Results for “Allow Lists” | Engineering Papers

DOE OSTI2025

Cyber-Informed Engineering (CIE) Guide for States

The Cyber-Informed Engineering (CIE) Guide for States provides state energy offices, public utility commissions, and partner organizations with a structured framework for integrating cyber-resilient engineering practices into energy planning, grantmaking, interconnection processes, and workforce development. As grid digitalization and the adoption of distributed energy resources accelerate, states face expanding cyber-physical risks that traditional cybersecurity measures alone cannot fully address. CIE offers a proactive, consequence-focused engineering methodology that emphasizes eliminating or mitigating high-impact failure modes through design, physical controls, and operational safeguards. The guide outlines the 12 core CIE principles, demonstrates their application through state-focused use cases—including grant evaluation rubrics, interconnection reviews, allow-list development, and training programs—and provides practical tools such as scoring frameworks, impact assessment methods, and implementation checklists. It also highlights pathways for state–utility collaboration and opportunities for technical assistance from national laboratories. By adopting CIE, states can enhance grid reliability, reduce lifecycle costs, strengthen supply-chain assurance, and foster a security-aware engineering culture that aligns with broader resilience and modernization goals. November 2025

29 - ENERGY PLANNING, POLICY AND ECONOMY↗

DOE OSTI2025

Cyber-Informed Engineering (CIE) Guide for States

The Cyber-Informed Engineering (CIE) Guide for States provides state energy offices, public utility commissions, and partner organizations with a structured framework for integrating cyber-resilient engineering practices into energy planning, grantmaking, interconnection processes, and workforce development. As grid digitalization and the adoption of distributed energy resources accelerate, states face expanding cyber-physical risks that traditional cybersecurity measures alone cannot fully address. CIE offers a proactive, consequence-focused engineering methodology that emphasizes eliminating or mitigating high-impact failure modes through design, physical controls, and operational safeguards. The guide outlines the 12 core CIE principles, demonstrates their application through state-focused use cases—including grant evaluation rubrics, interconnection reviews, allow-list development, and training programs—and provides practical tools such as scoring frameworks, impact assessment methods, and implementation checklists. It also highlights pathways for state–utility collaboration and opportunities for technical assistance from national laboratories. By adopting CIE, states can enhance grid reliability, reduce lifecycle costs, strengthen supply-chain assurance, and foster a security-aware engineering culture that aligns with broader resilience and modernization goals. November 2025

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Neutron Coincidence Measurements of Uranium-233 Oxide

Renewed international interest in thorium-fueled advanced reactors has challenged the safeguards community to address future proliferation concerns. Thorium-based technology presents many benefits but does not eliminate the proliferation risks associated with producing and processing fissile material. A byproduct of thorium-fueled reactors is uranium-233, which is classified as a direct-use material. As a result, the development of new or improved methods to characterize and measure materials containing 233U must mirror the pace of development of reactors and facilities that produce such material. Research is underway to assess, develop, and test approaches for safeguarding nuclear materials within the thorium fuel cycle. Neutron signatures from the nondestructive assay (NDA) of materials containing 233U are being quantified to inform the potential characterization of these materials. Using a traditional neutron coincidence counter and a series of well-documented 233U oxide samples, initial measurements have been made to assess the feasibility of 233U characterization and discrimination from other uranium isotopes, primarily 235U, using a combination of measurement techniques and analysis methods. Data acquisition is performed in list mode, allowing for a variety of analyses to be performed on the raw data that is not available using traditional shift register technology. Measurements were performed in passive and active configurations to quantify the strength of signal and to validate simulations in support of this work. This paper presents and discusses the results of the initial measurements of 233U oxide performed at Oak Ridge National Laboratory.

Lockhart, Madeline↗

DOE OSTI2020

Towards a classification of rank r $\mathscr{N}$ = 2 SCFTs. Part II. Special Kahler stratification of the Coulomb branch

We study the stratification of the singular locus of four dimensional $\mathscr{N}$ = 2 Coulomb branches. We present a set of self-consistency conditions on this stratification which can be used to extend the classification of scale-invariant rank 1 Coulomb branch geometries to two complex dimensions, and beyond. The calculational simplicity of the arguments presented here stems from the fact that the main ingredients needed - the rank 1 deformation patterns and the pattern of inclusions of rank 2 strata - are discrete topological data which satisfy strong self-consistency conditions through their relationship to the central charges of the SCFT. This relationship of the stratification data to the central charges is used here, but is derived and explained in a companion paper by one of the authors. We illustrate the use of these conditions by re-analyzing many previously-known examples of rank 2 SCFTs, and also by finding examples of new theories. The power of these conditions stems from the fact that for Coulomb branch stratifications a conjecturally complete list of physically allowed “elementary slices” is known. By contrast, constraining the possible elementary slices of symplectic singularities relevant for Higgs branch stratifications remains an open problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

OrthoPhylo

This software builds on PHAME developed at LANL to generate phylogenetic trees of bacterial whole genome sequences. Where PHAME uses whole genome alignments to generate informative sites to base tress on, PHAME-OuS annotates bacterial genes, identifies orthologous sequences, aligns related proteins, uses those alignments to inform transcript alignments, then builds trees with several methods. The first is a conventional gene concatenation and ML tree estemation method. The second attempts to reconcile gene tree with a unified species tree using quartets (ASTRAL). Both methods allow filtering of gene lists on number of species represented, length, and gappiness in order to tune noise-to-signal for tree estimation

Middlebrook, Earl↗

DOE OSTI2023

Using Current Data to Detect Hardware Faults at Solar Plants

Monitoring amperage data is an effective means of detecting faults in PV plant data. Utilizing amperage data collected at the combiner box gives plant operators an up-to-date list of faulted equipment, allowing them to coordinate maintenance needs at much shorter intervals than previously. Shorter maintenance intervals will increase PV plant production levels, narrowing the gap between expected and actual PV plant performance. The amperage monitoring method performs at a high level, with a string-outage related fault detection True Positive Rate of 46% and False Positive Rate of 8%.

14 SOLAR ENERGY↗

DOE OSTI2022

Computationally efficient zero-noise extrapolation for quantum-gate-error mitigation

Zero noise extrapolation (ZNE) is a widely used technique for gate error mitigation on near term quantum computers because it can be implemented in software and does not require knowledge of the quantum computer noise parameters. Traditional ZNE requires a significant resource overhead in terms of quantum operations. A recent proposal using a targeted (or random) instead of fixed identity insertion method (riim versus fiim) requires significantly fewer quantum gates for the same formal precision. We start by showing that riim can allow for ZNE to be deployed on deeper circuits than fiim but requires many more measurements to maintain the same statistical uncertainty. We develop two extensions to fiim and riim. The List Identity Insertion Method (liim) allows to mitigate the error from certain cnot gates, typically those with the largest error. Set Identity Insertion Method (siim) naturally interpolates between the measurement-efficient fiim and the gate-efficient riim allowing to trade off fewer cnot gates for more measurements. Finally, we investigate a way to boost the number of measurements, namely to run ZNE in parallel, utilizing as many quantum devices as are available. We explore the performance of riim in a parallel setting where there is a non-trivial spread in noise across sets of qubits within or across quantum computers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Updates to Relevance Vector Machine: Multiclass Classification, Variable Selection, and Proof-of-Concept Application to Safeguards Fresh Fuel Verification using List-Mode Neutron Collar Data

To expand the capabilities of safeguards authorities to verify the integrity of fresh fuel assemblies, Oak Ridge National Laboratory has retrofit the existing electronics of the JCC-71 uranium neutron coincidence collar, which contains 18 3 He neutron detectors and an external 241 AmLi(α, n) neutron interrogation source arranged to surround a fresh nuclear fuel assembly. The new electronics system allows analysts to record list-mode neutron multiplicity data in addition to the singles and doubles rates that are currently measured. Based on previous proof-of-concept research, analysis of these new data will identify off-normal fuel configurations in an assembly and characterize or localize the specific partial fuel defects. The purpose of this report it to document the analysis algorithm development and then to demonstrate its capability for the safeguards verification of fresh fuel assemblies using list mode neutron collar data. To analyze the complex list-mode data collected with the upgraded uranium neutron collar, multivariate classification algorithms are being developed using a novel classification method, the relevance vector machine. This approach may be applied to multiclass problems to estimate the probability that test data belongs to one of many possible classes of data. In addition, our method identifies the most useful variables/channels for making predictions, which illuminates the basis for the model’s predictions, and this interpretability is largely unique among data analytics methods. Variable selection occurs during model training and parameter tuning and does not need any external hyperparameter tuning routines. Finally, we apply the modified relevance vector machine to a simulated dataset of list-mode neutron collar data generated with the radiation transport code MCNP. The method can correctly identify off-normal fuel configurations, categorize the data according to four fuel defect scenarios, and rank the channels in the data according to prediction utility. For nuclear safeguards applications, it is concluded that this method has the potential to increase the sensitivity and reliability to detect missing fuel rods from a standard 17 x 17 Pressurized Water Reactor (PWR) fresh fuel assembly. Within this analysis, “off-normal” (i.e., missing fuel rods) were correctly classified in 17 simulated test scenarios with one quarter (25%) of the fresh fuel rods missing using a training data set of 58 simulated measurements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

GraphTango: A Hybrid Representation Format for Efficient Streaming Graph Updates and Analysis

Abstract Streaming graph processing performs batched updates and analytics on a time-evolving graph. The underlying representation format of the graph largely determines the throughputs of these updates and analytics phases. Existing representation formats usually employ variations of hash tables or adjacency lists. However, a recent study showed that the adjacency-list-based approaches perform poorly on heavy-tailed graphs, and the hash table-based approaches suffer on short-tailed graphs. We propose GraphTango, a hybrid representation format that provides excellent update and analytics throughput regardless of the graph’s degree distribution. GraphTango dynamically switches among three different formats based on a vertex’s degree: (i) Low-degree vertices store the edges directly with the neighborhood metadata, confining accesses to a single cache line, (2) Medium-degree vertices use adjacency lists, and (3) High-degree vertices use hash tables as well as adjacency lists. In this case, the adjacency list provides fast traversal during the analytics phase, while the hash table provides constant-time lookups during the update phase. We further optimized the performance by designing an open-addressing-based hash table that fully utilizes every fetched cache line. In addition, we developed a thread-local lock-free memory pool that allows fast growing/shrinking of the adjacency lists and hash tables in a multi-threaded environment. We evaluated GraphTango with the help of the SAGA-Bench framework and compared it with four other representation formats: Stinger, Degree-aware Robin Hood Hashing, and two adjacency list-based formats with different workload balancing scheme. On average, GraphTango provides 4.5x higher insertion throughput, 3.2x higher deletion throughput, and 1.1x higher analytics throughput over the next best format. Furthermore, we integrated GraphTango with the state-of-the-art graph processing frameworks DZiG and RisGraph. Compared to the vanilla DZiG and vanilla RisGraph , [ GraphTango + DZiG ] and [ GraphTango + RisGraph ] reduces the average batch processing time by 2.3x and 1.5x, respectively.

Ahmed, Alif↗

DOE OSTI2023

Advancing wildlife connectivity in land use planning: a case study with four-toed salamanders

Stable habitat connections that wildlife can safely traverse are essential to biodiversity conservation and healthy ecosystems. We developed high-resolution landscape connectivity models to predict resistance to movement by a threatened wetland-obligate amphibian, the four-toed salamander ( Hemidactylium scutatum ), and identified priority management areas on the 13,000-ha Department of Energy Oak Ridge Reservation (ORR) from 2019 to 2022. We developed a resistance surface based on aerial light detection and ranging data (LiDAR), >30 years of field-based mapping of forest, hydrologic, and geologic features, and contemporary population surveys, alongside derived predictors at <1-m resolution. We then modeled predicted movement corridors using a circuit theory-based modeling approach. We worked closely with land management and natural resources personnel to integrate ecological modeling with broader land use priorities, monetary costs, and feasibility. We identified important terrestrial and aquatic areas on ORR and simulated management scenarios to promote stable connections for four-toed salamanders. This approach allowed us to narrow down a list of 438 potential habitat manipulation sites to 10 sites where open-bottomed culverts and buffers could be implemented. This smaller-scale restoration approach produced a similar increase in landscape connectivity while costing <20% of a larger-scale approach based on barrier removal. We successfully identified feasible, cost-effective management strategies that integrated knowledge from a variety of sources. In conclusion, we offer a strategy that permitted integration of wildlife management goals into infrastructure upgrades wherein wildlife was not an initial consideration.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

slewpy

slewpy is a Python package that allows the simulation of the science operations of an astrophysics space satellite mission. slewpy allows users to specify an astronomical target list with observing priorities and a satellite configuration (i.e., orbit and various satellite parameters). Taking these inputs, slewpy can be used to run a time-resolved simulation of an astrophysics mission and outputs simulated target observations given constraints such as satellite slewing rates between targets, observing time on a given target, and Sun-, Earth-, and Moon-limb observing constraints. slewpy provides the tools to test astrophysics space satellite mission designs against observing requirements for a given science case.

Geringer-Sameth, Alex [Lawrence Livermore National↗

DOE OSTI2020

DISCo-microbe: design of an identifiable synthetic community of microbes

Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).

16S rRNA↗

DOE OSTI2020

Designing Flexibility into the Authorized Radioactive Contents of the 9982 Shipping Package

The 9982 radioactive material shipping package, or the 9982, differs from the others by allowing a multitude of radionuclides instead of a single defined set. While allowing flexibility, this requires more justification on why these contents would be worthwhile and why they would not cause various safety hazards when shipped together. The latter was covered through mass limit calculations, and the potential uses for the package are shown through comparison with historical shipments. Here, the mass limits were already calculated[1] and used to show three example shipments are suitable for the 9982 as well. Plutonium stored in 3013 containers[2], training sources shipped in 9977 packages[3], and americium standards shipped in 9978 packages[4] were all analyzed. The mass of each radionuclide and the corresponding mass limit were used to first determine if the listed content could be shipped. If so, the maximum allowed mass of such contents is also calculated in order to see if the 200-gram fissile limit for the 9982 would be violated if additional material was packed. The sum-of-the-fractions method produces contents that do not violate the mass limits or exceed the 200-gram fissile limit. These sets also serve as realistic examples of what may be shipped in the 9982. Well-founded example contents will help the approval of the package by showing its compatibility with previously shipped material. Unfounded hypothetical contents would not show the usefulness of having a wide variety of allowed radionuclides. More contents may be developed in order to incorporate other radionuclides that were not present in these three examples. The light elements will also need to be evaluated due to their exclusion currently preventing some materials from being allowed in the 9982.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Investigating Application of LiDAR for Nuclear Power Plants

Many evaluation, assessment, and modeling tasks at nuclear power plants require spatial in-formation; this often requires physical visits to locations within the facility because the 2D or 3D schematics and current models do not contain enough detail or do not capture as-built and real-world conditions. These visits require extensive manual labor for not only the requesting party, but also support groups, such as security. Light Detection and Ranging (LiDAR) mapping is trying to solve that problem by providing very detailed 3D models for low costs. However, the use of these models can be very limited because either component reference information is missing and too costly to add or there is no way to extract specific spatial data needed for other tools. This report outlines two main efforts. First, to reduce the effort of “Tagging” data in large 3D models, a general Application Programming Interface (API) was developed to import a variety of existing plant database information into a 3D-visualization engine. Filters allow the user to have only zone-specific items listed; then, they can simply click and assign the information to a specific spot or component in the 3D model. The second part of the work is the development of an interface for importing pieces from the3D-LiDAR model into other systems needed for modeling and simulation, outlined around fire modeling. This interface allows for the retrieval of item location and boundaries, enabling the auto generation of models for varying tools.

3D Modelling↗

DOE OSTI2021

VTK-m User's' Guide (V.1.7)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.This book includes contributions from the VTK-m community including the VTK-m development team and the user community.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

The VTK-m Users' Guide (V.1.9)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

The VTK-m Users' Guide (V.2.0)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.

97 MATHEMATICS AND COMPUTING↗