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DOE OSTI2025

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗

DOE OSTI2022

ROAM: A Remotely Operated Accelerator Monitor

Monitoring accelerators in operation is a well known challenge due to the radiation environment. However, there are significant benefits in being able to deploy particular sensors in specific locations of accelerator enclosures for monitoring or troubleshooting purposes. Learning from experience at other labs, we used Commercial Off The Shelf (COTS) components and an open source robot control software framework (ROS) to build a remotely controlled robot platform including a standard suite of instruments such as cameras, LIDAR, and ultrasound, with the ability to incorporate other ad-hoc sensors for specific measurements, such as a Gamma radiation monitor. Special attention was given to the robot's ability to maintain safety in the high risk environment of an accelerator, with multiple failure contingencies in place to ensure collision free operation. Testing was performed to prove the platform's viability and showcase its capability for accelerator monitoring.

Thayer, Thomas C.↗

DOE OSTI2024

Reconfigurable Network Slicing Orchestration in Network Function Virtualization Compatible Operational Technology Environment

The ongoing transition to Industry 4.0, which is characterized by increased inter-connectivity of cyber-physical systems, requires having time-sensitive, high throughput, and secure transfer of critical data in industrial sites. In this context, network slicing emerges as a critical tool to ensure timely data delivery by provisioning the network resources to cater to specific applications’ requirements and mitigating potential cyber attacks. To address these challenges, this paper aims to tackle two key questions essential for the successful implementation of network slicing in industrial environments. First, it investigates architectural considerations for developing a network infrastructure capable of supporting network slicing functionalities effectively. The proposed approach significantly improves deployment efficiency over traditional manual configurations. Second, it delves into the automated orchestration process, elucidating the steps and components involved in transitioning from a static network management approach to dynamically leverage network function virtualization schemes for creating network slices in ad-hoc manner. The system demonstrates high throughput suitable for production-level solutions and maintains exceptionally low latency, making it ideal for ultra-reliable low-latency communications. Even with increased network demands, the system remains stable, with effective Quality of Service (QoS) management, ensuring reliable performance under varying conditions. The proposed architecture outlines the necessary components, services, and communication protocols required for a production-level orchestrator for network segmentation in SCADA environments.

Rodiles Delgado, Brian G.↗

DOE OSTI2023

A Mobile Edge Computing Framework for Traffic Optimization At Urban Intersections Through Cyber-Physical Integration

The stop-and-go traffic pattern on urban roads often results in excessive energy consumption because of unnecessary vehicle braking, idling, and accelerations. With the widespread and increased use of automobiles, this traffic pattern creates many negative impacts (e.g., delayed travel time, air pollution, and additional carbon emission) on the sustainability of our cities. Taking advantage of the recent emerging Internet of Things (IoT) and edge computing paradigms, we propose a mobile edge computing framework that integrates the capability of real-time vehicle-to-infrastructure communication and intelligent speed optimization algorithms into a mobile app to optimize individual vehicles' driving speed at signalized intersections. The optimization aims to mitigate the stop-and-go traffic pattern and its undesirable consequences in urban transportation systems. The framework consists of (1) a cyberinfrastructure-enabled dynamic messaging system for retrieving and delivering real-time traffic and signal phase and timing information from IoT-connected signal controllers and sensors, (2) a real-time speed optimization algorithm for generating intelligent speed advisory using vehicle's information (e.g., GPS and driving directions from mobile sensing) and corresponding signal and traffic information, and (3) an ad-hoc mobile computing environment that converts drivers' smartphones into edge devices to host the speed optimization algorithms for enabling intelligent advisory on the vehicle's driving speed within signalized corridors. The paper presents the design and implementation of the proposed framework. Finally, we demonstrate the feasibility, usefulness, and energy-saving benefits of our proposed framework and its prototyping mobile app on urban transportation systems through traffic simulation, real-vehicle laboratory experiments, an evaluative survey, and field communication tests. The simulation-based energy evaluation results show that the 100% usage of the mobile app can achieve 24% energy savings in the transportation system.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Learning Robust Marking Policies for Adaptive Mesh Refinement

Here in this work, we revisit the marking decisions made in the standard adaptive finite element method (AFEM). Experience shows that a naïve marking policy leads to inefficient use of computational resources for adaptive mesh refinement (AMR). Consequently, using AMR in practice often involves ad-hoc or time-consuming offline parameter tuning to set appropriate parameters for the marking subroutine. To address these practical concerns, we recast AMR as a Markov decision process in which refinement parameters can be selected on-the-fly at run time, without the need for pre-tuning by expert users. In this new paradigm, the refinement parameters are also chosen adaptively via a marking policy that can be optimized using methods from reinforcement learning. We use the Poisson equation to demonstrate our techniques on h- and hp-refinement benchmark problems, and our experiments suggest that superior marking policies remain undiscovered for many classical AFEM applications. Furthermore, an unexpected observation from this work is that marking policies trained on one family of PDEs are sometimes robust enough to perform well on problems far outside the training family. For illustration, we show that a simple hp-refinement policy trained on 2D domains with only a single re-entrant corner can be deployed on far more complicated 2D domains, and even 3D domains, without significant performance loss. For reproduction and broader adoption, we accompany this work with an open-source implementation of our methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Hyperdiffusion of dust particles in a turbulent tokamak plasma

The effect of plasma turbulence on the trajectories of dust particles is investigated for the first time. The dynamics of dust particles is computed using the ad-hoc developed Dust Injection Simulator code, using a 3D turbulent plasma background computed with the TOKAM3X code. As a result, the evolution of the particle trajectories is governed by the ion drag force, and the shape of the trajectory is set by the Stokes number $St\propto a_d/n_0$, with $a_d$ the dust radius and $n_0$ the density at the separatrix. The plasma turbulence is observed to scatter the dust particles, exhibiting a hyperdiffusive regime in all cases. The amplitude of the turbulent spread of the trajectories $\Delta r^2$ is shown to depend on the ratio $Ku/St$, with $Ku\propto u_{rms}$ the Kubo number and $u_{rms}$ the fluctuation level of the plasma flow. These results are compared with a simple analytical model, predicting $\Delta r^2\propto (Ku/St)^2t^3$, or $\Delta r^2\propto (u_{rms}n_0/a_d)^2t^3$. As the dust is heated by the plasma fluxes, thermionic emission sets the dust charge, originally negative, to slightly positive values. This results in a substantial reduction of the ion drag force through the suppression of its Coulomb scattering component. The dust grain inertia is then no longer negligible, and drives the transition from a hyperdiffusive regime towards a ballistic one.

dust↗

DOE OSTI2023

sfapi_client v1.0

This software is a client designed to interact with the Superfacility API developed at NERSC. It allows users to easily access the api in python and programmatically interact with the compute resources available at NERSC. Other implementations are ad-hoc and made by our user base, the goal of the project is to encourage more users to adopt the API by making it easier to start building complex HPC workflows.

Tyler, Nicholas↗

DOE OSTI2023

Spectral Peak Enhancement by Combining Trusted Response Elements via Machine Learning (SPECTRE-ML) v0.8.0

SPECTRE-ML (Spectral Peak Enhancement by Combining Trusted Response Elements via Machine Learning) is a machine learning based program for finding optimal clusters of radiation detector segments (i.e., pixels or voxels) in order to improve spectral performance. It provides facilities for pre-processing and analyzing training datasets, running ML algorithms, and evaluating and visualizing outputs. SPECTRE-ML outperforms simpler ad-hoc segmentation methods such as uniform depth clusters, learning detector performance trends such as dead layers, edge effects, and gain shifts. Although extensible to arbitrary highly-segmented spectroscopic radiation detectors, SPECTRE-ML currently focuses on improving spectral performance in highly-segmented CdZnTe (CZT) detectors for International Atomic Energy Agency (IAEA) non-destructive assay (NDA) safeguards tasks.

Vavrek, Jayson↗

DOE OSTI2025

FAIR to WISE (F2W) v1.0.0

FAIR to WISE (F2W) is an iterative, large-language model (LLM) driven pipeline that turns unstructured research PDFs into structured, queryable knowledge graphs (KGs). Core features include schema-driven extraction to a LinkML model; full provenance capture; ontology-grounded enrichment (e.g., chemical validation and ChEBI lookup); graph construction to JSON-LD with stable IDs; and KG-RAG question answering with evidence-aware retrieval. The system is engineered for reproducibility and accessibility (open-source Ollama models, temperature=0, NVTX/Nsight profiling) with robust QA (relation verification, deduplication, and deterministic outputs). Primary uses are literature-to-KG automation, knowledge-grounded Q&A, and experimental steering support. We demonstrate the approach in organic photovoltaics, where the pipeline ingests papers, builds a domain KG, and evaluates answers against expert competency questions to guide experimental planning and interpretation. Compared with off-the-shelf LLMs and ad-hoc NLP tools, F2W addresses ontology gaps and reduces hallucination risk by grounding responses in extracted evidence and enforcing schema constraints; it also offers deterministic, provenance-linked outputs and open, cost-aware deployment. Evidence-aware ranking further improves answer quality over pure vector search.

Abramov, David [Lawrence Berkeley National Laborat↗

DOE OSTI2026

AQDrop Quantum Service (AQDrop) v1.0

AQDrop is a job management system designed to streamline access to the Advanced Quantum Testbed (AQT) at NERSC (National Energy Research Scientific Computing Center). It serves as a centralized middleware layer between researchers and quantum processing hardware. Key Features: AQDrop provides a FastAPI-based server backed by PostgreSQL for job submission, queue management, and role-based access control (members, operators, and administrators). Users submit Qiskit circuits via JSON payloads, which are queued, dispatched to the QPU through the Qubic API, and returned as measurement counts. A Python client library and web dashboard round out the interface options. Primary Use: Researchers submit quantum circuit jobs from a laptop or login node; an operator client executes those jobs on the AQT's physical QPU and returns results — all coordinated through the central API. Advantages: Compared to ad-hoc or direct hardware access, AQDrop adds structured queue management, auditable job-status tracking and OAuth2 authentication — reducing scheduling conflicts and unauthorized access. Its containerized deployment also improves reproducibility and scalability. Overall, AQDrop functions as a purpose-built quantum job broker tailored to NERSC's specific hardware and institutional access requirements.

Caplinger, Evan [Lawrence Berkeley National Labora↗

DOE OSTI2021

Towards a Unified theory of Fractional and Nonlocal Vector Calculus

Nonlocal and fractional-order models capture effects that classical partial differential equations cannot describe; for this reason, they are suitable for a broad class of engineering and scientific applications that feature multiscale or anomalous behavior. This has driven a desire for a vector calculus that includes nonlocal and fractional gradient, divergence and Laplacian type operators, as well as tools such as Green’s identities, to model subsurface transport, turbulence, and conservation laws. In the literature, several independent definitions and theories of nonlocal and fractional vector calculus have been put forward. Some have been studied rigorously and in depth, while others have been introduced ad-hoc for specific applications. The goal of this work is to provide foundations for a unified vector calculus by (1) consolidating fractional vector calculus as a special case of nonlocal vector calculus, (2) relating unweighted and weighted Laplacian operators by introducing an equivalence kernel, and (3) proving a form of Green’s identity to unify the corresponding variational frameworks for the resulting nonlocal volume-constrained problems. Here, the proposed framework goes beyond the analysis of nonlocal equations by supporting new model discovery, establishing theory and interpretation for a broad class of operators, and providing useful analogues of standard tools from the classical vector calculus.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Theoretical justification for heat flux limiter 0.15

In this section, we describe a semi-nonlocal kinetic model for the electron heat flux. The model has no free parameters. It takes the more physically motivated approach of placing a limiter on the perturbation to the electron distribution function, rather than the usual ad-hoc limiter on the heat flux. If the kinetic model is fitted by a heat flux limiter model, we find that the higher value of f e = 0.15 is a much closer fit than other models with f e ≃ 0.02.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

A Micromorphic Length-Scale Coupling Framework for the Determination of Higher-Order Constitutive Models and the Multi-Scale Simulation of Heterogeneous Materials [Thesis]

Heterogeneous materials and materials with complex microstructures pose a unique challenge in the development of accurate models of their response to external stimuli. These difficulties principally arise due to the difficulty in characterizing and modeling the constituents and their interactions. It is usually possible, though non-trivial, to construct an explicit representation of the microstructure (a direct numeric simulation or DNS) but the method by which the complex modes of deformation and other processes can be homogenized to a reduced-order approximation is frequently unclear. Many homogenization approaches are ad-hoc and lack a strong justification beyond ease of computation. Furthermore, the homogenization approach can, in some cases, not utilize the full breadth of information available in the computation of the macro-scale stresses and deformation measures. It is also noteworthy that homogenization, by its very nature, will tend to obfuscate details of processes occurring at the lower length-scale. It is therefore of interest to include as much information as possible in the construction of the reduced-order model so as to be predictive in a variety of loading environments. We here present a length-scale bridging technique based upon the micromorphic continuum mechanics of Eringen which incorporates volume and surface area averages as a part of its construction. This approach enforces the balance equations at the micro-scale and then studies the effect of the spatially varying nature on the macro-scale. This leads, naturally, to further balance equations which are solved at the macro-scale. This work details a homogenization framework which arises naturally from the micromorphic construction of Eringen attempting to introduce no definitions beyond which are justifiable from micro-structural considerations. One of the results of this effort is the so-called “micromorphic filter” which has been developed and applied to several DNS to demonstrate its effectively. In order to determine the macroscopic degrees of freedom we utilize the special case of an overlap coupling technique where the macro-scale is fully constrained to the micro-scale. This enables us to study the resulting material properties as expected but also allows us to further study the boundary conditions on the additional degrees of freedom at the macro-scale.

42 ENGINEERING↗

DOE OSTI2024

A Model for Optimally Allocating Curbside Space Among Competing Uses

The emergence of various new forms of urban mobility services in recent years is leading to new pressures on curbside space. Municipalities, the entities typically responsible for managing the curbside, are in many instances handling these growing pressures by reallocating portions of the curbside away from traditional uses (such as metered and residential parking) in favor of uses such as ridehailing, scooter and bike-share corrals. As yet, however, such actions are being undertaken on an ad-hoc basis, due to the rapidly growing complexity of the curbside and the lack of standard analytical approaches. This lack of analytical capability is due to the traditional focus of transportation network modeling being focused predominantly on the interaction of supply and demand on links and nodes, with limited focus on link edges (the curbside). In this paper we address this research need by proposing a framework for modeling inter-modal competition for curbside space, inspired by the classical Bid-Rent Model of urban land use, intended to support curb managers to move towards maximizing the aspects of economic welfare that relate to curb access. In the bi-level model, choices made by the curbside manager impact travelers’ mode choices, and vice versa. We then present a simple numerical case study to demonstrate the properties of the proposed model, showing its tractability, flexibility, and intuitive sensitivity to systematic variation in inputs. The framework demonstrates the type of adaptive and evolving approach needed to maximize benefits from increasingly dynamic curb management strategies. The paper concludes with a brief discussion of future research needs to advance this line of inquiry.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

ChargeX Prescribed Testing Program at CharIN June 2024 Testival: Outcomes & Future Recommendations

In June 2024, the ChargeX Consortium developed an optional prescribed testing program for electric vehicle (EV) and electric vehicle supply equipment (EVSE) manufacturers that attended the CharIN Testival as testers. There were two driving purposes of this program; to introduce a new hybrid approach to testing events with both ad-hoc and prescribed testing offered, and to demonstrate the test cases and structure effectiveness of the EV-EVSE Interoperability Test Plan (EEITP) document developed within the ChargeX Testing Task Force. This program contained eight test scenarios to be performed during the final 30-minutes of a 90-minute testing slot with details like purpose, setup, pass criteria, etc. included within a written test plan document. A $2,000 rebate was offered to those who participated, and a ChargeX moderation force was present to collect EV and EVSE meta data, testing meta data, and testing results.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

The HTAP_v3.2 emission mosaic: merging regional and global monthly emissions (2000–2020) to support air quality modelling and policies

This study, performed under the umbrella of the Task Force on Hemispheric Transport of Air Pollution (TF-HTAP), responds to the need of the global and regional atmospheric modelling community of having a mosaic emission inventory of air pollutants that conforms to specific requirements: global coverage, long time series, spatially distributed emissions with high time resolution, and a high sectoral resolution. The mosaic approach of integrating official regional emission inventories based on locally reported data, with a global inventory based on a globally consistent methodology, allows modellers to perform simulations of a high scientific quality while also ensuring that the results remain relevant to policymakers. HTAP_v3.2, an ad-hoc global mosaic of anthropogenic inventories, is an update to the HTAP_v3 global mosaic inventory and has been developed by integrating official inventories over specific areas (North America, Europe, Asia including China, Japan and Korea) with the independent Emissions Database for Global Atmospheric Research (EDGAR) inventory for the remaining world regions. The results are spatially and temporally distributed emissions of SO 2 , NO x , CO, NMVOC, NH 3 , PM 10 , PM 2.5 , Black Carbon (BC), and Organic Carbon (OC), with a spatial resolution of 0.1 × 0.1° and time intervals of months and years covering the period 2000–2020 (https://doi.org/10.5281/zenodo.17086684, Crippa, 2025, https://edgar.jrc.ec.europa.eu/dataset_htap_v32, last access: 27 October 2025). The emissions are further disaggregated to 16 anthropogenic emitting sectors. This paper describes the methodology applied to develop such an emission mosaic, reports on source allocation, differences among existing inventories, and best practices for the mosaic compilation. One of the key strengths of the HTAP_v3.2 emission mosaic is its temporal coverage, enabling the analysis of emission trends over the past two decades. The development of a global emission mosaic over such long time series represents a unique product for global air quality modelling and for better-informed policy making, reflecting the community effort expended by the TF-HTAP to disentangle the complexity of transboundary transport of air pollution.

Guizzardi, Diego [European Commission, Ispra (Ital↗

DOE OSTI2022

Quantifying uncertainty in Pareto estimates of global lake area

This software contains the code for Bayesian uncertainty analysis of global lake area. Computed uncertainties are compared against more conventional estimation using lake size-abundance distributions. Routines are included to explore sensitivity to observational errors and ad-hoc "censoring" strategies.

Stachelek, Jemma↗

DOE OSTI2022

A Knowledge-based Framework for Building Energy Model Performance Verification

Building energy modeling (BEM) has been widely used by researchers, regulators, and engineers to quantify building energy performance. Quality assurance (QA) and quality control (QC) of the model's performance are essential parts of such analysis. Currently, QA/QC is done in a manual and ad-hoc manner, which is tedious, error-prone, and time-consuming when QA/QC a large number of models. To solve these challenges, we propose a a dAta-driveN buIlding perforMance verificATion framEwork (ANIMATE), which conducts automated output-based verification of building operations requirements (especially for time-series output-based verification of control requirements). While this framework was developed for verifying energy model performance, it can be extended for other applications such as BEM software testing and performance verification of real buildings in the field.

Chen, Yan↗