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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Bounce-averaged theory in arbitrary multi-well plasmas: solution domains and the graph structure of their connections

Bounce-averaged theories provide a framework for simulating relatively slow processes, such as collisional transport and quasilinear diffusion, by averaging these processes over the fast periodic motions of a particle on a closed orbit. This procedure dramatically increases the characteristic time scale and reduces the dimensionality of the modelled system. The natural coordinates for such calculations are the constants of motion (COM) of the fast particle motion, which by definition do not change during an orbit. However, for sufficiently complicated fields – particularly in the presence of local maxima of the electric potential and magnetic field – the COM are not sufficient to specify the particle trajectory. In such cases, multiple domains in COM space must be used to solve the problem, with boundary conditions enforced between the domains to ensure continuity and particle conservation. Previously, these domains have been imposed by hand, or by recognising local maxima in the fields, limiting the flexibility of bounce-averaged simulations. Here, we present a general set of conditions for identifying consistent domains and the boundary condition connections between the domains, allowing the application of bounce-averaged theories in arbitrarily complicated and dynamically evolving electromagnetic field geometries. We also show how the connections between the domains can be represented by a directed graph, which can help to succinctly represent the trajectory bifurcation structure.

fusion plasma↗
DOE OSTI2025

Defect Diffusion Graph Neural Networks for Materials Discovery in High-Temperature Energy Applications

Here, the migration of crystallographic defects dictates material properties and performance for a plethora of technological applications. Density functional theory (DFT)-based nudged elastic band (NEB) calculations are a powerful computational technique for predicting defect migration activation energy barriers, yet they become prohibitively expensive for high-throughput screening of defect diffusivities. Without introducing hand-crafted (i.e., chemistry- or structure-specific) descriptors, we propose a generalized deep learning approach to train surrogate models for NEB energies of vacancy migration by hybridizing graph neural networks with transformer encoders and simply using pristine host structures as input. With sufficient training data, computationally efficient and simultaneous inference of vacancy defect thermodynamics and migration activation energies can be obtained to compute temperature-dependent vacancy diffusivities and to down-select candidates for more thorough DFT analysis or experiments. Thus, as we specifically demonstrate for potential water-splitting materials, candidates with desired defect thermodynamics, kinetics, and host stability properties can be more rapidly targeted from open-source databases of experimentally validated or hypothetical materials.

14 SOLAR ENERGY↗
DOE OSTI2025

HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions

Hydrolysis is a fundamental family of chemical reactions where water facilitates the cleavage of bonds. The process is ubiquitous in biological and chemical systems, owing to water’s remarkable versatility as a solvent. However, accurately predicting the feasibility of hydrolysis through computational techniques is a difficult task, as subtle changes in reactant structure like heteroatom substitutions or neighboring functional groups can influence the reaction outcome. Furthermore, hydrolysis is sensitive to the pH of the aqueous medium, and the same reaction can have different reaction properties at different pH conditions. In this work, we have combined reaction templates and high-throughput ab initio calculations to construct a diverse data set of hydrolysis free energies. The developed framework automatically identifies reaction centers, generates hydrolysis products, and utilizes a trained graph neural network (GNN) model to predict ΔG values for all potential hydrolysis reactions in a given molecule. The long-term goal of the work is to develop a data-driven, computational tool for high-throughput screening of pH-specific hydrolytic stability and the rapid prediction of reaction products, which can then be applied in a wide array of applications including chemical recycling of polymers and ion-conducting membranes for clean energy generation and storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Cluster-Graph Fingerprinting: A Framework for Quantitative Analysis of Machine-Learned Interatomic Model Training and Simulation Data

Machine-learned interatomic models represent a significant advancement in simulation methods, extending the predictive ability of first-principles methods to previously inaccessible length and time scales. However, the data-driven nature of these models can lead to difficult-to-detect errors that can compromise prediction accuracy. To address this challenge, we introduce a novel fingerprinting approach based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES) ML-IAM graph-based descriptor. Our strategy enables efficient and statistically rigorous analysis of system configurations used in ML-IAM training and those generated by their application, e.g., in molecular dynamics simulations. We demonstrate that these fingerprints can effectively assess novelty of a configuration relative to an existing data set and determine dissimilarity among individual configurations, which are two key tasks in workflows for active learning-based ML-IAM training, data set curation, and on-the-fly uncertainty quantification.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Deciphering the Solvation Structure of Aqueous ZnCl 2 Solutions from X-ray Absorption Spectra Using the Interpretable Graph Neural Network

Machine learning (ML) provides powerful pathways for predicting spectroscopic observables from atomic structures, but its broader impact depends on making model predictions interpretable in terms of physical and chemical principles. Here, we introduce a physics-guided graph neural network (GNN) model that predicts Zn K-edge X-ray spectroscopy (XAS) spectra of aqueous ZnCl 2 solutions. Training data are generated from ab initio XAS calculations on molecular dynamics snapshots obtained using a machine learning interatomic potential. The GNN reproduces experimental spectra across concentrations from dilute (<0.1 m) to highly concentrated (30 m, “water-in-salt”) regimes and scales efficiently to large, disordered liquid systems beyond the reach of conventional ab initio approaches. Gradient-based attribution analysis reveals that the model learns physically meaningful structure-spectrum relationships. Ligand-specific attributions reflect orbital hybridization patterns and the origin of the excitations derived from the density functional theory. Bond-length attributions recover spectral shifts consistent with multiple-scattering theory. Finally, this work bridges data-driven prediction with electronic-structure theory, establishing a general paradigm for interpretable ML that links atomic structure, electronic structure, and spectroscopic observables.

25 ENERGY STORAGE↗
DOE OSTI2024

Moiré Patterns in Pt Overlayers on Gold: A Graph Neural Network Interatomic Potential Study

Overlayer structures in bimetallic catalysts are relevant to a variety of catalytic reactions, particularly in electrocatalysis for fuel cell applications. Previous computational studies largely consider these overlayer structures to be those of a pseudomorphic overlayer, where there is a 1:1 atomic ratio between the overlayer and the support metal. Our previous work based on density functional theory (DFT) has shown that there exist nonstoichiometric overlayer structures that are more stable than the stoichiometric ones. Here, in this work, we developed a graph neural network interatomic potential (GNN-IP) to analyze structures formed in Pt overlayers on Au(111). The GNN-IP was used to explore properties of nonstoichiometric overlayers at length scales that are prohibitively expensive to pursue with planewave DFT calculations. In particular, we examined large Pt islands on top of a 48 × 48 Au(111) unit cell to explore the influence of the rotational angle (α) between the Pt overlayer and support Au(111) on both the stability of and the preferred atomic density in the overlayer. Island structures with smaller rotational angles between the Pt overlayer and Au(111) tend to be more stable. Further, smaller rotational angles tend to result in lower atomic density in the Pt overlayer.

chemical structure↗
DOE OSTI2026

Effects of Dissolution Regimes on Flow Channelization and Solute Transport in 3D Fracture Networks: Insights From Graph‐Based Reactive Transport Modeling

We investigate how mineral dissolution reshapes flow pathways and solute transport in three‐dimensional discrete fracture networks using a computationally efficient graph‐based reactive transport model. The DFNs are inspired by field‐site observations of fractured carbonate and represent realistic connectivity and structural heterogeneity. Flow is simulated with the Reynolds equation, and dissolution follows first‐order kinetics with diffusive limitations captured through an effective mass‐transfer coefficient. By systematically varying two key dimensionless parameters, the effective Damköhler number (Da), governing reaction versus advection rates, and a transport parameter (Da), analogous to the Thiele modulus, distinct flow channelization regimes emerge: mildly channelized at low G, highly channelized at intermediate Da, and extreme wormhole formation at high Da and low G. Eulerian and Lagrangian analyses, including breakthrough curves, particle tortuosity, dispersivity, and flow channeling indicators quantitatively characterize the progression of dissolution‐driven network restructuring. Across all regimes, initial fracture heterogeneity persists. The results underscore how the interplay between this initial structure, advection, reaction, and diffusion critically shapes subsurface flow pathways, with implications for applications ranging from groundwater remediation to enhanced geothermal systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Towards accurate prediction of configurational disorder properties in materials using graph neural networks

Abstract The prediction of configurational disorder properties, such as configurational entropy and order-disorder phase transition temperature, of compound materials relies on efficient and accurate evaluations of configurational energies. Previous cluster expansion methods are not applicable to configurationally-complex material systems, including those with atomic distortions and long-range orders. In this work, we propose to leverage the versatile expressive capabilities of graph neural networks (GNNs) for efficient evaluations of configurational energies and present a workflow combining attention-based GNNs and Monte Carlo simulations to calculate the disorder properties. Using the dataset of face-centered tetragonal gold copper without and with local atomic distortions as an example, we demonstrate that the proposed data-driven framework enables the prediction of phase transition temperatures close to experimental values. We also elucidate that the variance of the energy deviations among configurations controls the prediction accuracy of disorder properties and can be used as the target loss function when training and selecting the GNN models. The work serves as a fundamental step toward a data-driven paradigm for the accelerated design of configurationally-complex functional material systems.

Chemistry↗
DOE OSTI2024

An open source knowledge graph ecosystem for the life sciences

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

A low-latency graph computer to identify metastable particles at the Large Hadron Collider for real-time analysis of potential dark matter signatures

Abstract Image recognition is a pervasive task in many information-processing environments. We present a solution to a difficult pattern recognition problem that lies at the heart of experimental particle physics. Future experiments with very high-intensity beams will produce a spray of thousands of particles in each beam-target or beam-beam collision. Recognizing the trajectories of these particles as they traverse layers of electronic sensors is a massive image recognition task that has never been accomplished in real time. We present a real-time processing solution that is implemented in a commercial field-programmable gate array using high-level synthesis. It is an unsupervised learning algorithm that uses techniques of graph computing. A prime application is the low-latency analysis of dark-matter signatures involving metastable charged particles that manifest as disappearing tracks.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Knowledge graph-aided Bayesian active learning for top- K genetic interaction discovery

In silico methods for predicting the effects of multi-gene perturbations hold great promise for advancing functional genomics, computational drug discovery, and disease modeling. However, the development of these predictive algorithms for mammalian systems has been hampered by limited datasets and high experimental costs. In this study, we present a Bayesian active learning framework designed to discover pairwise host gene knockdowns that effectively inhibit viral proliferation in an in vitro HIV-1 infection model. Our method leverages a biological knowledge graph as side information and employs a computationally efficient batch diversification approach. We evaluated this framework using a dataset of viral load measurements obtained from multi-day dual-gene depletion experiments, encompassing all possible pairwise knockdowns of over 350 host genes associated with HIV infection. We demonstrate that our framework rapidly identifies the most effective gene knockdown pairs for reducing viral load. Furthermore, we show that incorporating side information enhances performance during the early stages of active learning (low data regime), while our batch diversification strategy significantly boosts performance in later stages (high data regime). This framework is general and can be adapted to explore gene interactions in other contexts, such as synthetic lethality prediction and mapping epistatic effects across quantitative trait loci.

Computational biology and bioinformatics↗
DOE OSTI2026

Citation network datasets for benchmarking spiking graph neural networks on experimental neuromorphic hardware

Spiking neural networks (SNNs) running on neuromorphic computers offer an energy-efficient alternative for AI tasks. Recently, spiking graph neural networks (S-GNNs) have been shown to produce encouraging results on benchmark citation network datasets such as Cora, CiteSeer, and PubMed for node classification tasks. These S-GNNs were run on SNN simulators only because they contain up to tens of thousands of neurons and up to millions of synapses, translating poorly to neuromorphic hardware. Therefore, in this paper, we create a suite of benchmark datasets from the CiteSeer dataset that can be accommodated on current neuromorphic hardware platforms. Our contribution consists of a collection of three datasets. First, we have an induced subgraph of CiteSeer, which we call MiniSeer, containing 2110 papers, 3604 binary features, and 6 topics. Second, MicroSeer is a very small dataset consisting of 84 papers, 1227 features, and 6 topics. Lastly, BiteSeer is a collection of 15 binary classification datasets. We present creation of these datasets along with accuracies, running times, and spike counts when simulated. We believe that our results in this paper will be used by the neuromorphic community to benchmark, test, and develop neuromorphic hardware and simulators.

Zhu, Kevin [George Mason University, Virginia]↗
DOE OSTI2024

Uncertainty quantification for molecular property predictions with graph neural architecture search

Graph Neural Networks (GNNs) have emerged as a prominent class of data-driven methods for molecular property prediction. However, a key limitation of typical GNN models is their inability to quantify uncertainties in the predictions. This capability is crucial for ensuring the trustworthy use and deployment of models in downstream tasks. To that end, we introduce AutoGNNUQ, an automated uncertainty quantification (UQ) approach for molecular property prediction. AutoGNNUQ leverages architecture search to generate an ensemble of high-performing GNNs, enabling the estimation of predictive uncertainties. Our approach employs variance decomposition to separate data (aleatoric) and model (epistemic) uncertainties, providing valuable insights for reducing them. In our computational experiments, we demonstrate that AutoGNNUQ outperforms existing UQ methods in terms of both prediction accuracy and UQ performance on multiple benchmark datasets, and generalizes well to out-of-distribution datasets. Additionally, we utilize t-SNE visualization to explore correlations between molecular features and uncertainty, offering insight for dataset improvement. AutoGNNUQ has broad applicability in domains such as drug discovery and materials science, where accurate uncertainty quantification is crucial for decision-making.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Expediting field-effect transistor chemical sensor design with neuromorphic spiking graph neural networks

Improving the sensitive and selective detection of analytes in a variety of applications requires accelerating the rational design of field-effect transistor (FET) chemical sensors. Achieving high-performance detection relies on identifying optimal probe materials that can effectively interact with target analytes, a process traditionally driven by chemical intuition and time-consuming trial-and-error methods. To address the difficulties in probe screening for FET sensor development, this work presents a methodology that combines neuromorphic machine learning (ML) architectures, specifically a hybrid spiking graph neural network (SGNN), with an enriched dataset of physicochemical properties through semi-automated data extraction using large language models. Achieving a classification accuracy of 0.89 in predicting sensor sensitivity categories, the SGNN model outperformed traditional ML techniques by leveraging its ability to capture both global physicochemical properties and sparse topological features through a hybrid modeling framework. Next-generation sensor design was informed by the actionable insights into the connections between material properties and sensing performance offered by the SGNN framework. Through virtual screening for the detection of per- and polyfluoroalkyl substances (PFAS) as a use case, the effectiveness of the SGNN model was further validated. Density functional theory simulations confirmed graphene as a promising active material for PFAS detection as suggested by the SGNN framework. By bridging gaps in predictive modeling and data availability, this integrated approach provides a strong foundation for accelerating advancements in FET sensor design and innovation.

Ferreira, Rodrigo Pires [Univ. of Chicago, IL (Uni↗
DOE OSTI2025

Spin-informed universal graph neural networks for simulating magnetic ordering

The screening and discovery of magnetic materials are hindered by the computational cost of first-principles density-functional theory (DFT) calculations required to find the ground state magnetic ordering. Although universal machine-learning interatomic potentials (uMLIPs), also known as atomistic foundation models, offer high-fidelity models of many atomistic systems with significant speedup, they currently lack the inputs required for predicting magnetic ordering. In this work, we present a data-efficient, spin-informed graph neural network framework that incorporates spin degrees of freedom as inputs and preserves physical symmetries, extending the functionality of uMLIPs to simulate magnetic orderings. This framework speeds up DFT calculations through better initial guesses for magnetic moments, determines the ground-state ordering of bulk materials and even generalizes to magnetic ordering in surfaces. Furthermore, we implement a closed-loop anomaly detection approach that effectively addresses the classic "chicken-and-egg" problem of creating a high-quality dataset while developing a uMLIP, unearthing anomalies in large benchmark datasets and boosting model accuracy.

Xu, Wenbin↗