool the air entering the compressor stage of a gas combustion turbine. This process, known as turbine inlet cooling (TIC), boosts power production during periods of high temperature and high-power demand. Such systems can enhance grid reliability and reduce the cost for peak-demand power. A simulation model of the power plant was developed in IPSEpro software and validated against operational data from the plant. This model allowed the team to estimate the additional power that could be produced by applying TIC under different operating and ambient conditions. Absorption chiller performance was estimated from vendor sources to determine the production rate of chilled water from the geothermal resource. Geothermal drilling and development costs were estimated using NREL's GEOPHIRES 2.0. The expected lower drilling costs in this region led to an estimated cost of geothermal heat of about $4/MMBtu (1.4 cents/kWh t ). The estimated cost for the absorption chillers and TIC hardware were obtained from literature sources and project partners. Hourly data were obtained for weather, natural gas and electricity prices, and plant operating state for 2017, which served as a representative year. NREL estimated the capital cost, operating cost, and additional electricity production and revenue for different combinations of geothermal capacity, chiller capacity, and water storage-tank size. The analysis drove toward smaller geothermal and chiller systems to reduce equipment cost. A relatively low-cost water storage tank accumulated the near-continuous chilled water output for later use when TIC was most valued.

15 GEOTHERMAL ENERGY↗

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗

A variant selection framework for genome graphs

Abstract Motivation Variation graph representations are projected to either replace or supplement conventional single genome references due to their ability to capture population genetic diversity and reduce reference bias. Vast catalogues of genetic variants for many species now exist, and it is natural to ask which among these are crucial to circumvent reference bias during read mapping. Results In this work, we propose a novel mathematical framework for variant selection, by casting it in terms of minimizing variation graph size subject to preserving paths of length α with at most δ differences. This framework leads to a rich set of problems based on the types of variants [e.g. single nucleotide polymorphisms (SNPs), indels or structural variants (SVs)], and whether the goal is to minimize the number of positions at which variants are listed or to minimize the total number of variants listed. We classify the computational complexity of these problems and provide efficient algorithms along with their software implementation when feasible. We empirically evaluate the magnitude of graph reduction achieved in human chromosome variation graphs using multiple α and δ parameter values corresponding to short and long-read resequencing characteristics. When our algorithm is run with parameter settings amenable to long-read mapping (α = 10 kbp, δ = 1000), 99.99% SNPs and 73% SVs can be safely excluded from human chromosome 1 variation graph. The graph size reduction can benefit downstream pan-genome analysis. Availability and implementation https://github.com/AT-CG/VF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

PyPop: a mature open-source software pipeline for population genomics

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations.

59 BASIC BIOLOGICAL SCIENCES↗

Bridging Python to Silicon: The SODA Toolchain

Systems performing scientific computing, data analysis, and machine learning tasks have a growing demand for application-specific accelerators that can provide high computational performance while meeting strict size and power requirements. However, the algorithms and applications that need to be accelerated are evolving at a rate that is incompatible with manual design processes based on hardware description languages. Agile hardware design tools based on compiler techniques can help by quickly producing an application-specific integrated circuit (ASIC) accelerator starting from a high-level algorithmic description. Here, we present the software-defined accelerator (SODA) synthesizer, a modular and open-source hardware compiler that provides automated end-to-end synthesis from high-level software frameworks to ASIC implementation, relying on multilevel representations to progressively lower and optimize the input code. Our approach does not require the application developer to write any register-transfer level code, and it is able to reach up to 364 giga floating point operations per second (GFLOPS)/W efficiency (32-bit precision) on typical convolutional neural network operators.

97 MATHEMATICS AND COMPUTING↗

Efforts to enhance reproducibility in a human performance research project

Background: Ensuring the validity of results from funded programs is a critical concern for agencies that sponsor biological research. In recent years, the open science movement has sought to promote reproducibility by encouraging sharing not only of finished manuscripts but also of data and code supporting their findings. While these innovations have lent support to third-party efforts to replicate calculations underlying key results in the scientific literature, fields of inquiry where privacy considerations or other sensitivities preclude the broad distribution of raw data or analysis may require a more targeted approach to promote the quality of research output. Methods: We describe efforts oriented toward this goal that were implemented in one human performance research program, Measuring Biological Aptitude, organized by the Defense Advanced Research Project Agency's Biological Technologies Office. Our team implemented a four-pronged independent verification and validation (IV&V) strategy including 1) a centralized data storage and exchange platform, 2) quality assurance and quality control (QA/QC) of data collection, 3) test and evaluation of performer models, and 4) an archival software and data repository. Results: Our IV&V plan was carried out with assistance from both the funding agency and participating teams of researchers. QA/QC of data acquisition aided in process improvement and the flagging of experimental errors. Holdout validation set tests provided an independent gauge of model performance. Conclusions: In circumstances that do not support a fully open approach to scientific criticism, standing up independent teams to cross-check and validate the results generated by primary investigators can be an important tool to promote reproducibility of results.

59 BASIC BIOLOGICAL SCIENCES↗

A Knowledge-based Framework for Building Energy Model Performance Verification

Building energy modeling (BEM) has been widely used by researchers, regulators, and engineers to quantify building energy performance. Quality assurance (QA) and quality control (QC) of the model's performance are essential parts of such analysis. Currently, QA/QC is done in a manual and ad-hoc manner, which is tedious, error-prone, and time-consuming when QA/QC a large number of models. To solve these challenges, we propose a a dAta-driveN buIlding perforMance verificATion framEwork (ANIMATE), which conducts automated output-based verification of building operations requirements (especially for time-series output-based verification of control requirements). While this framework was developed for verifying energy model performance, it can be extended for other applications such as BEM software testing and performance verification of real buildings in the field.

Chen, Yan↗

Economic and embodied energy analysis of integrated circuit manufacturing processes

Integrated circuits (ICs) are the fundamental microelectronic building blocks of typical information and communication technology (ICT) devices such as laptops and smartphone. With the emergence of faster and cheaper low-power ICs for the growing ICT market, there is a limited information on their manufacturing energy and economic impacts owing to the lack of recurrent upgradation of proprietary IC manufacturing process data. In this work, economic and life cycle energy assessments (LCAs) of IC manufacturing and assembly processes were conducted using the latest bill of materials (BOM) manufacturing data in a state-of-the-art IC manufacturing cost software tool developed by IC Knowledge, LLC. IC manufacturing cost was estimated to be $\$$1.00-$\$$5.00/cm 2 ; the high-end cost represents the most advanced 3D NAND IC technology with the Wafer Level Chip Scale Package cost of $4/cm 2 . Total cumulative energy demand (CED) estimates of IC manufacturing using the OpenLCA software ranged from 9 to 38 MJ/cm 2 or 56–235 BJ/month with the largest share (~ 75%) from on-site energy. The IC manufacturing CED is projected to increase with the progress in IC technology node, which has increased by more than two times for technology node evolution from 110 to 14 nm. Furthermore, the representative detailed BOM data were considered to reduce the CED uncertainties of the estimated standard deviation of 35%- 42%.

97 MATHEMATICS AND COMPUTING↗

Tools for analysis of optimization models

The software is code for analyzing, debugging, and solving optimization models. The code implements several algorithms and provides convenient APIs to apply these algorithms to optimization models. The algorithms are primarily based on graph theory. They compute well-known partitions of graphs, and use these partitions to provide the user information about their optimization model, including diagnosing certain types of structural modeling errors. Some algorithms may be used as a subroutine to solve an optimization problem, and may call an optimization solver to facilitate this. Well-known linear algebra routines are called to provide further diagnostics. The software contains no data and no models other than toy models used for testing.

Parker, Robert↗

CMLM (Co-Optimized Machine-Learned Manifolds) [SWR-23-41]

Co-optimized Machine-Learned Manifolds (CMLM) is a data-driven approach for developing reduced-order manifold models for high-dimensional chemically reacting systems. It involves a specially designed neural network, the training of which simultaneously optimizes linear combinations of species that define the manifold, nonlinear mapping to outputs of interest such as reaction rates, and (optionally) subfilter closure for large eddy simulation. This software package provides an implementation of the CMLM approach in Python using the PyTorch machine learning library. A few example cases are included, showing how the tool can be applied to different types of data from 0D and 1D reacting simulations performed using Cantera. The neural networks can be saved in a format that is readable by the Pele suite of combustion solvers for use in reacting computational fluid dynamics simulations. This software repository contains several python scripts to perform various tasks associated with the Co-optimized Machine Learned Manifolds (CMLM) model, which is described in Perry, Henry de Frahan, and Yellapantula, CNF, 2022 (https://doi.org/10.1016/j.combustflame.2022.112286). This includes not only the code that defines the CMLM model, but also scripts to generate suitable training data, scripts to pre-process the data, scripts to train the CMLM model, and scripts to plot the output, as well as various other helper files. The scripts depend on several commonly used python libraries for data analysis and chemical reaction computations. The trained models that result from this tool are designed to work with the an interface being implemented in the Pele suite of reacting flow solvers (https://github.com/AMReX-Combustion).

Perry, Bruce↗

A hierarchical evaluation framework for assessing climate simulations relevant to the energy-water-land nexus (Final Report)

The overarching goal was to construct a hierarchy of new and well-tested metrics and analysis tools that support both fundamental and use-inspired research. Motivating this goal was a convergence of needs from climate scientists and stakeholders alike for a systematic, robust framework of model evaluation and diagnosis to provide scientific insights, inform model development, support best practices for the use of climate model outputs, and facilitate communication of climate information in the evolving landscapes of multi-model, multi-resolution, and large ensemble simulations that generate terabytes of data for any single climate run. Steps toward attaining these goals benefited from expertise and established capability of the project team, which included leadership of the North American Regional Climate Change Assessment Program (NARCCAP) and the Coordinated Regional Downscaling Experiment (CORDEX), development of hierarchical model evaluation approaches, and successful research in the analysis and diagnosis of climate model skill, as well as the understanding and modeling of regional climate processes in North America. As part of the overarching goal, the project worked to disseminate a suite of methodologies, algorithms, and software components that the wider community can employ to advance climate science and applications. With rigorous demonstration, the evaluation framework and the mix of standard and high risk / high reward approaches helped form the basis for future development of a computationally enabled user-friendly system for community use.

17 WIND ENERGY↗

Red Noise–based False Alarm Thresholds for Astrophysical Periodograms via Whittle’s Approximation to the Likelihood

Astronomers who search for periodic signals using Lomb–Scargle periodograms rely on false alarm level (FAL) estimates to identify statistically significant peaks. Although FALs are often calculated from white noise models, many astronomical time series suffer from red noise. Prewhitening is a statistical technique in which a continuum model is subtracted from the log power spectrum estimate, after which the observer can proceed with a white-noise treatment. Here we present a prewhitening-based method of calculating frequency-dependent FALs. We fit power laws and autoregressive models of order 1 to each Lomb–Scargle periodogram by minimizing the Whittle approximation to the negative log-likelihood (NLL), then calculate FALs based on the best-fit model power spectrum. Our technique is a novel extension of the Whittle NLL to datasets with uneven time sampling. We demonstrate FAL calculations using observations of α Cen B, GJ 581, HD 192310, synthetic data from the radial velocity (RV) fitting challenge, and Kepler observations of a differential rotator. The Kepler data analysis shows that only true rotation signals are detected by red noise FALs, while white noise FALs suggest all spurious peaks in the low-frequency range are significant. A high-frequency sinusoid injected into α Cen B logR$'$ HK observations exceeds the 1% red noise FAL despite having only 8.9% of the power of the dominant rotation signal. In a periodogram of HD 192310 RVs, peaks associated with differential rotation and planets are detected against the 5% red noise FAL without iterative model fitting or subtraction. The software for calculating red noise–based FALs is available on GitHub.

Astrostatistics (1882)↗