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At least 559 records · Page 31

BLEECAM™ (Benchmarking Life Cycle Environmental, Economic, and Social Metrics for Critical and Advanced Minerals and Materials) [SWR-25-125]

The National Laboratory of the Rockies' (NLR) Benchmarking Life Cycle Environmental, Economic, and Social Metrics for Critical and Advanced Minerals and Materials (BLEECAM™) is an open-source, integrated decision-support tool for evaluating the impacts, risks, and trade-offs across U.S. and global materials supply chains. Funded by the U.S. Department of Energy, BLEECAM supports supply chain and market analysis. The tool integrates multi-objective supply chain optimization, system dynamics, network design, lifecycle assessment, techno-economic modeling, and social impact assessment methods to evaluate how supply chains evolve over time, geography, and deployment scenarios. BLEECAM also supports analysis related to energy infrastructure, data centers and digital infrastructure, advanced manufacturing, and other sectors that depend on critical materials.

Khalifa, SherifA. [National Laboratory of the Rock↗

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson’s R and Spearman’s ρ coefficients as well as Kendall’s τ and Top–Down correlation. We also test the behavior of association measures, including the coefficient of determination R 2 , Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spear man’s ρ, Kendall’s τ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R 2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.

59 BASIC BIOLOGICAL SCIENCES↗

Gaussian Process Optimization of Sensitivity-Based Similarity Metrics between New Nuclear Applications and New/Existing Benchmarks

Confidently designing safe, new nuclear criticality experiments requires expert judgement, which could take years of experience. Sensitivity/uncertainty (S/U) analysis can be utilized by less experienced individuals to conservatively estimate uncertainties in important parameters, such as k eff , in newly proposed nuclear applications. This type of analysis relies on matching new nuclear applications with existing benchmark experiments. The Whisper-1.1 software package included in MCNP6.2 ®1 contains more than 1,100 International Criticality Safety Benchmark Evaluation Project (ICSBEP) benchmarks. These benchmarks however rarely match new nuclear applications. The number of benchmarks available to match a given set of materials or geometric configurations varies significantly. Furthermore, recently performed benchmark experiments may not have had enough time to be properly documented and published. Benchmarks are vital for determining the accuracy of nuclear data and can assist nuclear physics and evaluators in improving nuclear data libraries. Exhaustively exploring the parameter space using simulations with software such as MCNP is too computationally expensive. In this work, Gaussian process optimization was implemented to reduce the number of simulations needed for optimization over multiple parameters. This optimization scheme was designed to selectively generate new benchmarks with high sensitivity-based similarity metrics to user-defined nuclear applications. Two benchmark models of spherically nested shells containing plutonium, uranium, tantalum, and water were used in the optimization to match an application containing plutonium plates, stacked in a tantalum reflector, surrounded by water.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Columbia River Surface Water and Pore Water Unaligned FTICR-MS Data Associated with “Using Community Assembly Metrics from Metacommunity Ecology to Understand Environmental Metabolomes”

Surface water and pore water samples were collected at five sites along a shoreline transect of the Columbia River, southeastern WA, USA in 2017. This dataset is comprised of (1) high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) and (2) a metadata csv file. The FTICR-MS files are .xml, and the data package includes instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user’s specific needs. The data are associated with the publication “Using community assembly metrics from metacommunity ecology to understand environmental metabolomes” that will be published in Nature Communications (Danczak et al.). The study aimed to investigate gaps in understanding the spatiotemporal organization of environmental metabolomes to improve the ability to predict ecosystem function. Associated sequencing data will be published via NCBI. The access information for NCBI and the publication DOI will be added to this abstract when they are available. Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.

54 ENVIRONMENTAL SCIENCES↗

LTE-P-19 Comparison Metrics and Terms for Low Temperature Electrolysis

Defines a standard set of definitions, metrics, units, and conventions for low temperature electrolysis (LTE). The goal is to ensure that the literature is consistent from research group to research group, and data is reported in similar formats, such that results can be compared on a similar basis.

Electryolyzer↗

Developing Metrics to Evaluate the Skill and Credibility of Downscaling

In this project, our overarching goal was to evaluate the skill and credibility of statistical and dynamical downscaling techniques for reconstructing the historical climate record and projecting future climate change. This report summarizes our approach and accomplishments. In the first year of the project, the priority was to generate new data sets. For Year 2, the overall goal was to focus comparisons during the historical period and for a subset of variables, especially temperature and precipitation. In Year 3 and beyond, the focus was mainly on comparisons and metrics for future climate change simulations. To quantify the uncertainty associated with gridded dataset choice, the UCLA group compared eight gridded temperature datasets, examining climatologies, variability, and trends. The Scripps group completed statistical downscaling of NARR with the LOCA method, and UCLA and Scripps collaborated on a comparison of historical and end-of-century temperature and precipitation patterns over California from WRF, LOCA-WRF, and LOCA-Livneh. In addition to downscaling temperature and precipitation, the Scripps group has spent considerable time working on near-surface wind and humidity downscaling. The Santa Clara group assembled the Variable Infiltration Capacity (VIC) for nine snow-dominated river basins draining the western slopes of the Sierra Nevada range and assessed the role of snow albedo feedback in their VIC simulations. The results will help inform future downscaling studies.

54 ENVIRONMENTAL SCIENCES↗

Developing Metrics to Evaluate the Skill and Credibility of Downscaling (Final Report)

In this project, our overarching goal was to evaluate the skill and credibility of statistical and dynamical downscaling techniques for reconstructing the historical climate record and projecting future climate change. This report summarizes our approach and accomplishments. In the first year of the project, the priority was to generate new data sets. For Year 2, the overall goal was to focus comparisons during the historical period and for a subset of variables, especially temperature and precipitation. In Year 3 and beyond, the focus was mainly on comparisons and metrics for future climate change simulations. To quantify the uncertainty associated with gridded dataset choice, the UCLA group compared eight gridded temperature datasets, examining climatologies, variability, and trends. The Scripps group completed statistical downscaling of NARR with the LOCA method, and UCLA and Scripps collaborated on a comparison of historical and end-of-century temperature and precipitation patterns over California from WRF, LOCA-WRF, and LOCA-Livneh. In addition to downscaling temperature and precipitation, the Scripps group has spent considerable time working on near-surface wind and humidity downscaling. The Santa Clara group assembled the Variable Infiltration Capacity (VIC) for nine snow-dominated river basins draining the western slopes of the Sierra Nevada range and assessed the role of snow albedo feedback in their VIC simulations. The results will help inform future downscaling studies.

54 ENVIRONMENTAL SCIENCES↗

LDMS-GPU: Lightweight Distributed Metric Service (LDMS) for NVIDIA GPGPUs

GPUs are now a fundamental accelerator for many high-performance computing applications. They are viewed by many as a technology facilitator for the surge in fields like machine learning and Convolutional Neural Networks. To deliver the best performance on a GPU, we need to create monitoring tools to ensure that we optimize the code to get the most performance and efficiency out of a GPU. Since NVIDIA GPUs are currently the most commonly implemented in HPC applications and systems, NVIDIA tools are the solution for performance monitoring. The Light-Weight Distributed Metric System (LDMS) at Sandia is an infrastructure widely adopted for large-scale systems and application monitoring. Sandia has developed CPU application monitoring capability within LDMS. Therefore, we chose to develop a GPU monitoring capability within the same framework. In this report, we discuss the current limitations in the NVIDIA monitoring tools, how we overcame such limitations, and present an overview of the tool we built to monitor GPU performance in LDMS and its capabilities. Also, we discuss our current validation results. Most of the performance counter results are the same in both vendor tools and our tool when using LDMS to collect these results. Furthermore, our tool provides these statistics during the entire runtime of the tool as a time series and not just aggregate statistics at the end of the application run. This allows the user to see the progress of the behavior of the applications during their lifetime.

97 MATHEMATICS AND COMPUTING↗

Distributed Wind Resilience Metrics for Electric Energy Delivery Systems: Comprehensive Literature Review

While most people have a general concept of what it means to be “resilient,” an examination of definitions from different sources reveals that there are key commonalities but key differences as well. The lack of a generally accepted definition and application of resilience extends to electric energy delivery systems. Without an accepted definition, it is difficult to implement programs or processes to improve resiliency. In this paper, existing work from industry, regulatory bodies, and national laboratories to define and apply resilience to electric energy delivery systems is studied to understand the key components to define resilience and better understand associated metrics. This understanding is then applied to distributed wind for a specific example of how resilience of a system is affected by the technologies and generation sources used to support it. A key finding is that there is no “one size fits all” process for resilience. Each system has a “distinctiveness” characteristic, which qualifies the possibility of differences in resilience due to different threats, geography, stakeholders, risk tolerance, and mitigations. The distinctiveness characteristic extends to distributed wind, where different configurations may lend the distributed wind to contribute to the resilience of systems in a variety of ways. The findings of this research demonstrate the need for a resilience framework that can be readily applied by stakeholders to improve resilience based on the specific system, threat, risk tolerance and stakeholders.

17 WIND ENERGY↗

GaAs Neutron Response Functions and Radiation Damage Metrics

The radiation effects community needs clear, well-documented, neutron energy-dependent responses that can be used in assessing radiation-induced material damage to GaAs semiconductors and for correlating observed radiation-induced changes in the GaAs electronic properties with computed damage metrics. In support of the objective, this document provides: a) a clearly defined set of relevant neutron response functions for use in dosimetry applications; b) clear mathematical expressions for the defined response functions; and c) updated quantitative values for the energy- dependent response functions that reflect the best current nuclear data and modelling. This document recaps the legacy response functions. It then surveys the latest nuclear data and updates the recommended response function to support current GaAs damage studies. A detailed tabulation for six of the energy-dependent response functions is provided in an Appendix.

36 MATERIALS SCIENCE↗

Empirical Performance Analysis of HPC Applications with Portable Hardware Counter Metrics [Thesis]

In this dissertation, we demonstrate that it is possible to develop methods of empirical hardware-counter-based performance analysis for scientific applications running on diverse types of CPUs. Although hardware counters have been used in performance analysis for at least 30 years, the methods used are still limited to particular CPU vendors or even particular generations of CPUs from the same vendor. Our motivating hypothesis is that hardware counter-based measurements could be developed to provide consistent performance information on diverse CPU types. This dissertation proves the hypothesis was correct by demonstrating one such set of metrics.

97 MATHEMATICS AND COMPUTING↗

Graph-Based Similarity Metrics for Comparing Simulation Model Causal Structures

The causal structure of a simulation is a major determinant of both its character and behavior, yet most methods we use to compare simulations focus only on simulation outputs. We introduce a method that combines graphical representation with information theoretic metrics to quantitatively compare the causal structures of models. The method applies to agent-based simulations as well as system dynamics models and facilitates comparison within and between types. Comparing models based on their causal structures can illuminate differences in assumptions made by the models, allowing modelers to (1) better situate their models in the context of existing work, including highlighting novelty, (2) explicitly compare conceptual theory and assumptions to simulated theory and assumptions, and (3) investigate potential causal drivers of divergent behavior between models. We demonstrate the method by comparing two epidemiology models at different levels of aggregation.

97 MATHEMATICS AND COMPUTING↗

Developing and applying quantifiable metrics for diagnostic and experiment design on Z

This project applies methods in Bayesian inference and modern statistical methods to quantify the value of new experimental data, in the form of new or modified diagnostic configurations and/or experiment designs. We demonstrate experiment design methods that can be used to identify the highest priority diagnostic improvements or experimental data to obtain in order to reduce uncertainties on critical inferred experimental quantities and select the best course of action to distinguish between competing physical models. Bayesian statistics and information theory provide the foundation for developing the necessary metrics, using two high impact experimental platforms on Z as exemplars to develop and illustrate the technique. We emphasize that the general methodology is extensible to new diagnostics (provided synthetic models are available), as well as additional platforms. We also discuss initial scoping of additional applications that began development in the last year of this LDRD.

97 MATHEMATICS AND COMPUTING↗

AI-Assisted Conceptual Development of a Pre-Geometric Cosmological Model - An Exercise in AI-Assisted Conceptual Framework Generation, Paper II: Local Geometry and Metric Structure

This paper develops the geometric sector of the replication-driven cosmogenesis framework introduced in Paper I. Starting from a pre-geometric spectral substrate and a minimal set of replication axioms, we show how coherent self-replicating units generate a spatial adjacency graph whose continuum limit acquires an effective Riemannian structure. The replication dynamics determines a characteristic correlation length that seeds the local metric, while overlap relations among coherent units produce an isotropic neighborhood geometry with an emergent dimensionality $d_{\rm eff}\simeq 3$ across a broad range of replication factors. As replication slows and causal order stabilizes, a limiting signal speed $c_\ast$ appears, providing the basis for the Lorentzian structure of spacetime without assuming a pre-existing light cone. We derive conditions under which the adjacency graph converges to a smooth three-dimensional manifold, describe the transition from Euclidean to Lorentzian propagation, and identify geometric invariants controlled by the replication parameters. This work establishes the geometric and causal layer of the replication cosmogenesis program, bridging the spectral axioms of Paper I to the cosmological dynamics explored in Paper III.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE BSSD Performance Management Metrics Report Q2

The vision of the National Microbiome Data Collaborative (NMDC) centers on the concept of connecting data, people, and ideas to advance microbiome innovation and discovery. Building data infrastructure, while key to NMDC’s ability to execute on our vision, can only go so far in creating scientific impact. By fostering strong community partnerships and developing a set of robust community outreach and training programs, we are able to turn our products – the Submission Portal, NMDC EDGE, and the Data Portal – into tools that empower the scientific community. Our multi-pronged community building approach spans individual researchers, research teams, consortia and scientific societies, and institutions and federal agencies. To foster a collaborative and inclusive community-centered environment, we have identified three strategic objectives to promote an inclusive and connected community: (1) recognize and support the diverse research needs and perspectives of the microbiome research community; (2) promote best practices across the microbiome community, from researchers to funders, through community-driven practices (FAIR, CARE, and TRUST); and (3) build a microbiome ecosystem that enables scientific discovery and innovation across stakeholders. These strategic objectives allow our team to focus on impact across a diverse range of activities, from launching the American Society for Microbiology (ASM) Microbiome Data Prize to supporting the Ambassador and Champions programs fostering learning and building a collaborative network. We broadly communicate our work through social media (X/Twitter, LinkedIn, and Instagram), The Microbiome Standard (our quarterly newsletter), and Annual Reports. All our work is underpinned by a strong commitment to diversity, equity, and inclusion as articulated in our Action Plan that tracks progress towards key metrics. A core component of our engagement strategy is user research. User research ensures the Submission Portal, NMDC EDGE, Data Portal, and the new Field Notes mobile app are designed with and for the scientific community. Our user research efforts consist of asking researchers exploratory questions to collect information on researcher priorities, methodologies, and perceptions to ensure that we are aware of the current state of microbiome research. Our usability testing provides researchers with prototypes or test environments of the NMDC products, and we capture valuable information on how users interact with the products to make improvements. Given the diverse nature of microbiome work, we acknowledge that we are not aware of all pressing data challenges and thus rely on the research community to help us identify the most important issues to prioritize. To date, we have conducted 24 interviews and one beta-testing call with 10 participants across all NMDC products, which have generated 321 insights and 120 action items. Herein, we describe the ways we engage with the microbiome research community to advance the NMDC mission.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics

Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.

59 BASIC BIOLOGICAL SCIENCES↗

Development and Application of Schema Based Occupant-Centric Building Performance Metrics

Occupant behavior can significantly influence the operation and performance of buildings. Many occupant-centric key performance indicators (KPIs) rely on having accurate counts of the number of occupants in a building, which is very different to how occupancy information is currently collected in the majority of buildings today. To address this gap, the authors develop a standardized methodology for the calculation of percent space utilization for buildings, which is formulated with respect to two prevalent operational data schemas: the Brick Schema and Project Haystack. The methodology is scalable across different levels of spatial granularity and irrespective of sensor placement. Moreover, the methods are intended to make use of typical occupancy sensors that capture presence level occupancy and not counts of people. Since occupant-hours is a preferable metric to use in KPI calculations, a method to convert between percent space utilization and occupant-hours using the design occupancy for a space is also developed. The methodology is demonstrated on a small commercial office space in Boulder, Colorado using data collected between June 2018 and February 2019. A multiple linear regression is performed that shows strong evidence for a relationship between building energy consumption and percent space utilization.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Battery Energy Storage Systems: A Review of Energy Management Systems and Health Metrics

With increasing concerns about climate change, there is a transition from high-carbon-emitting fuels to green energy resources in various applications including household, commercial, transportation, and electric grid applications. Even though renewable energy resources are receiving traction for being carbon-neutral, their availability is intermittent. To address this issue to achieve extensive application, the integration of energy storage systems in conjunction with these resources is becoming a recommended practice. Additionally, in the transportation sector, the increased demand for EVs requires the development of energy storage systems that can deliver energy for rigorous driving cycles, with lithium-ion-based batteries emerging as the superior choice for energy storage due to their high power and energy densities, length of their life cycle, low self-discharge rates, and reasonable cost. As a result, battery energy storage systems (BESSs) are becoming a primary energy storage system. The high-performance demand on these BESS can have severe negative effects on their internal operations such as heating and catching on fire when operating in overcharge or undercharge states. Reduced efficiency and poor charge storage result in the battery operating at higher temperatures. To mitigate early battery degradation, battery management systems (BMSs) have been devised to enhance battery life and ensure normal operation under safe operating conditions. Some BMSs are capable of determining precise state estimations to ensure safe battery operation and reduce hazards. Precise estimation of battery health is computed by evaluating several metrics and is a central factor in effective battery management systems. In this scenario, the accurate estimation of the health indicators (HIs) of the battery becomes even more important within the framework of a BMS. This paper provides a comprehensive review and discussion of battery management systems and different health indicators for BESSs, with suitable classification based on key characteristics.

Nazaralizadeh, Solmaz (ORCID:0009000737004039)↗