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DOE OSTI2025

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence↗

DOE OSTI2025

ERF: Energy Research and Forecasting Model

High performance computing (HPC) architectures have undergone rapid development in recent years. As a result, established software suites face an ever increasing challenge to remain performant on and portable across modern systems. Many of the widely adopted atmospheric modeling codes cannot fully (or in some cases, at all) leverage the acceleration provided by General-Purpose Graphics Processing Units, leaving users of those codes constrained to increasingly limited HPC resources. Energy Research and Forecasting (ERF) is a regional atmospheric modeling code that leverages the latest HPC architectures, whether composed of only Central Processing Units (CPUs) or incorporating GPUs. ERF contains many of the standard discretizations and basic features needed to model general atmospheric dynamics. The modular design of ERF provides a flexible platform for exploring different physics parameterizations and numerical strategies. ERF is built on a state-of-the-art, well-supported, software framework (AMReX) that provides a performance portable interface and ensures ERF's long-term sustainability on next generation computing systems. This paper details the numerical methodology of ERF, presents results for a series of verification/validation cases, and documents ERF's performance on current HPC systems. The roughly 5× speed up of ERF (using GPUs) over Weather Research and Forecasting (CPUs only) for a 3D squall line test case highlights the significance of leveraging GPU acceleration.

17 WIND ENERGY↗

DOE OSTI2024

Shifting Between Compute and Memory Bounds: A Compression-Enabled Roofline Model

In the evolving landscape of high-performance computing, especially to fight the end of Moore’s Law and Dennard’s Scaling, the ability to shift between compute-bound and memory-bound states is critical for enhancing adaptability and flexibility to diverse system and domain-specific architectures. Such capability is vital for optimizing performance across distinguished hardware configurations, such as accelerators, memory hierarchies, and cache systems. Despite that ad hoc optimization techniques, such as compressed/approximate computation, have been enabled for compute-/data-intensive computing for improved performance in distinct hardware settings, there lacks an understanding of 1) the rational behind performance improvement; 2) capability of different optimizations; 3) what optimization to respond to specific computational and memory demands. This work proposes a compression-enabled roofline model to facilitate this adaptability with data compression techniques to balance and transform between computational and memory demands. This model enables applications to adjust in response to the specific strengths and limitations of the underlying hardware and system to optimize resource utilization. The effectiveness of this approach is demonstrated with matrix multiplication kernels on different input sizes, with turning on/off various compression techniques, including 1) low-precision floating point; 2) sparse matrix formulation; and 3) compressed arrays with ZFP. By reducing memory transfer volumes and cache misses and increasing data locality and computational intensity through compression, the specific roofline model can transform between compute and memory bounds to align more efficiently with system capabilities. This advancement not only improves overall performance but also maximizes adaptability in diverse computing environments.

Naraparaju, Ramasoumya [University of Washington]↗

DOE OSTI2020

High operating temperature heat transfer fluids for solar thermal power generation. Final report

This is the final technical report for the DOE MURI project on developing high-operating temperature heat transfer fluids for solar thermal power generation. This project aimed to evaluate liquid metals as a heat-transport fluid and potential energy storage medium for concentrated solar powered (CSP) systems. The project consisted of five phases, starting with fluid selection and screen and ending with potential CSP integration. The initial fluid selection arrived at heavy liquid metals as candidate fluids such as lead bismuth eutectic (LBE) as the prime liquid-alloy candidate to be studied, given the conditions above. Fifty-seven liquid compositions were initially identified with liquidus temperatures lower than 200°C, composed of elements that provide no driving force to the reduction of Cr 2 O 3 or Al 2 O 3 passivation layers in pipe material which is required for corrosion prevention. LBE was identified as the primary candidate fluid after these compositions were compared against computational thermodynamic modeling to screen all of the selected systems that would be compatible with our design objectives. Twenty-eight of these compositions were also investigated with the rapid characterization methods; the accuracies of the liquidus temperature and the specific heats predicted by the computations were better than 3 percent and 9 percent, respectively. We conducted numerus corrosion tests of various Fe-Cr-Al based steels in LBE and its variants at temperate as high as 800°C. It was found that minor additions to the liquid did not provide sufficient corrosion protection to warrant their use in real applications. Furthermore, we investigated the detailed mechanism of corrosion between heavy liquid metal and the pipe material at these very high temperatures. A liquid metal loop was constructed to operate at these high temperatures. The loop construction and operation lead to valuable lessons learned that will be needed for industrial scale loops. Furthermore, we learned that electromagnetic pumps at these extreme temperatures will have to be reengineered and redesigned to be used for CSP applications.

14 SOLAR ENERGY↗

DOE OSTI2022

Approximating a linear multiplicative objective in watershed management optimization

Implementing management practices in a cost-efficient manner is critical for regional efforts to reduce the amount of pollutants entering the Chesapeake Bay. We study the problem of selecting a subset of practices that minimizes pollutant load—subject to budgetary and environmental constraints—as simulated in a widely used regulatory watershed model. Mimicking the computation of pollutant load in the regulatory model, we formulate this problem as a continuous optimization model with a linear multiplicative objective function and linear constraints. To lay the groundwork for incorporating additional stakeholder requirements in the future, especially those that would require integer variables, we present and study a continuous linear optimization model that approximates the nonlinear model. The linear model, which requires an exponential number of variables, arises naturally as an alternative model for the same underlying physical process. We examine the theoretical behavior of these optimization models and investigate restrictions of the linear model to handle its large number of variables. Through extensive computational tests on real and randomly generated instances, we demonstrate that the linear model and its restrictions provide optimal solutions close to those of the nonlinear model in practice, despite poor approximation properties in the worst case. We conclude that the linear model—together with our approach to handling its large number of variables—provides a viable framework from which to extend the optimization model to better meet the needs of the Chesapeake Bay watershed management stakeholders.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Singlet Fission

This report summarizes key findings from DOE Award DE‑SC0007004 – Singlet Fission, documenting more than a decade of research led by Professor Josef Michl. The project advanced foundational understanding of singlet fission (SF) through integrated synthetic, spectroscopic, crystallographic, and computational studies. Across a diverse set of chromophores—including tetracenes, cibalackrot derivatives, BODIPY dimers, TDPPs, and fluorinated isobenzofurans—the team identified structural and packing features that enable or inhibit SF, clarified the roles of charge‑transfer intermediates and excimer formation, and developed simplified theoretical models and computational screening tools for predicting optimal geometries and excited‑state-energetics. The work significantly broadened design principles for SF‑active materials and provided insights relevant to next‑generation solar energy conversion and molecular photophysics.

14 SOLAR ENERGY↗

DOE OSTI2025

Effective Defect Detection Using Instance Segmentation for NDI

Ultrasonic testing is a common Non-Destructive Inspection (NDI) method used in aerospace manufacturing. However, the complexity and size of the ultrasonic scans make it challenging to identify defects through visual inspection or machine learning models. Using computer vision techniques to identify defects from ultrasonic scans is an evolving research area. In this study, we used instance segmentation to identify the presence of defects in the ultrasonic scan images of composite panels that are representative of real components manufactured in aerospace. We used two models based on Mask- RCNN (Detectron 2) and YOLO 11 respectively. Additionally, we implemented a simple statistical pre-processing technique that reduces the burden of requiring custom-tailored pre-processing techniques. Our study demonstrates the feasibility and effectiveness of using instance segmentation in the NDI pipeline by significantly reducing data pre-processing time, inspection time, and overall costs.

computer vision techniques↗

DOE OSTI2023

Revisiting Néel 60 years on: The magnetic anisotropy of L1 0 FeNi (tetrataenite)

The magnetocrystalline anisotropy energy of atomically ordered L1 0 FeNi (the meteoritic mineral tetrataenite) is studied within a first-principles electronic structure framework. Two compositions are examined: equiatomic Fe 0.5 Ni 0.5 and an Fe-rich composition, Fe 0.56 Ni 0.44 . It is confirmed that, for the single crystals modeled in this work, the leading-order anisotropy coefficient K 1 dominates the higher-order coefficients K 2 and K 3 . To enable comparison with experiment, the effects of both imperfect atomic long-range order and finite temperature are included. While our computational results initially appear to undershoot the measured experimental values for this system, careful scrutiny of the original analysis due to Néel et al. [J. Appl. Phys. 35, 873 (1964)] suggests that our computed value of K 1 is, in fact, consistent with experimental values, and that the noted discrepancy has its origins in the nanoscale polycrystalline, multivariant nature of experimental samples, that yields much larger values of K 2 and K 3 than expected a priori. These results provide fresh insight into the existing discrepancies in the literature regarding the value of tetrataenite’s uniaxial magnetocrystalline anisotropy in both natural and synthetic samples.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Prevention of resistive wall tearing mode major disruptions with feedback

Resistive wall tearing modes (RWTMs) can cause major disruptions. A signature of RWTMs is that the rational surface is sufficiently close to the wall to interact with it. For (m,n) = (2,1) modes, a RWTM requires normalized minor radius of the rational surface ρ q2 ≥ 0.75, which can also be expressed as q 75 ≤ 2. Major disruptions can occur when the criterion is satisfied. This is confirmed in simulations and theory and in a DIII-D locked mode disruption database. The q 75 < 2 criterion is valid at high β as well as at low β. A very important feature of RWTMs is that they can be feedback stabilized. If the ρ q2 criterion is not satisfied, or if the wall is ideally conducting, then the mode does not produce a major disruption, although it can produce a minor disruption. Feedback, or rotation of the mode at the wall by complex feedback, can emulate an ideal wall, preventing major disruptions. The ρ q2 criterion depends weakly on the wall radius. A simple geometric model of its dependence on wall radius is given.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Data Assimilation for Robust UQ Within Agent-Based Simulation on HPC Systems

Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.

Spannaus, Adam [ORNL] (ORCID:0000000225213657)↗

DOE OSTI2023

Accurate computational design of three-dimensional protein crystals

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here, in this study, we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Modeling Single and Two-Phase Transport in Thin Porous Layers Using a Composite Continuum-Pore Network Formulation

In this work, a composite continuum-pore network formulation is presented to model single and two-phase transport thin porous layers, such as gas diffusion layers in polymer electrolyte fuel cells (PEFCs) and active electrodes in redox flow batteries (RFBs). The formulation can be integrated into CFD codes, thus combining the ease of implementation of continuum-based modeling and the computational power of pore-network modeling. The composite model includes a control volume (CV) mesh at the layer scale, which embeds a cubic pore network [1,2]. The pore-network model is used to determine analytically local anisotropic effective transport properties (local effective diffusivity and permeability), which are mapped onto the CV mesh to simulate transport in the porous transport layer [3,4]. Good agreement is found between the predicted global effective transport properties (global effective diffusivity and permeability) under dry and wet conditions and previous experimental data reported in the literature for Toray TGP-H series carbon paper. Water saturation distributions are also compared with results obtained using X-ray computed tomography [4]. [1] P.A. García-Salaberri, I.V. Zenyuk, J.T. Gostick, A.Z. Weber, Modeling Gas Diffusion Layer in Polymer Electrolyte Fuel Cells Using a Continuum-Based Pore-Network Formulation, ECS Trans. 97 (2020) 615. [2] P.A. García-Salaberri, Modeling diffusion and convection in thin porous transport layers using a composite continuum-network model: Application to gas diffusion layers in polymer electrolyte fuel cells, Int J. Heat Mass Transf. (2020), submitted. [3] P.A. García-Salaberri, J.T. Gostick, G. Hwang, A.Z. Weber, M. Vera, Effective diffusivity in partially-saturated carbon-fiber gas diffusion layers: Effect of local saturation and application to macroscopic continuum models, J. Power Sources 296 (2015) 440–453. [4] P.A. García-Salaberri, G. Hwang, M. Vera, A.Z. Weber, J.T. Gostick, Effective diffusivity in partially-saturated carbon-fiber gas diffusion layers: Effect of through-plane saturation distribution, Int. J. Heat Mass Transf. 86 (2015) 319–333.

Garcia-Salaberri, Pablo↗

DOE OSTI2022

Fast estimation of ion-pairing for screening electrolytes: A cluster can approximate a bulk liquid

The propensity for ion-pairing can often dictate the thermodynamic and kinetic properties of electrolyte solutions. Fast and accurate estimates of ion-pairing can thus be extremely valuable for supplementing design and screening efforts for novel electrolytes. We introduce an efficient cluster model to estimate the local ion-pair potential-of-mean-force between ionic solutes in electrolytes. The model incorporates an ion-pair and a few layers of explicit solvent in a gas-phase cluster and leverages an enhanced sampling approach to achieve high efficiency and accuracy. We employ harmonic restraints to prevent solvent escape from the cluster and restrict sampling of large inter-ion distances. We develop a cluster ion-pair sampling tool that implements our cluster model and demonstrate its potential utility for screening simple and poly-electrolyte systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Reduced Order Model of Transactive Bidding Loads

Transactive energy (TE) has been identified to provide better grid efficiency and reliability by market-based transactive exchanges between energy producers and energy consumers. Simulations of TE systems are crucial to evaluate the benefits and impacts of different transactive mechanisms. However, such simulations can be time consuming due to the information exchange between various participants and complex co-simulation environments. In this paper, we develop a reduced order model to speed up the simulation of transactive systems in TE simulation platform (TESP) while achieving very low error between the reduced order and full model results. Specifically, the developed reduced order model consists of an aggregate responsive load agent which utilizes two Recurrent Neural Networks (RNNs) with Long Short-Term Memory units (LSTMs) to enable transactive elements to collectively participate in the TE system. The proposed aggregate responsive load (ARL) agent is able to produce similar transactive behaviors to the full simulation model while achieving significant simulation time reduction. Finally, we also show that the developed model enables generalization of simulation results across different dates and across different number of loads included in the simulations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

Machine learning at the Spallation Neutron Source accelerator and target

We describe the ongoing efforts to apply Machine Learning techniques to improve the performance of our accelerator and target. Specially, we are looking to minimize halo beam losses in the absence of a proper physics model, automatically detect and log anomalies in the target support systems such as cooling, and detect and prevent errant beam pulses in the linac. We also describe the infrastructure we use to acquire and stream data to the GPU cluster for training, our code development cycle, and edge computing for model inference. To minimize halo beam losses, we use a Reinforcement Learning technique tested on a virtual accelerator. The target anomaly detection is trained on archived data using incomplete physics models and is made part of the existing target reporting system. The errant beam prevention analyzes beam current and beam phase waveforms as well as accelerator configuration data to predict errant pulses. We also develop continual learning to adapt to changes in the accelerator.

Accelerator Physics↗

DOE OSTI2020

Functional Requirements for the Modeling and Simulation of Advanced (Non-LWR) Reactor Mechanistic Source Term

A number of industry vendors are leading a resurgence in advanced reactor development. As the assurance of public safety from the accidental release of radionuclides to the environment is central to regulatory licensing and the reactor design process, the development of a mechanistic source term (MST) assessment has been identified by the advanced reactor industry as a foremost priority. In contrast to historic light-water reactor (LWR) source term analysis efforts, an MST attempts to realistically model the release and transport of radionuclides from the source to the environment for specific scenarios, while accounting for retention or transmutation phenomena and associated uncertainties. This work seeks to aid in the development of MST modeling and simulation tools by performing a preliminary identification of functional requirements for the major advanced reactor types.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2021

Application of Quantum Machine Learning to High Energy Physics Analysis at LHC using IBM Quantum Computer Simulators and IBM Quantum Computer Hardware

One of the major objectives of the experimental programs at the LHC is the discovery of new physics. This requires the identification of rare signals in immense backgrounds. Using machine learning algorithms greatly enhances our ability to achieve this objective. With the progress of quantum technologies, quantum machine learning could become a powerful tool for data analysis in high energy physics. In this study, using IBM gate-model quantum computing systems, we employ the quantum variational classifier method and the quantum kernel estimator method in two recent LHC flagship physics analyses: $t\bar{t}H$ (Higgs boson production in association with a top quark pair) and $H\rightarrow\mu\mu$ (Higgs boson decays to two muons). We have obtained early results with 10 qubits on the IBM quantum simulator and the IBM quantum hardware. On the quantum simulator, the quantum machine learning methods perform similarly to classical algorithms such as SVM (support vector machine) and BDT (boosted decision tree), which are often employed in LHC physics analyses. On the quantum hardware, the quantum machine learning methods have shown promising discrimination power, comparable to that on the quantum simulator. This study demonstrates that quantum machine learning has the ability to differentiate between signal and background in realistic physics datasets.

Chan, Jay↗

DOE OSTI2021

Converting tabular data into images for deep learning with convolutional neural networks

Abstract Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded in the order of features, such as speech and imaging. However, most tabular data do not assume a spatial relationship between features, and thus are unsuitable for modeling using CNNs. To meet this challenge, we develop a novel algorithm, image generator for tabular data (IGTD), to transform tabular data into images by assigning features to pixel positions so that similar features are close to each other in the image. The algorithm searches for an optimized assignment by minimizing the difference between the ranking of distances between features and the ranking of distances between their assigned pixels in the image. We apply IGTD to transform gene expression profiles of cancer cell lines (CCLs) and molecular descriptors of drugs into their respective image representations. Compared with existing transformation methods, IGTD generates compact image representations with better preservation of feature neighborhood structure. Evaluated on benchmark drug screening datasets, CNNs trained on IGTD image representations of CCLs and drugs exhibit a better performance of predicting anti-cancer drug response than both CNNs trained on alternative image representations and prediction models trained on the original tabular data.

59 BASIC BIOLOGICAL SCIENCES↗