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At least 829 records · Page 46

Systems and methods for automatically identifying and linking names in digital resources

The present invention provides systems and methods for automatically identifying name-like-strings in digital resources, matching these name-like-string against a set of names held in an expertly curated database, and for those name-like-strings found in said database, enhancing the content by associating additional matter with the name, wherein said matter includes information about the names that is held within said database and pointers to other digital resources which include the same name and it synonyms.

97 MATHEMATICS AND COMPUTING↗

Deep Learning for Modeling Enhanced Geothermal Systems

Enhanced Geothermal Systems (EGS) offer a vast potential to expand the use of geothermal energy. Heat is extracted from this engineered system by injecting cold water into a subsurface fractures, which are in contact with the hot dry rock, and pulled through the production wells. Creating EGS requires improving the natural permeability of hot crystalline rocks. To develop economically viable EGS reservoirs, significant technical barriers (e.g., better stimulation technologies without adequate water and/or permeability) and non-technical barriers (e.g., land access and permitting) must be overcome. In this short conference paper, we present a workflow to address a part of this challenge – “How to develop economically viable EGS using existing technologies?”. Our workflow called the GeoThermalCloud (GTC) for EGS, leverages recent advances in machine learning, deep learning, and cloud computing. This GTC framework is open-source and available at https://github.com/SmartTensors/GeoThermalCloud.jl. The GTC framework provides trained deep learning (DL) models to estimate the net present value of a given EGS design scenario. The Geothermal Design Tool (https://github.com/GeoDesignTool/GeoDT.git), a fast and simplified multi-physics solver, is used to develop a database for training DL models. The database consists of EGS design parameters (inputs to DL model) and their net present value (output of DL model) in uncertain geologic systems. The EGS design parameters for constructing this training database are based on Utah FORGE but include the options of more wells and deeper depths. The DL models are trained by ingesting the EGS design parameters and estimating the corresponding net present value. Such an emulation allows us to screen various EGS designs quickly and identify good development strategies by coupling them with optimization techniques. Our preliminary results show promise in DL emulation of net present value. However, a lot more work is needed to improve the predictive capability of DL models (i.e., extensive hyperparameter tuning is necessary). This will be the primary focus of our future work.

artificial neural networks, geothermal↗

The 2022 Russian Invasion of Ukraine: Nuclear Supply Chains vs. Sanctions

The United States and European countries are unlikely to collectively approve of sanctions against Russian exports of nuclear fuel assemblies and uranium in the near term despite the 2022 invasion of Ukraine. Rather than bearing the costs that cutting off Russian imports would have on domestic nuclear energy production, the United States and European countries are more likely to prefer developing alternative supply chains of nuclear fuel and enriched uranium to reduce dependence on Russian resources. This outlook is primarily based on two areas of evaluation: (1) comparison of the Russian-made reactor fuel supply chain within the European Union (EU) in 2014 following the annexation of Crimea and in 2022 following the invasion of Ukraine, and (2) the dependence of France and the United States on Russia’s exports of enriched uranium. Additionally, the potential impacts to Kazakh uranium exports if trade routes for nuclear resources through Russia became unavailable were considered as an additional factor in the push for disentanglement from Russian nuclear resources. This work utilized BACI, a database of harmonized international trade data at the product level drawn from the United Nations Comtrade Database and created by the French international economics research institute CEPII.1 Comparisons of imports and exports were based on the trade value in U.S. dollars as reported in BACI instead of the quantity of the traded product. This evaluation only considers import and export data up until 2021, since the trade data for 2022 is incomplete within the Comtrade Database for several of the key countries presented in this work, including Australia, Canada, Namibia, Niger, and Russia.

Political science↗

Recent Metallic Fuel Data Recovery in FIPD

The Metallic Fuels Irradiation and Physics Database (FIPD) [1] is an organized collection of metallic fuel test pin data (U-xPu-yZr, = 0 ~ 28; y = 2 ~ 10) and documentation available to industry. FIPD mainly contains three types of data: (1) Fuel pin fabrication data, including fuel slug diameter, fuel slug length, cladding diameter, smear density, etc. (2) Fuel pin operation conditions, including axial distributions for power, temperatures, fluences, burnup, and isotopic densities, etc. and (3) Fuel pin post-irradiation examination (PIE) data, including fission gas release and gas chemistry, profilometry, and neutron radiography, etc. The operating conditions for pins with PIE data available in FIPD span significant ranges across key parameters. The fuel peak burnup extends from less than 5% up to 20 at%. The cladding peak temperature varies from about 490°C to 660°C. Finally, the cladding peak DPA shows a wide range from less than 5 to 120. These broad ranges reflect the diverse testing conditions and operational parameters captured in the available PIE data. More detail about FIPD can be found in ref. [2]. The database development is an ongoing effort covering metallic fuel experiments from the Experimental Breeder Reactor II (EBR-II) and the Fast Flux Test Facility (FFTF). As reported in the ref. [3, 4], most of the PIE data generated during the IFR program [5] has been collected, reviewed, processed, and integrated into FIPD. The most recently added PIE data can be found in ref. [4], which shows the collection of over 95% of the PIE data by the time of this paper. The recent improvements to the database are summarized in this paper.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Summary of Graphite Data Stored within NDMAS

The Graphite Technology Development Project provides data to support the design of graphite core components within specific reactor service conditions of the next generation of high-temperature, gas-cooled nuclear reactors. Physical, mechanical, and thermal properties of nuclear grade graphite were characterized for specimens that were unirradiated, irradiated, and irradiated under various stress conditions. The material properties include diameter, length, mass, density, compressive strength, tensile strength, flexural strength, modulus, resistivity, thermal diffusivity, and thermal expansion coefficient. Baseline graphite specimens are unirradiated from different grades (2114, IG-110, NBG-17, NBG-18, and PCEA) and different types used in different characterization tests (compressive, flexural, tensile, one-inch cylinder, and quarter-inch cylinder). The Advanced Graphite Creep (AGC) irradiation specimens are from a much larger number of grades and cylinder types (creep, piggyback, and pencil). For baseline graphite, characterization data for 7,756 specimens extracted from thirteen graphite billets were captured to the NDMAS database. For AGC experiments, four irradiation campaigns have been completed: AGC-1, AGC-2, AGC-3, and AGC-4. The ongoing HDG-1 (High-Dose Graphite) experiment, which began irradiation with Cycle 168B on August 26, 2020, includes specimens previously irradiated in AGC-2 in addition to the specimens originally destined for AGC-5.. Besides the characterization data, the AGC data includes irradiation monitoring and physics data representing the irradiation conditions of AGC specimens. Currently, all data for AGC-1, AGC-2, and AGC-3 have been captured to the NDMAS database. Only AGC-4 pre-irradiation and irradiation monitoring data have been captured, and HDG-1 pre-irradiation data are in process of being captured for unirradiated specimens. To date, a total of 38,149 material property records have been captured into NDMAS database for baseline and AGC specimens. All characterization data are qualified for use according to their perspective data verification reports. For the AGC irradiation campaigns, a total of 41,502 qualified physics calculation records were added for AGC-1, AGC-2, and AGC-3. Finally, a total of 173,698,505 AGC irradiation monitoring data records (thermocouple temperature, gas flow rate, gas pressure, gas moisture, applied load, and specimen displacement) have been captured to NDMAS; the majority of those records (~94%) are qualified data records.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Intern Poster: STIG Shouldn't Drop ACID

STIG (Structured Threat Intelligence Graph) is an open-source graph database tool from INL. It’s used to create and process cyber intelligence graphs, which are shared in the cyber threat intelligence community and used to train INL machine learning products like @DisCo. For quality machine learning and critical infrastructure defense, STIG’s database must be ACID: Atomic, Consistent, Isolated, Durable. Various ACID tests were designed and applied to STIG to ensure its behavior follows these properties.

99 - GENERAL AND MISCELLANEOUS↗

Do we have globally representative data to understand soil processes?

Understanding and modeling soils and soil organic matter (SOM) are central to a variety of human needs, from food production to ecosystem management. Soil data have been collected for over a century, but the global spatial and process representativeness of soil data remains unclear. We assessed the representativeness of currently available soil data that could be used to understand a variety of SOM processes. We used 16 open-source soil databases and data from over 281,000 unique locations globally, categorizing the databases into three main data types necessary to understand SOM processes: soil carbon stocks and fluxes, mechanistic drivers of these stocks and fluxes, and soil carbon gain or loss potential. We found that stock and driver data have extensive global coverage. However, data on soil carbon gain or loss potential, particularly data describing change in soils over time such as time series data, are severely limited in their global coverage. We conclude that while significant strides have been made in measuring soil carbon stocks and fluxes, and their drivers, we are limited in global data related to changes in soils over time. Our recommendations for soil data generators are to ensure precise metadata reporting and prioritizing sampling in underrepresented areas like tropical, arctic, mountainous, wetland and arid regions. We also encourage designing revisit schemes that explicitly support change detection and reporting multi-modal datasets that can aid in model development. Targeted measurement of low coverage soil data types and regions is necessary for a range of applications including current and future biogeochemical predictions, and their management and policy implications.

carbon fluxes↗

A centralized resource for bacterial–fungal interactions research

Research on bacterial-fungal interactions (BFIs) has revealed that fungi and bacteria frequently interact with one another within diverse ecosystems and microbiomes. Assessing the current state of knowledge within the field of BFI research, particularly with respect to what interactions between bacteria and fungi have been previously described, is very challenging and time consuming. This is largely due to a lack of any centralized resource, with reports of BFIs being spread across publications in numerous journals using non-standardized text to describe the relationships. To address this issue, we have developed the BFI Research Portal, a publicly accessible database of previously reported interactions between bacterial and fungal taxa to serve as a centralized resource for the field. Users can query bacterial or fungal taxa to see what members from the other kingdom have been observed as interaction partners. Search results are accompanied by interactive and intuitive visual outputs, and the database is a dynamic resource that will be updated as new BFIs are reported.

59 BASIC BIOLOGICAL SCIENCES↗

Applying U.S. metal fuel experience to new fuel designs for fast reactors

With the increasing interest in small modular reactors or microreactors, developers are working to design and submit licensing approval requests of U–10Zr-fueled fast reactors. The developers and their proponents cite prior metal fuel experience (worldwide, but U.S. experience in particular for many developers) as the motivation and justification for their reactor concepts. The experience with metal fuel deployment in sodium-cooled fast reactors as well as the underlying irradiation testing database, provide a suitable basis for analytically justifying the use of metal fuel in new reactors. The evolution of metal fuel design and capability illustrates the importance of key fuel design parameters to consider in new applications of the prior experience: fuel smeared density, plenum-to-fuel volume ratio, the ratio of cladding radius to thickness, fuel composition, and cladding and duct materials. In-service operating and deployment conditions to be considered include fuel linear heat generation rate, fuel temperature, cladding temperature, peak burnup and peak fast fluence. Fuel designs and in-service conditions that are bounded by the database and experience are most easily addressed, but deviations from those previous parameters and conditions can be addressed by considering impacts on previously established behavior and applying other mitigating conservatisms, as appropriate. Here, the authors recommend any new deployment proceed with fuel surveillance and monitoring to mitigate risk, application of conservative measures to address uncertainties, and a fuel qualification program that addresses a range of in-service operating conditions with production fuel. The work reported should be of interest to students and regulators unfamiliar with metal fuel in fast reactors.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Proxy Method to Bridge LCA Data Gaps Using Automated Material Classification and Probabilistic Under-Specification

Life cycle assessments (LCAs) are essential for understanding the environmental impacts of material production. However, gaps in life cycle inventory (LCI) data for material and chemical inputs present a key challenge for LCA practitioners, especially in the early design stages. Strategies for filling in these gaps require additional time and expertise, which can hinder the LCA’s completion. This study combined automatic material classification and probabilistic under-specification to create a time-efficient method to fill material LCI data gaps. To illustrate the proposed method, proxy environmental impact distributions were generated using publicly available material LCI data classified into the ChemOnt chemical taxonomy using the open-source chemical classification software ClassyFire. Input materials with data gaps were then classified into the same taxonomy, where proxy environmental impact values could be selected from the available distributions to quickly fill in any data gaps. Although these methods were applied to classify material production processes available in the Federal LCA Commons and Ecoinvent databases, they can be applied to any LCA database. This study shows that classifying materials by their chemical structure produces taxonomies with increased granularity relative to industrial classification, improving the ability of under-specified proxy data to be used for differentiating the environmental impacts of competing designs.

biological databases↗

Accurate Thermochemistry of Complex Lignin Structures via Density Functional Theory, Group Additivity, and Machine Learning

A molecular-level understanding of lignin structures and bond dissociation energies could facilitate depolymerization technologies. Still, this information is currently limited due to the lack of databases and the simplification of surrogate models. Here, substitution effects on seven common linkages in lignin polymers are systematically investigated. An automated reaction network generator is employed to create a database of structures. A new group additivity (GA) model based on principal component analysis (PCA) descriptors is introduced and trained on gas-phase density functional theory data of 4100 species at the M06-2X/6-311++G(d,p) level. Hydrogen bonds, local steric, and nonaromatic ring contributions are also incorporated. Lastly, we improve the accuracy of the group additivity model to reach the G4 theory by computing a data set of 770 species at this level and using a data fusion approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in $\mathrm{METLIN}$

We report Neutral loss (NL) spectral data presents a mirror of MS 2 data and is a valuable yet largely untapped resource for molecular discovery and similarity analysis. Tandem mass spectrometry (MS 2 ) data is effective for the identification of known molecules and the putative identification of novel, previously uncharacterized molecules (unknowns). Yet, MS 2 data alone is limited in characterizing structurally related molecules. To facilitate unknown identification and complement the METLIN-MS 2 fragment ion database for characterizing structurally related molecules, we have created a MS 2 to NL converter as a part of the METLIN platform. The converter has been used to transform METLIN’s MS 2 data into a neutral loss database (METLIN-NL) on over 860 000 individual molecular standards. The platform includes both the MS 2 to NL converter and a graphical user interface enabling comparative analyses between MS 2 and NL data. Examples of NL spectral data are shown with oxylipin analogues and two structurally related statin molecules to demonstrate NL spectra and their ability to help characterize structural similarity. Mirroring MS 2 data to generate NL spectral data offers a unique dimension for chemical and metabolite structure characterization.

59 BASIC BIOLOGICAL SCIENCES↗

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗

Enabling Scalable and Extensible Memory-mapped Datastores in Userspace

Exascale workloads are expected to incorporate data-intensive processing in close coordination with traditional physics simulations. These emerging scientific, data-analytics and machine learning applications need to access a wide variety of datastores in flat files and structured databases. Programmer productivity is greatly enhanced by mapping datastores into the application process's virtual memory space to provide a unified “in-memory” interface. Currently, memory mapping is provided by system software primarily designed for generality and reliability. However, scalability at high concurrency is a formidable challenge on exascale systems. Also, there is a need for extensibility to support new datastores potentially requiring HPC data transfer services. In this article, we present UMap , a scalable and extensible userspace service for memory-mapping datastores. Furthermore, through decoupled queue management, concurrency aware adaptation, and dynamic load balancing, UMap enables application performance to scale even at high concurrency. We evaluate UMap in data-intensive applications, including sorting, graph traversal, database operations, and metagenomic analytics. Our results show that UMap as a userspace service outperforms an optimized kernel-based service across a wide range of intra-node concurrency by 1.22-1.9 × . We performed two case studies to demonstrate UMap 's extensibility. First, a new datastore residing in remote memory is incorporated into UMap as an application-specific plugin. Second, we present a persistent memory allocator Metall built atop UMap for unified storage/memory.

97 MATHEMATICS AND COMPUTING↗

High-throughput virtual laboratory for drug discovery using massive datasets

Time-to-solution for structure-based screening of massive chemical databases for COVID-19 drug discovery has been decreased by an order of magnitude, and a virtual laboratory has been deployed at scale on up to 27,612 GPUs on the Summit supercomputer, allowing an average molecular docking of 19,028 compounds per second. Over one billion compounds were docked to two SARS-CoV-2 protein structures with full optimization of ligand position and 20 poses per docking, each in under 24 hours. GPU acceleration and high-throughput optimizations of the docking program produced 350× mean speedup over the CPU version (50× speedup per node). GPU acceleration of both feature calculation for machine-learning based scoring and distributed database queries reduced processing of the 2.4 TB output by orders of magnitude. The resulting 50× speedup for the full pipeline reduces an initial 43 day runtime to 21 hours per protein for providing high-scoring compounds to experimental collaborators for validation assays.

97 MATHEMATICS AND COMPUTING↗

Simulation Tools for Characterizing Stress Distribution in Laser Welded Dissimilar Joints

This project focuses on developing a thermo-metallurgical-mechanical modeling method to accurately predict the microstructural evolution and residual stress in laser welding between dissimilar metals, such as HSLA steel and high carbon equivalent (CE) gear steel. The method leverages a comprehensive material database to model the temperature and rate dependent phase transformations, along with their associated effects on material properties, such as thermal expansion and flow stress, throughout the welding process. A key innovation is the incorporation of phase transformation and phase-specific properties, which enhances the accuracy of residual stress predictions. The mixture material in the fusion zone due to the dissimilar metals will also be addressed in the numerical model. This is especially critical in scenarios involving phase transformations in the fusion zone and heat-affected zone (HAZ), where the phase changes can induce substantial residual stress variations. The material database has been generated using JMatPro. The modeling approach is implemented through a custom User Material (UMAT) subroutine, executed with the commercial finite element software Abaqus.

36 MATERIALS SCIENCE↗

A Play-Based Exploration of CO 2 Storage in the Illinois Basin (Final Technical Report)

This report documents the results of "A Play-Based Exploration of CO₂ Storage in the Illinois Basin" (DE-FE0032366), a project funded by the U.S. Department of Energy Office of Fossil Energy and Carbon Management and conducted by the Illinois State Geological Survey (ISGS) at the University of Illinois Urbana-Champaign in partnership with Visage Energy. The project adapted play-based exploration (PBE), a systematic basin-scale evaluation methodology from the petroleum industry, to screen areas of Illinois for commercial geologic carbon storage (GCS) in Cambro-Ordovician strata. The traditional play concept was expanded to encompass three play element groups, subsurface geologic factors, surface features, and societal factors, yielding 24 play elements with defensible suitability criteria applied through a five-tier classification scheme. An integrated geospatial database was assembled from ISGS, MGSC, MRCI, NATCARB, and public data sources, supported by significant data-improvement work including correction of legacy well locations, digitization of more than 1,300 well construction records using the DOE CATALOG team's OGRRE tool, compilation of a statewide 2D seismic database, and production of a refined fault and fold geodatabase.

58 GEOSCIENCES↗

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.

59 BASIC BIOLOGICAL SCIENCES↗