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DOE OSTI2017

Dry Storage Cask Inventory Assessment

The report, Commercial Spent Nuclear Fuel and High-Level Radioactive Waste Inventory Report [FCRDNFST-2013-000263, Vinson/Metzger/Carter 2017], provides information on the inventory of commercial spent nuclear fuel (SNF) as well as Government-owned SNF and High Level Waste (HLW) in the U.S. Department of Energy (DOE) complex. Inventory forecasts for commercial SNF were made for a few selected scenarios of future commercial nuclear power generation involving the existing reactor fleet including one scenario involving reactors under construction. This Dry Storage Cask Inventory Assessment report uses the data contained in FCRD-NFST-2013- 000263 to define the existing inventory of SNF in dry storage. This information is integrated with data on dry storage canisters and casks from the report, Storage and Transport Cask Data for Used Commercial Nuclear Fuel, 2013 U. S. Edition [ATI-TR-13047 2013] in a Microsoft Access database (hereinafter referred to as the Dry Storage Cask/Inventory Database). The Dry Storage Cask/Inventory Database is used to produce queries for assessing the various systems used for the existing inventory of dry storage casks. The database and this report will be revised in the future as the inventory of fuel in dry storage changes and as additional information becomes available. Both bare fuel and canistered dry storage casks are currently used to dry store SNF. Only 4 utilities currently use bare fuel storage systems for dry storage at 5 reactor sites. Seven unique bare fuel storage cask systems are used to store a total of 9,694 spent fuel assemblies in 212 total casks.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2018

Sirepo : an open-source cloud-based software interface for X-ray source and optics simulations

Sirepo , a browser-based GUI for X-ray source and optics simulations, is presented. Such calculations can be performed using SRW ( Synchrotron Radiation Workshop ), which is a physical optics computer code, allowing simulation of entire experimental beamlines using the concept of a `virtual beamline' with accurate treatment of synchrotron radiation generation and propagation through the X-ray optical system. SRW is interfaced with Sirepo by means of a Python application programming interface. Sirepo supports most of the optical elements currently used at beamlines, including recent developments in SRW . In particular, support is provided for the simulation of state-of-the-art X-ray beamlines, exploiting the high coherence and brightness of modern light source facilities. New scientific visualization and reporting capabilities have been recently implemented within Sirepo , as well as automatic determination of electron beam and undulator parameters. Publicly available community databases can be dynamically queried for error-free access to material characteristics. These computational tools can be used for the development and commissioning of new X-ray beamlines and for testing feasibility and optimization of experiments. The same interface can guide simulation on a local computer, a remote server or a high-performance cluster. Sirepo is available online and also within the NSLS-II firewall, with a growing number of users at other light source facilities. Our open source code is available on GitHub.

99 GENERAL AND MISCELLANEOUS↗

NASA NTRS1993

A parallel data management system for large-scale NASA datasets

The past decade has experienced a phenomenal growth in the amount of data and resultant information generated by NASA's operations and research projects. A key application is the reprocessing problem which has been identified to require data management capabilities beyond those available today (PRAT93). The Intelligent Information Fusion (IIF) system (ROEL91) is an ongoing NASA project which has similar requirements. Deriving our understanding of NASA's future data management needs based on the above, this paper describes an approach to using parallel computer systems (processor and I/O architectures) to develop an efficient parallel database management system to address the needs. Specifically, we propose to investigate issues in low-level record organizations and management, complex query processing, and query compilation and scheduling.

Srivastava, Jaideep↗

DOE OSTI2023

The Coastal Carbon Library and Atlas: Open source soil data and tools supporting blue carbon research and policy

Abstract Quantifying carbon fluxes into and out of coastal soils is critical to meeting greenhouse gas reduction and coastal resiliency goals. Numerous ‘blue carbon’ studies have generated, or benefitted from, synthetic datasets. However, the community those efforts inspired does not have a centralized, standardized database of disaggregated data used to estimate carbon stocks and fluxes. In this paper, we describe a data structure designed to standardize data reporting, maximize reuse, and maintain a chain of credit from synthesis to original source. We introduce version 1.0.0. of the Coastal Carbon Library, a global database of 6723 soil profiles representing blue carbon‐storing systems including marshes, mangroves, tidal freshwater forests, and seagrasses. We also present the Coastal Carbon Atlas, an R‐shiny application that can be used to visualize, query, and download portions of the Coastal Carbon Library. The majority (4815) of entries in the database can be used for carbon stock assessments without the need for interpolating missing soil variables, 533 are available for estimating carbon burial rate, and 326 are useful for fitting dynamic soil formation models. Organic matter density significantly varied by habitat with tidal freshwater forests having the highest density, and seagrasses having the lowest. Future work could involve expansion of the synthesis to include more deep stock assessments, increasing the representation of data outside of the U.S., and increasing the amount of data available for mangroves and seagrasses, especially carbon burial rate data. We present proposed best practices for blue carbon data including an emphasis on disaggregation, data publication, dataset documentation, and use of standardized vocabulary and templates whenever appropriate. To conclude, the Coastal Carbon Library and Atlas serve as a general example of a grassroots F.A.I.R. (Findable, Accessible, Interoperable, and Reusable) data effort demonstrating how data producers can coordinate to develop tools relevant to policy and decision‐making.

Holmquist, James R.↗

NASA NTRS1989

A rapid prototyping/artificial intelligence approach to space station-era information management and access

Applications of rapid prototyping and Artificial Intelligence techniques to problems associated with Space Station-era information management systems are described. In particular, the work is centered on issues related to: (1) intelligent man-machine interfaces applied to scientific data user support, and (2) the requirement that intelligent information management systems (IIMS) be able to efficiently process metadata updates concerning types of data handled. The advanced IIMS represents functional capabilities driven almost entirely by the needs of potential users. Space Station-era scientific data projected to be generated is likely to be significantly greater than data currently processed and analyzed. Information about scientific data must be presented clearly, concisely, and with support features to allow users at all levels of expertise efficient and cost-effective data access. Additionally, mechanisms for allowing more efficient IIMS metadata update processes must be addressed. The work reported covers the following IIMS design aspects: IIMS data and metadata modeling, including the automatic updating of IIMS-contained metadata, IIMS user-system interface considerations, including significant problems associated with remote access, user profiles, and on-line tutorial capabilities, and development of an IIMS query and browse facility, including the capability to deal with spatial information. A working prototype has been developed and is being enhanced.

Carnahan, Richard S., Jr.↗

DOE OSTI2025

Role of Uncertainty Quantification in the Explainability of Large Language Models for the Nuclear Industry

The meteoric rise of generative artificial intelligence (AI) large language models (LLMs) has created an opportunity to utilize them to increase efficiencies in a multitude of industries. While LLMs carry great potential to revolutionize the manner in which work is performed, numerous known deficiencies limit their utility, including the black box nature of the models, the stochastic nature of the response (i.e., presenting the same prompt multiple times results in different responses), and the potential for hallucination. Widespread adoption of LLMs in safety-critical industries such as nuclear will require some form of explainability to assure end users that the LLM’s response to a given query is valid. Model uncertainty is inherently linked to the concepts of trust and explainability, and can be used to identify situations in which the model is insufficiently certain about its answer. Although uncertainty is not enough in and of itself to determine the suitability of an answer—a model can be very certain of an inaccurate answer—it still provides valuable supporting information. Practical methodologies for gauging or quantifying the uncertainty in LLM outputs are presented herein, along with examples based on nuclear-specific prompts.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2015

Continuous Security and Configuration Monitoring of HPC Clusters

Continuous security and configuration monitoring of information systems has been a time consuming and laborious task for system administrators at the High Performance Computing (HPC) center. Prior to this project, system administrators had to manually check the settings of thousands of nodes, which required a significant number of hours rendering the old process ineffective and inefficient. This paper explains the application of Splunk Enterprise, a software agent, and a reporting tool in the development of a user application interface to track and report on critical system updates and security compliance status of HPC Clusters. In conjunction with other configuration management systems, the reporting tool is to provide continuous situational awareness to system administrators of the compliance state of information systems. Our approach consisted of the development, testing, and deployment of an agent to collect any arbitrary information across a massively distributed computing center, and organize that information into a human-readable format. Using Splunk Enterprise, this raw data was then gathered into a central repository and indexed for search, analysis, and correlation. Following acquisition and accumulation, the reporting tool generated and presented actionable information by filtering the data according to command line parameters passed at run time. Preliminary data showed results for over six thousand nodes. Further research and expansion of this tool could lead to the development of a series of agents to gather and report critical system parameters. However, in order to make use of the flexibility and resourcefulness of the reporting tool the agent must conform to specifications set forth in this paper. This project has simplified the way system administrators gather, analyze, and report on the configuration and security state of HPC clusters, maintaining ongoing situational awareness. Rather than querying each cluster independently, compliance checking can be managed from one central location.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1990

CLIPS: A tool for corn disease diagnostic system and an aid to neural network for automated knowledge acquisition

This paper describes the building of a corn disease diagnostic expert system using CLIPS, and the development of a neural expert system using the fact representation method of CLIPS for automated knowledge acquisition. The CLIPS corn expert system diagnoses 21 diseases from 52 symptoms and signs with certainty factors. CLIPS has several unique features. It allows the facts in rules to be broken down to object-attribute-value (OAV) triples, allows rule-grouping, and fires rules based on pattern-matching. These features combined with the chained inference engine result to a natural user query system and speedy execution. In order to develop a method for automated knowledge acquisition, an Artificial Neural Expert System (ANES) is developed by a direct mapping from the CLIPS system. The ANES corn expert system uses the same OAV triples in the CLIPS system for its facts. The LHS and RHS facts of the CLIPS rules are mapped into the input and output layers of the ANES, respectively; and the inference engine of the rules is imbedded in the hidden layer. The fact representation by OAC triples gives a natural grouping of the rules. These features allow the ANES system to automate rule-generation, and make it efficient to execute and easy to expand for a large and complex domain.

Wu, Cathy↗

DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

NASA NTRS2008

Moving Away from Ones and Zeros, Designing a Ground Data System Based on Higher Levels of Abstraction

Previous JPL ground systems have been designed with the Ground Data System (GDS) engineer in mind. The focus on these systems has been on packaging and delivery of low level information (frames, packets, telemetry values) to the end user. It was not that long ago when project teams would be huddled over a workstation, examining crude displays of telemetry bits organized in various ways, trying to determine the status of a spacecraft. Understanding the data often required additional levels of GDS expertise, or worse, transformation of the raw data into alternative formats followed by ingestion into other tools so that the data became meaningful. The primary focus was often to answer these types of questions: "Why did this particular frame fail Reed-Solomon decode? Why did this packet get marked as invalid? Why am I missing a block of telemetry from my query?" -- which are completely valid questions to ask from a GDS Engineer's point of view, and large families of tools have been designed to help answer these questions. But these are not the questions that most users care about - which are more like: "Why is the battery state of charge trending down? Show me a summary image report for the last traverse to the target. Show me a data accountability summary for the last DSN pass." Answers to these questions, which are what users are looking for, requires a higher level of abstraction and supporting tools than mining through ones and zeros. JPL has created a next generation capability called the Mission Data Processing and Control System (MPCS) which is designed to support this higher level of abstraction by providing customizable views of the ground system combining collections of lower level information into more meaningful ways. Instead of examining frames, packets, and individual telemetry data points -- MPCS is capable of providing comprehensive summary reports, product status, overall flight/ground event status, as well as payload health summaries. Based on these higher level views, end users can make tactical or strategic decisions, or drop into detailed analysis as needed. System designers need to continue building systems that support low level GDS troubleshooting - but the basic design of a GDS should be geared towards what end users actually need to see. This paper will describe the capabilities of MPCS that directly support these higher levels of abstraction, and which are being used today in missions such as the Mars Science Laboratory and other NASA missions.

MPCS↗

NASA NTRS2016

A Strategic Approach to Medical Care for Exploration Missions

Exploration missions will present significant new challenges to crew health, including effects of variable gravity environments, limited communication with Earth-based personnel for diagnosis and consultation for medical events, limited resupply, and limited ability for crew return. Providing health care capabilities for exploration class missions will require system trades be performed to identify a minimum set of requirements and crosscutting capabilities which can be used in design of exploration medical systems. Current and future medical data, information, and knowledge must be cataloged and put in formats that facilitate querying and analysis. These data may then be used to inform the medical research and development program through analysis of risk trade studies between medical care capabilities and system constraints such as mass, power, volume, and training. These studies will be used to define a Medical Concept of Operations to facilitate stakeholder discussions on expected medical capability for exploration missions. Medical Capability as a quantifiable variable is proposed as a surrogate risk metric and explored for trade space analysis that can improve communication between the medical and engineering approaches to mission design. The resulting medical system approach selected will inform NASA mission architecture, vehicle, and subsystem design for the next generation of spacecraft.

Antonsen, E.↗

NASA NTRS2003

Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation: Second Year Progress Report

Mesh generation has long been recognized as a bottleneck in the CFD process. While much research on automating the volume mesh generation process have been relatively successful,these methods rely on appropriate initial surface triangulation to work properly. Surface discretization has been one of the least automated steps in computational simulation due to its dependence on implicitly defined CAD surfaces and curves. Differences in CAD peometry engines manifest themselves in discrepancies in their interpretation of the same entities. This lack of "good" geometry causes significant problems for mesh generators, requiring users to "repair" the CAD geometry before mesh generation. The problem is exacerbated when CAD geometry is translated to other forms (e.g., IGES )which do not include important topological and construction information in addition to entity geometry. One technique to avoid these problems is to access the CAD geometry directly from the mesh generating software, rather than through files. By accessing the geometry model (not a discretized version) in its native environment, t h s a proach avoids translation to a format which can deplete the model of topological information. Our approach to enable models developed in the Denali software environment to directly access CAD geometry and functions is through an Application Programming Interface (API) known as CAPRI. CAPRI provides a layer of indirection through which CAD-specific data may be accessed by an application program using CAD-system neutral C and FORTRAN language function calls. CAPRI supports a general set of CAD operations such as truth testing, geometry construction and entity queries.

Afjeh, Abdollah A.↗

DOE OSTI2017

Software-defined Quantum Networking Ecosystem

The software enables a user to perform modeling and simulation of software-defined quantum networks. The software addresses the problem of how to synchronize transmission of quantum and classical signals through multi-node networks and to demonstrate quantum information protocols such as quantum teleportation. The software approaches this problem by generating a graphical model of the underlying network and attributing properties to each node and link in the graph. The graphical model is then simulated using a combination of discrete-event simulators to calculate the expected state of each node and link in the graph at a future time. A user interacts with the software by providing an initial network model and instantiating methods for the nodes to transmit information with each other. This includes writing application scripts in python that make use of the software library interfaces. A user then initiates the application scripts, which invokes the software simulation. The user then uses the built-in diagnostic tools to query the state of the simulation and to collect statistics on synchronization.

Humble, Travis S.↗

DOE OSTI2025

Computationally efficient models for aqueous organic redox flow batteries

The rising usage of intermittent energy has garnered the need for large scale energy storage systems. Redox flow batteries (RFB) based energy storage system shows promising potential. Numerical simulations and machine learning approaches have been widely used to study RFB performance. The development of autonomous material discovery framework and digital twin of energy storage system usually needs to query cell performance through fast response models. In this study, two computationally efficient models are introduced: a physics-based analytical flow battery model (EZBattery), and a machine learning operator model (Deep Operator Network, denoted by DeepONet). Both models can provide cell performance near instantly, and prediction accuracy was systematically examined on an application of evaluating the performances of a 780 cm 2 aqueous organic redox flow battery (AORFB), using potential anolyte candidates in dihydroxyphenazine (DHP)-based family of organic materials. A validated computationally expansive 3-dimensional multi-physics finite element model by COMSOL was used as the ground truth and provided the training data set for the DeepONet. 1280 samples were generated with 10 properties to mimic the different possible anolyte candidates, and the cell performances were evaluated under 10 different combined operating conditions. The accuracy comparisons for the two computationally efficient models show that both models can provide comparable accuracy in predicting cell charging/discharging voltage curves. DeepONet can provide slightly higher overall accuracy than EZBattery with faster calculation speed, but highly relies on the training dataset. EZBattery does not need a training dataset and can provide interpretable physics-based explanations of the results, while being more flexible to adjust to adapt any different cell designs, flow battery architectures, and electrolyte materials.

Analytical model↗

DOE OSTI2015

Global prevalence and distribution of genes and microorganisms involved in mercury methylation

Mercury methylation produces the neurotoxic, highly bioaccumulative methylmercury (MeHg). Recent identification of the methylation genes (hgcAB) provides the foundation for broadly evaluating microbial Hg-methylation potential in nature without making explicit rate measurements. We first queried hgcAB diversity and distribution in all available microbial metagenomes, encompassing most environments. The genes were found in nearly all anaerobic, but not in aerobic, environments including oxygenated layers of the open ocean. Critically, hgcAB was effectively absent in ~1500 human microbiomes, suggesting a low risk of endogenous MeHg production. New potential methylation habitats were identified, including invertebrate guts, thawing permafrost, coastal dead zones, soils, sediments, and extreme environments, suggesting multiple routes for MeHg entry into food webs. Several new taxonomic groups potentially capable of Hg-methylation emerged, including lineages having no cultured representatives. We then begin to address long-standing evolutionary questions about Hg-methylation and ancient carbon fixation mechanisms while generating a new global view of Hg-methylation potential.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

Massively parallel support for a case-based planning system

Case-based planning (CBP), a kind of case-based reasoning, is a technique in which previously generated plans (cases) are stored in memory and can be reused to solve similar planning problems in the future. CBP can save considerable time over generative planning, in which a new plan is produced from scratch. CBP thus offers a potential (heuristic) mechanism for handling intractable problems. One drawback of CBP systems has been the need for a highly structured memory to reduce retrieval times. This approach requires significant domain engineering and complex memory indexing schemes to make these planners efficient. In contrast, our CBP system, CaPER, uses a massively parallel frame-based AI language (PARKA) and can do extremely fast retrieval of complex cases from a large, unindexed memory. The ability to do fast, frequent retrievals has many advantages: indexing is unnecessary; very large case bases can be used; memory can be probed in numerous alternate ways; and queries can be made at several levels, allowing more specific retrieval of stored plans that better fit the target problem with less adaptation. In this paper we describe CaPER's case retrieval techniques and some experimental results showing its good performance, even on large case bases.

Kettler, Brian P.↗

DOE OSTI2025

Differentially Private Map Matching (DPMM) v1.0

Human mobility trajectories provide valuable information for developing mobility applications, as they contain diverse and rich information about the users. User mobility data is valuable for various applications such as intelligent transportation systems (ITS), commercial business models, and disease-spread models. However, such spatio-temporal traces may pose a threat to user privacy. GPS trajectories in their raw form are not suitable for transportation studies, as they require matching locations with nearest road links — a process called map-matching. This software implements a differential privacy (DP)-based map-matching algorithm, called DPMM, that generates link-level location trajectories in a privacy-preserving manner to protect users' origin destinations (OD) and travel paths. OD privacy is achieved by injecting Planar Laplace noise to the user OD GPS points. Travel-path privacy is provided with randomized travel path construction using exponential DP mechanism. The injected noise level is selected adaptively, by considering the link density of the location and the functional category of the localized links. For path privacy, our mechanism samples waypoints and selects candidate paths between waypoints. DPMM provides privacy effectively with respect to link density instead of other trajectory samples in the database compared to other privacy mechanisms. Compared to the different baseline models our DP-based privacy model offers closer query responses to the raw data in terms of individual and aggregate trajectory-level statistics with an average at absolute deviation from the baseline for individual statistics on ϵ = 1.0. Beyond individual trajectory statistics, the DPMM outperforms the other benchmark DP-based mechanisms on different aggregate statistics with up to 8x improvement in utility.

Peisert, Sean [Lawrence Berkeley National Laborato↗

DOE OSTI2014

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell. Various computational models rely on random gene selection to infer such networks from microarray data. While incorporation of prior knowledge into data analysis has been deemed important, in practice, it has generally been limited to referencing genes in probe sets and using curated knowledge bases. We investigate the impact of augmenting microarray data with semantic relations automatically extracted from the literature, with the view that relations encoding gene/protein interactions eliminate the need for random selection of components in non-exhaustive approaches, producing a more accurate model of cellular behavior. A genetic algorithm is then used to optimize the strength of interactions using microarray data and an artificial neural network fitness function. The result is a directed and weighted network providing the individual contribution of each gene to its target. For testing, we used invasive ductile carcinoma of the breast to query the literature and a microarray set containing gene expression changes in these cells over several time points. Our model demonstrates significantly better fitness than the state-of-the-art model, which relies on an initial random selection of genes. Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships. The p53 pathway results were manually validated in the literature. 60% of nonKEGG relationships were supported (74% for highly weighted interactions). The method was then applied to yeast data and our model again outperformed the comparison model. Our results demonstrate the advantage of combining gene interactions extracted from the literature in the form of semantic relations with microarray analysis in generating contribution-weighted gene regulatory networks. This methodology can make a significant contribution to understanding the complex interactions involved in cellular behavior and molecular physiology.

59 BASIC BIOLOGICAL SCIENCES↗