Final Phase I Technical Report - Deep Learning Enabled FAIR Data Management for Center for Functional Nanomaterials
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Sun, Yu↗
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MF Approach to Open Science: FAIR Data , Persistent Identifiers
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Boehnlein, Amber↗
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems
Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.
59 BASIC BIOLOGICAL SCIENCES↗
Biased degenerate ground-state sampling of small Ising models with converged quantum approximate optimization algorithm
The quantum alternating operator ansatz, a generalization of the quantum approximate optimization algorithm (QAOA), is a quantum algorithm used for approximately solving combinatorial optimization problems. QAOA typically uses the transverse field mixer as the driving Hamiltonian. One of the interesting properties of the transverse field driving Hamiltonian is that it results in nonuniform sampling of degenerate ground states of optimization problems. In this study, we numerically examine the fair sampling properties of the transverse field mixer QAOA, and Grover mixer QAOA (GM-QAOA), which provides theoretical guarantees of fair sampling of degenerate optimal solutions, up to a large enough p such that the mean expectation value converges to an optimal approximation ratio of 1. This comparison is performed with high-quality heuristically computed, but not necessarily optimal, QAOA angles, which give strictly monotonically improving solution quality as p increases. These angles are computed using the Julia based numerical simulation software JuliQAOA. Fair sampling of degenerate ground states is quantified using the Shannon entropy of the ground-state amplitudes distribution. The fair sampling properties are reported on several quantum signature Hamiltonians from previous quantum annealing fair sampling studies. Small random fully connected spin glasses are shown, which exhibit exponential suppression of some degenerate ground states with transverse field mixer QAOA. The transverse field mixer QAOA simulations show that some problem instances clearly saturate the Shannon entropy of 0 with a maximally biased distribution that occurs when the learning converges to an approximation ratio of 1 while other problem instances never deviate from a maximum Shannon entropy (uniform distribution) at any p step. Published by the American Physical Society 2025
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Sampling on NISQ Devices: "Who’s the Fairest One of All?"
Modern NISQ devices are subject to a variety of biases and sources of noise that degrade the solution quality of computations carried out on these devices. A natural question that arises in the NISQ era, is how fairly do these devices sample ground state solutions. To this end, we run five fair sampling problems (each with at least three ground state solutions) that are based both on quantum annealing and, on the Grover Mixer, -QAOA algorithm for gate-based NISQ hardware. In particular, we use seven IBM Q devices, the Aspen-9 Rigetti device, the IonQ device, and three D-Wave quantum annealers. For each of the fair sampling problems, we measure the ground state probability, the relative fairness of the frequency of each ground state solution with respect to the other ground state solutions, and the aggregate error as given by each hardware provider. Overall, our results show that NISQ devices do not achieve fair sampling yet. Furthermore, we also observe differences in the software stack with a particular focus on compilation techniques that illustrate what work will still need to be done to achieve a seamless integration of frontend (i.e., quantum circuit description) and backend compilation.
Computer Science↗
2D Dam-Break Analysis of L Lake and PAR Pond Dams Using HEC-RAS
In 1991 a dam-break study was conducted for the high hazard dams located at L Lake and PAR Pond on the Savannah River Site. Two scenarios were considered, over topping from a Probable Maximum Flood (PMF), and a fair weather dam-break for either or both dams. Unfortunately, no inundation map was developed from the study. The purpose of this project was to redo the original dam-break study with improved data and methodology to generate Inundation maps to assist with emergency response and evacuation plans. The Hydrologic Engineering Center's River Analysis System (HEC-RAS) is a free to download river analysis modeling program developed by the US Army Corps of Engineers capable of 1D and 2D hydraulic calculations. Version 5.0.7 (released March 2019) was used for this project. Digital elevation models for the area were retrieved from the US Geological Survey database and converted to a .hdf file within the program. Then the 2D flood area was identified from the contours. Both L Lake and PAR Pond were inputted as 1D storage areas because DEM data does not contain elevation values under water bodies. An elevation vs volume curve was available for both storage areas. Initial elevations were set for both scenarios. Both dams are earthen dams. The Steel Creek dam at L Lake has 6 ft diameter conduit with an upper and lower sluice gate. PAR pond dam consist of a weir and sluice gate connected to an 8 x 8 ft channel. Both outlets were modeled with a pool elevation vs discharge curve. The steel creek dam sluice gates were assumed to be fully open in all cases. As in the previous study, the dams were set to breach when they were overtopped by 1.5 ft during PMF conditions (Figure 1). A fair weather breach was set to be due to a piping failure (Figure 1). In the dual dam break during fair weather conditions the PAR pond dam fails 3 hours after Steel Creek to achieve maximum flooding in the down stream reaches. Simulation was run 3 days for each case and with a 1 minute computational interval. Maximum flooding occurs under PMF conditions with the failure of both dams. PAR pond dam fails first 16 hours and 32 minutes after the start of the simulation with the Steel creek dam failing 6 minutes later. In all cases, the bridges and roads spanning Steel Creek and Lower Three Runs will be inundated and potentially washed away. The Burtons Ferry Highway south of the storage areas will be partially flooded during PMF failure, dual fair weather failure, and PAR pond failure under fair weather conditions.
54 ENVIRONMENTAL SCIENCES↗
Deriving Transmissibility Functions from Finite Elements for Specifications
This work explores deriving transmissibility functions for a missile from a measured location at the base of the fairing to a desired location within the payload. A pressure on the outside of the fairing and the rocket motor’s excitation creates an acceleration at a measured location and a desired location. Typically, the desired location is not measured. In fact, it is typical that the payload may change, but measured acceleration at the base of the fairing is generally similar to previous test flights. Given this knowledge, it is desired to use a finite-element model to create a transmissibility function which relates acceleration from the previous test flight’s measured location at the base of the fairing to acceleration at a location in the new payload. Four methods are explored for deriving this transmissibility, with the goal of finding an appropriate transmissibility when both the pressure and rocket motor excitation are equally present. In conclusion, these methods are assessed using transient results from a simple example problem, and it is found that one of the methods gives good agreement with the transient results for the full range of loads considered.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
A tri-level distribution locational marginal price-based demand response framework
Here, in this paper, we propose a tri-level, nested, two-stage price-based demand response (PBDR) framework that considers distribution locational marginal price (DLMP) as DR enabler between load-serving entities (LSE), demand response providers (DRPs), and customers in the day-ahead distribution market. It enables LSE and customer interactions by using multiple DRPs, positioned in-between, and independently optimizes their objectives. The problem is formulated using linear power flow with approximated power losses and its application in DLMP as DR pricing. The tri-level problem is solved using a nested reformulation & decomposition (R&D) method and tested on the real Indian-108 bus distribution system under various dynamic pricings. Further, the temporal–spatial variations in DLMPs are assessed using fairness criteria. Numerical analyses demonstrate that DLMP applications can effectively improve economic efficiency, and transparency in DR programs valuation with a favorable fairness margin. The results show that DLMP as DR pricing signal induces (0-2) % variation in DLMP for DR participation up to 10 %. Further, it gives over 90 % fairness over temporal–spatial variation for all the customers.
24 POWER TRANSMISSION AND DISTRIBUTION↗
CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis
Abstract Background Many organizations face challenges in managing and analyzing data, especially when relevant datasets arise from multiple sources and methods. Analyzing heterogeneous datasets and additional derived data requires rigorous tracking of their interrelationships and provenance. This task has long been a Grand Challenge of data science and has more recently been formalized in the FAIR principles: that all data objects be Findable, Accessible, Interoperable, and Reusable, both for machines and for people. Adherence to these principles is necessary for proper stewardship of information, for testing regulatory compliance, for measuring the efficiency of processes, and for facilitating reuse of data-analytical frameworks. Findings We present the Contextual Ontology-based Repository Analysis Library (CORAL), a platform that greatly facilitates adherence to all 4 of the FAIR principles, including the especially difficult challenge of making heterogeneous datasets Interoperable and Reusable across all parts of a large, long-lasting organization. To achieve this, CORAL's data model requires that data generators extensively document the context for all data, and our tools maintain that context throughout the entire analysis pipeline. CORAL also features a web interface for data generators to upload and explore data, as well as a Jupyter notebook interface for data analysts, both backed by a common API. Conclusions CORAL enables organizations to build FAIR data types on the fly as they are needed, avoiding the expense of bespoke data modeling. CORAL provides a uniquely powerful platform to enable integrative cross-dataset analyses, generating deeper insights than are possible using traditional analysis tools.
97 MATHEMATICS AND COMPUTING↗
SetGo: Metadata Readiness for Scientific AI Datasets
Scientific datasets intended for AI use require both computational readiness for model training and metadata readiness for discovery, sharing, and reuse. The Readiness Engine for Data Integration (REDI) addresses computational readiness, but no corresponding tool evaluates whether a dataset’s metadata are sufficiently complete, governed, and standards-compliant for publication and agent-based consumption. Existing FAIR assessors operate only on published repository records, and no single system covers FAIR compliance, licensing, provenance, governance, reproducibility, and catalog readiness together. We present SetGo, an open-source Python toolkit that assesses and repairs metadata readiness across these six dimensions before a dataset is published or archived. Applied to four scientific corpora, SetGo surfaces deficiencies that general-purpose tools do not detect: ERA5 climate metadata scores 4% on ACDD 1.3 compliance; materials datasets fail OPTIMADE species-definition requirements; and PDB-derived proteomics data carries licensing terms incompatible with standard SPDX identifiers. Guided enrichment raises overall FAIR scores from 52–57% to 81–91%, and a single setgo publish command pushes to Hugging Face Hub, CKAN, or OpenMetadata with ML Commons Croissant 1.0 metadata sidecars. To support interactive and automated workflows, SetGo integrates with coding agents powered by large language models (LLMs) through a /setgo skill that enables natural-language execution of the full assess–enrich–publish loop, with user involvement limited to supplying missing metadata values.
Wilkinson, Sean [ORNL] (ORCID:0000000214437479)↗
Codebase release 2.0 for UFOManager
Research in the data-intensive discipline of high energy physics (HEP) often relies on domain-specific digital contents. Reproducibility of research relies on proper preservation of these digital objects. This paper reflects on the interpretation of principles of Findability, Accessibility, Interoperability, and Reusability (FAIR) in such context and demonstrates its implementation by describing the development of an end-to-end support infrastructure for preserving and accessing Universal FeynRules Output (UFO) models guided by the FAIR principles. UFO models are custom-made python libraries used by the HEP community for Monte Carlo simulation of collider physics events. Our framework provides simple but robust tools to preserve and access the UFO models and corresponding metadata in accordance with the FAIR principles.
Neubauer, Mark S.↗
Equity Considerations in Siting Consolidated Interim Storage Facilities for Commercial Spent Nuclear Fuel
Questions of equity and fairness are often raised by representatives from State, Tribal and local governments and members of the public when resolving conflicts over siting of nuclear facilities. However, the two terms are not synonymous: equity can be quantified while fairness is much more subjective. The Department of Energy's (DOE) December 2021 Request for Information sought input on how to site federal facilities for the temporary, consolidated storage of spent nuclear fuel (SNF) using a consent-based approach. It is anticipated that just such questions about equity and fairness associated with the potential emergence of more than one host site may be raised by the twelve groups of university, nonprofit and private sector partners (Consortia) working to support community engagement, inclusively involve stakeholders, build relationships, and develop innovative forms of mutual learning and public capacity to participate in the consent-based siting process for a federal consolidated interim storage facility during the current Planning & Capacity Building stage of the consent-based siting process. In terms of DOE's Integrated Waste Management System (IWMS), sociopolitical equity concepts are a factor in all aspects of IWMS development and operations and will be particularly applicable should two or more host sites become a possibility, either by the emergence of multiple volunteer hosts or by pursuit as a IWMS program strategy. This paper summarizes recent analyses that explore how four equity metrics - number of states, division of the projected SNF total by the year 2083, current population and land area - might be perceived by host communities, states and regions if two, three or four sites for hosting federal consolidated interim storage facilities were to be contemporaneously realized. Existing institutional arrangements, including Nuclear Regulatory Commission regions, Federal Energy Regulatory Commission regions and Low-Level Radioactive Waste Disposal Compacts, were selected to create hypothetically merged two, three and four-region scenarios to calculate how the four metrics balance out. Projected SNF burden was prioritized with regional contiguity of the consolidated regions a requirement for a functional scenario. The intent was not to promote or suggest any construct as a program objective; the configurations are geopolitical abstractions only to explore potential perceptions of equity. Understanding the possible issues of equity that could arise may benefit program efforts toward achieving a cooperative federalism wherein both the federal and multiple State governments share the goal of manifesting more than one federal consolidated interim storage facility. The main finding is that it is not possible to optimize for all four metrics simultaneously. The analyses demonstrate that trying to create a sense of equity by backfitting a solution to a random population and land distribution will always contain a degree of artificiality.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
ESS-DIVE reporting format for field measurements of soil respiration
This is a new data and metadata reporting format for soil respiration data, based on engagement with a wide range of researchers in the earth and ecological sciences as well as expert advisory panels. Reporting formats are intended to be ‘bottom-up’, community-developed documents and templates that can enable consistent, findable, accessible, interoperable, and reproducible (FAIR) data; our goal was a reporting format that would be relevant and useful for synthesis activities, optimizing data discoverability and usability while not placing an undue burden on data contributors. The format is split into two levels of information—metadata about chambers (used to measure soil respiration in the field), and the measured data themselves. The file data_reportingformat_template.xlsx contains information on how the data table should be structured, including field names, field descriptions, and units; the chammetadata_reportingformat_template.xlsx file contains similar information for the chamber-level metadata. Fundamentally, this format aims to enable FAIR data through an easy-to-use guide for data providers interested in formatting their data in a common way, and provide ‘future-proofing’ capabilities to support reanalyses of soil respiration data, a globally-important component of the carbon cycle.
54 ENVIRONMENTAL SCIENCES↗
FAIRLinked: Data FAIRification Tools for Materials Data Science
FAIRLinked is a software package created to support the FAIRification of materials science data, ensuring proper alignment with FAIR principles: Findable, Accessible, Interoperable, and Reusable. It is built to be compatible with MDS-Onto, an ontology designed to capture the semantics of various types of materials data, enabling integration and sharing across different research workflows. The package is subdivided into three subpackages: InterfaceMDS, RDFTableConversion, and QBWorkflow. The first subpackage, InterfaceMDS allows users to search for terms using either string search or various filters, explore different domains and subdomains, and add terms to MDS-Onto. RDFTableConversion is used for serialization and deserialization of data from CSV into JSONLDs and vice versa in a way that captures the semantics of the data using MDS-Onto. Lastly, QBWorkflow is a serialization and deserialization workflow that incorporates RDF Data Cube vocabulary, useful for working with multidimensional datasets. By offering these packages, FAIRLinked lowers the barrier of creating FAIR, machine-actionable data for researchers in the materials science community.
FAIR↗
Surface Chemistry of Liquid Bismuth under Oxygen and Water Vapor Studied by Ambient Pressure X-ray Photoelectron Spectroscopy
Bismuth (Bi) has a fairly low melting point of 544 K making it practical as a liquid metal medium in a number of applications. Under ambient atmospheric conditions the surface of solid Bi oxidizes. While the solid Bi interface has been fairly well characterized with surface science studies upon exposure to oxygen, to date little is known about the molecular level reactivity of the liquid interface. Here, using ambient pressure X-ray photoelectron spectroscopy the liquid-gas interfacial chemistry of Bi was examined upon exposure to oxygen gas and water vapor at 550 K up to a maximum pressure of 0.5 Torr. Water vapor remained unreactive towards the liquid interface over the entire pressure range. Oxygen remined unreactive up to 10 –4 Torr, whereas above this pressure oxidation was observed forming Bi 2 O 3 . The oxidation exposure onset was > 5 x 10 5 Langmuirs, significantly higher than what is required for solid Bi interfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Drive Cycles, Battery Pack Scaling, and Usage Considerations for Long-Haul and Regional-Haul Electric Trucks
Electrifying Class-8 heavy-duty trucks presents a promising opportunity to enhance energy efficiency and reduce freight transport costs. Battery electric trucks (BETs), once considered niche, are gaining traction due to advancements in battery technology and cost reductions. However, accurately predicting battery lifespan under realistic usage conditions remains a key challenge. Understanding battery failure mechanisms and their links to design, operation, and management is essential for developers and fleet operators. This study introduces a method to develop simplified, lab-testable dynamic stress test (DST) cycles for regional and long-haul Class-8 BETs, derived from real-world diesel truck usage. These DSTs enable benchmarking of battery technologies, identification of aging stressors, and optimization of battery design, life, and cost. The approach supports evaluation of key metrics such as levelized cost of driving and total cost of ownership, aiding fair comparisons and adoption decisions. We also propose feasible battery pack sizes that meet current driving demands with strategic charging, and a method to scale pack-level DSTs to cell-level cycles for lab-based testing. These tools facilitate tradeoff analysis across battery chemistries, pack sizing, and charging strategies, while offering means to get insights into battery aging under realistic conditions-ultimately supporting informed BET deployment decisions.
25 ENERGY STORAGE↗
Precise measurement of nuclear interaction cross sections towards neutron-skin determination with R 3 B
The R 3 B (Reactions with Relativistic Radioactive Beams) experiment as a major instrument of the NUSTAR collaboration for the research facility FAIR in Darmstadt is designed for kinematically complete studies of reactions with high-energy radioactive beams. Part of the broad physics program of R 3 B is to constrain the asymmetry term in the nuclear equation-of-state and hence improve the description of highly asymmetric nuclear matter (e.g., in neutron stars). For a precise determination of the neutron-skin thickness – an observable which is directly correlated with the symmetry energy in theoretical calculations – by measuring absolute fragmentation cross sections, it is essential to quantify the uncertainty and challenge the reaction model under stable conditions. During the successful FAIR Phase-0 campaign of R 3 B, we precisely measured the energy dependence of total interaction cross sections in 12 C + 12 C collisions, for a direct comparison with calculations based on the eikonal reaction theory.
Ponnath, L. (ORCID:0000000286742624)↗