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DOE OSTI2025

Machine Learning Thermodynamics And Kinetics of Defects For Accelerated Materials Discovery

Atomistic defects play a pivotal role in functional and structural materials’ performance across a myriad of technology applications. Quantitative prediction of the thermodynamics and kinetics of defect formation and migration, respectively, typically requires accurate but expensive first-principles approaches, such as density functional theory (DFT). Their computational expense limits the throughput needed to perform high-throughput materials discovery/screening exercises or to perform materials modeling tasks relying on extensive sampling techniques. Therefore, in this Sandia National Laboratories Laboratory Directed Research and Development (LDRD) project (Project #229366), we developed a variety of machine learning techniques, trained on density functional theory calculations, to accelerate the discovery and modeling of materials in which vacancy and interstitial defects primarily dictate material performance. These include applications such as metal oxides for water-splitting or mixed ionic-electronic conduction, metal hydrides for hydrogen storage, and transition metal dichalcogenides for electronics, and the approaches developed herein can further be applied to many other domains that similarly depend on materials’ thermodynamic and kinetic defect properties for their desired functionality.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Identifying Green Solvent Mixtures for Bioproduct Separation Using Bayesian Experimental Design

Liquid–liquid extraction (LLE) is a widely used technique for the separation and purification of liquid-phase products with applications in various industries, including pharmaceuticals, petrochemicals, and renewable chemistry. A critical step in the design of an LLE process is the selection of appropriate solvents. This study presents a new methodology for identifying solvent mixtures for bioproduct separation using Bayesian experimental design (BED). Motivated by the need for environmentally friendly and effective separation methods, we address the challenge of selecting solvent systems that balance separation efficiency, selectivity, and environmental impact while also tackling the difficulty of separating multiple bioproducts using complex solvent systems. Our approach specifically seeks to predict product partition coefficients (log10 Kp values) as thermodynamic parameters underlying solvent selection. The iterative approach integrates Bayesian optimization with experimental measurements to guide solvent selection and leverages COSMO-RS simulations to enhance high-throughput experimentation. Using the design of solvent systems for the separation of lignin-derived aromatic products via centrifugal partition chromatography (CPC) as a case study, we show that within seven iterations/cycles of the methodology, we can identify new mixtures of green solvents that align with CPC design principles. Furthermore, these results demonstrate the efficacy of the BED framework in optimizing green solvent systems for complex separations, highlighting the potential of this method to advance the field of green chemistry and contribute to the development of sustainable industrial processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities

ABSTRACT Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we presentMetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach—encompassing microenvironmental conditions, agent information, and metabolic pathways—we simulated different communities to showcase the potential of the model. Using ourin-silicoplatform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases.MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities. IMPORTANCE Our study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes inE. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.

Microbiology↗

DOE OSTI2025

Multiscale Characterization of Additive Manufacturing Components with Computed Tomography, 3D X-ray Microscopy, and Deep Learning

Additive manufacturing (AM) facilitates the creation of complex-geometry parts, driving advancements in lightweight aerospace components, high-efficiency engine cooling channels, and customized medical implants. However, ensuring the quality and reliability of AM parts remains challenging due to internal defects, surface irregularities, porosity, and residual trapped powder, which are often inaccessible to traditional inspection methods. Recent developments in X-ray computed tomography (XCT) and 3D X-ray microscopy (XRM), particularly systems equipped with resolution-at-a-distance (RaaD™) capabilities, enable high-resolution, non-destructive evaluation of AM components across multiple scales, from sub-micrometer to macroscopic levels. This paper explores modern XCT and XRM techniques for multiscale characterization of AM parts, focusing on their ability to detect and analyze defects such as porosity, cracks, inclusions, and surface roughness, while offering insights into defect formation mechanisms, material properties, and process-induced variations. The integration of deep learning (DL) frameworks, including Simurgh, DeepRecon, and DeepScout, enhances XCT/XRM workflows by reducing scan times, improving resolution recovery, and enabling accurate defect detection even with limited projection data. These DL-based methods overcome limitations of traditional reconstruction techniques, enabling faster, more reliable characterization of dense materials like Inconel 718 and novel alloys such as AlCe. Applications include process parameter optimization, high-throughput quality control, and multistage AM process evaluation, with DL-enhanced workflows accelerating analysis times from weeks to days. Correlative imaging approaches further validate XCT and XRM data against scanning electron microscopy (SEM) images of physically sectioned samples, confirming the accuracy of DL-based reconstructions and enabling comprehensive defect analysis. While challenges remain in generalizing DL models to diverse materials and imaging conditions, improvements in resolution, noise reduction, and defect detection highlight the transformative potential of these methods. This multiscale and correlative approach enables precise identification and correlation of microstructural features with the overall performance of AM components. By integrating advanced XCT, XRM, and DL techniques, this paper demonstrates a significant leap forward in AM characterization, offering valuable insights into the relationships between processing parameters, microstructure, and part performance, and driving innovations that enhance the quality and reliability of AM products for demanding industrial applications.

Additive manufacturing↗

DOE OSTI2025

FPGA-accelerated SpeckleNN with SNL for real-time X-ray single-particle imaging

We present the implementation of a specialized version of our previously published unified embedding model, SpeckleNN, for real-time speckle pattern classification in X-ray Single-Particle Imaging (SPI), using the SLAC Neural Network Library (SNL) on an FPGA platform. This hardware realization transitions SpeckleNN from a prototypic model into a practical edge solution, optimized for running inference near the detector in high-throughput X-ray free-electron laser (XFEL) facilities, such as those found at the Linac Coherent Light Source (LCLS). To address the resource constraints inherent in FPGAs, we developed a more specialized version of SpeckleNN. The original model, which was designed for broader classification across multiple biological samples, comprised ~5.6 million parameters. The new implementation, while reducing the parameter count to 64.6K (a 98.8% reduction), focuses on maintaining the model's essential functionality for real-time operation, achieving an accuracy of 90%. Furthermore, we compressed the latent space from 128 to 50 dimensions. This implementation was demonstrated on the KCU1500 FPGA board, utilizing 71% of available DSPs, 75% of LUTs, and 48% of FFs, with an average power consumption of 9.4W according to the Vivado post-implementation report. The FPGA performed inference on a single image with a latency of 45.015 microseconds at a 200 MHz clock rate. In comparison, running the same inference on an NVIDIA A100 GPU resulted in an average power consumption of ~73W and an image processing latency of around 400 microseconds. Our FPGA-accelerated version of SpeckleNN demonstrated significant improvements, achieving an 8.9 × speedup and a 7.8 × reduction in power consumption compared to the GPU implementation. Key advancements include model specialization and dynamic weight loading through SNL, which eliminates the need for time-consuming FPGA design re-synthesis, allowing fast and continuous deployment of models (re)trained online. These innovations enable real-time adaptive classification and efficient vetoing of speckle patterns, making SpeckleNN more suited for deployment in XFEL facilities. This implementation has the potential to significantly accelerate SPI experiments and enhance adaptability to evolving experimental conditions.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Design, Processing, and Properties of WTaCrV-Hf Multi-principal Element Alloys

Refractory multi-principal element alloys are candidates for high-temperature structural components due, in part, to their high strength and high melting points. Single-phase materials are initially preferred for isotropic material properties as a function of time and temperature in service conditions. This work outlines a computational rank-ordering and experimental validation methodology for single-phase body-centered-cubic phase stability in WTaCrV-Hf alloys using order–disorder transition temperature. Eight compositions were fabricated by arc-melting and heat-treated at 1400 °C for 24 hrs. X-ray diffraction, energy-dispersive x-ray spectroscopy, and Vickers hardness testing showed alloys with order–disorder transition temperatures below 600 °C formed a single-phase body-centered-cubic structure during solidification and remained single-phase after heat-treatment. The sample possessing the lowest order–disorder transition temperature exhibited slip traces suggestive of room-temperature plastic deformation under Vickers indentation, with both heat-treated single-phase samples exhibiting hardnesses over 800 HV with little cracking compared to tungsten. These results establish order–disorder transition temperature as a viable predictive parameter for multi-principal element alloy phase stability. The methodology outlined in this work provides a framework for future design, fabrication, and characterization of high-temperature structural multi-principal element alloys.

CALPHAD↗

DOE OSTI2026

A scalable framework for efficient coupling of thermal and microstructural simulations in additive manufacturing

Predicting microstructure evolution in metal additive manufacturing (AM) is important for process optimization, but spatiotemporal scale disparities between thermal transport and microstructure evolution create significant challenges for efficient data transfer between simulation codes. To address this, we present Stork, a scalable framework for coupling thermal and microstructural simulations. Stork uses a sparse data representation to identify and store active solidification sub-volumes, enabling highly parallel quad-linear interpolation from coarse thermal grids to fine microstructure grids without large intermediate storage. We demonstrate the framework by coupling the semi-analytic heat transfer code 3DThesis with the time-parallel cellular automata code Toucan. This approach achieves over two orders of magnitude reduction in data generation time and file size compared to prior workflows. Numerical studies show that quad-linear interpolation preserves grain morphology and crystallographic texture in laser powder bed fusion (LPBF) simulations for coarsening ratios up to 16. Overall, Stork provides a scalable pathway for high-throughput, component-scale AM simulations on modern high-performance computing systems.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Identifying high-impact and high-uncertainty parameters in MiniFuel model predictions

The MiniFuel irradiation platform at Oak Ridge National Laboratory's High Flux Isotope Reactor (HFIR) is a flexible, high-throughput separate effects test capability. Finite element thermal models are relied upon to design MiniFuel experiments and to achieve experimental objectives. Recent reports show good agreement in the model prediction of target fuel temperatures, but as the capability of the experiments is extended to higher temperatures, the uncertainty in the model predictions must be quantified. To that end, high-impact, high-uncertainty parameters that contribute the most uncertainty to the model are identified. The uncertainty quantification was accomplished through a series of screening and sensitivity analyses. The first analysis utilizes the method of Morris to perform a computationally efficient preliminary screening that considers uncertainty in a large number of the model inputs. The most important parameters identified in the Morris screening study were then considered in a Sobol sensitivity analysis that more robustly ranks and quantifies the uncertainty associated with each parameter. From these analyses, it was determined that thermal contact conductance between components is the parameter that contributes the highest uncertainty. The estimated uncertainty of the MiniFuel model fuel temperature predictions is ±80 °C in the removable beryllium and ±40 °C in the vertical experiment facilities. In conclusion, the framework established by the series of sensitivity analyses presented herein could easily be adapted to fit the needs of accelerated fuel qualification processes.

Fuel, Irradiation↗

DOE OSTI2025

An accelerated framework for predicting creep rupture lifetimes in engineering alloys

Confidently predicting high-temperature deformation, including creep and creep rupture, is paramount for the design and commercialization of candidate materials for advanced nuclear energy systems. To accelerate creep quantification, we introduce a framework that enables rapid, cost-effective, and reliable prediction of creep rupture lifetimes, minimizing reliance on time-intensive bulk creep testing. Unlike conventional creep analysis, which requires extensive time and resources, our method leverages a maximum of four short-term bulk creep tests as training data for prediction. This framework combines high-throughput nanoindentation up to 700 °C with these targeted bulk tests to inform our creep rupture model in order to predict rupture lifetimes. The strong agreement between our predictions and conventional experimental data demonstrates the effectiveness of our approach for accelerated creep analysis and lifetime prediction of structural components in high-temperature applications. Our multi-pronged approach motivates further integration of computational tools and advanced instrumentation to establish a universal framework for understanding high-temperature material responses.

36 MATERIALS SCIENCE↗

DOE OSTI2026

AutoLabs: cognitive multi-agent systems with self-correction for autonomous chemical experimentation

The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges. In this work, we introduce AutoLabs, a self-correcting, multi-agent architecture designed to autonomously translate natural-language instructions into executable protocols for a high-throughput liquid handler. The system engages users in dialogue, decomposes experimental goals into discrete tasks for specialized agents, performs tool-assisted stoichiometric calculations, and iteratively self-corrects its output before generating a hardware-ready file. We present a comprehensive evaluation framework featuring five benchmark experiments of increasing complexity, from simple sample preparation to multi-plate timed syntheses. Through a systematic ablation study of 20 agent configurations, we assess the impact of reasoning capacity, architectural design (single- vs. multi-agent), tool use, and self-correction mechanisms. Our results demonstrate that agent reasoning capacity is the most critical factor for success, reducing quantitative errors in chemical amounts (nRMSE) by over 85% in complex tasks. When combined with a multi-agent architecture and iterative self-correction, AutoLabs approaches expert-authored reference procedures on the benchmark (F1-score > 0.89) on challenging multi-plate syntheses. These findings establish a clear blueprint for developing robust and trustworthy AI partners for autonomous laboratories, highlighting the synergistic effects of modular design, advanced reasoning, and self-correction to ensure both performance and reliability in high-stakes scientific applications. Code: https://github.com/pnnl/autolabs

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Towards a self-driving trigger at the LHC: adaptive response in real time

Real-time data filtering and selection—or trigger—systems at high-throughput scientific facilities such as the experiments at the Large Hadron Collider must process extremely high-rate data streams under stringent bandwidth, latency, and storage constraints. Yet these systems are typically designed as static, hand-tuned menus of selection criteria grounded in prior knowledge and simulation. In this work, we further explore the concept of a self-driving trigger, an autonomous data-filtering framework that reallocates resources and adjusts thresholds dynamically in real-time to optimize signal efficiency, rate stability, and computational cost as instrumentation and environmental conditions evolve. We introduce a benchmark ecosystem to emulate realistic collider scenarios and demonstrate real-time optimization of a menu including canonical energy sum triggers as well as modern anomaly-detection algorithms that target non-standard event topologies using machine learning. Using simulated data streams and publicly available collision data from the Compact Muon Solenoid experiment, we demonstrate the capability to dynamically and automatically optimize trigger performance under specific cost objectives without manual retuning. Our adaptive strategy shifts trigger design from static menus with heuristic tuning to intelligent, automated, data-driven control, unlocking greater flexibility and discovery potential in future high-energy physics analyses.

Emami, Shaghayegh [Michigan U.] (ORCID:00090007589↗

DOE OSTI2026

MapsTorch : automatic differentiation for X-ray fluorescence data analysis

X-ray fluorescence (XRF) is a popular spectroscopy technique for elemental analysis. Spectrum fitting and parameter tuning are at the core of XRF analysis and are conventionally manually intensive, especially for synchrotron experiments involving large amounts of diverse samples. This work introduces the automatic differentiation (AD) technique to XRF and an open-source package called MapsTorch. By transforming an analytical model of the XRF spectrum into a differentiable computation graph with AD, MapsTorch enables robust optimization of parameters and elemental intensities. We evaluate MapsTorch by conducting computational experiments on a large number of historical synchrotron XRF datasets and compare its performance with the currently practiced fitting tool NLopt. The results show that MapsTorch consistently achieves high-quality fits and often leads to better fitting quality than NLopt, particularly in tasks such as initial spectrum fitting and elemental intensity refinement. The robust performance of MapsTorch paves the way for developing automated and high-throughput XRF data analysis workflows to handle the increasing data volumes expected from next-generation synchrotron facilities.

X-ray fluorescence↗

DOE OSTI2025

Network Slicing for Federated Learning in Operational Technology Environment

Industrial Control Systems (ICS) and Supervisory Control and Data Acquisition (SCADA) environments are essential to modern infrastructure, facing challenges in ensuring low-latency, high-throughput communication while mitigating cyber threats. This paper presents a framework integrating Federated Learning (FL) and network slicing with Quality of Service (QoS) to enable real-time monitoring without disrupting OT operations. Leveraging digital twin technology and Network Function Virtualization (NFV), the architecture supports predictive analytics and Industry 4.0 requirements. FL facilitates decentralized model training, preserving data privacy and scalability, though it introduces potential throughput constraints. Network slicing addresses this by creating dedicated virtualized segments optimized for performance and security. Advanced fault tolerance at the container and instance levels enhances system reliability. The proposed architecture ensures high throughput, low latency, and secure orchestration for real-time anomaly detection in OT networks. Performance evaluations validate its efficiency in throughput, deployment, and learning accuracy, providing a robust foundation for future ICS automation and data-driven decision-making.

Delgado, Brian G. Rodiles [University of Texas at ↗

DOE OSTI2025

Integrating and Characterizing HPC Task Runtime Systems for hybrid AI-HPC workloads

Scientific workflows increasingly involve both HPC and machine-learning tasks, combining MPI-based simulations, training, and inference in a single execution. Launchers such as Slurm’s srun constrain concurrency and throughput, making them unsuitable for dynamic and heterogeneous workloads. We present a performance study of RADICAL-Pilot (RP) integrated with Flux and Dragon, two complementary runtime systems that enable hierarchical resource management and high-throughput function execution. Using synthetic and production-scale workloads on Frontier, we characterize the task execution properties of RP across runtime configurations. RP+Flux sustains up to 930 tasks/s, and RP+Flux+Dragon exceeds 1,500 tasks/s with over 99.6% utilization. In contrast, srun peaks at 152 tasks/s and degrades with scale, with utilization below 50%. For IMPECCABLE.v2 drug discovery campaign, RP+Flux reduces makespan by 30–60% relative to srun/Slurm and increases throughput more than four times on up to 1,024. These results demonstrate hybrid runtime integration in RP as a scalable approach for hybrid AI-HPC workloads.

HPC-AI↗

DOE OSTI2026

wastewater_virus

This repo contains software used to clean and assemble high-throughput sequencing data containing viruses. The input is raw illumina sequencing reads and the output is a database of high-quality viral genomes. The specific application is to wastewater viral concentrates but it is not restricted to that sample type. The software is composed of Nextflow workflows and a set of custom Python and bash scripts that call publicly available bioinformatics tools to accomplish obvious tasks in data analysis in a high performance computing environment. For detailed information, please see the repo's README file.

Kantor, Rose [Lawrence Livermore National Laborato↗

DOE OSTI2025

jaxhps: An elliptic PDE solver built with machine learning in mind

Elliptic partial differential equations (PDEs) can model many physical phenomena, such as electrostatics, acoustics, wave propagation, and diffusion. In scientific machine learning settings, a high-throughput PDE solver may be required to generate a training dataset, run in the inner loop of an iterative algorithm, or interface directly with a deep neural network. To provide value to machine learning users, such a PDE solver must be compatible with standard automatic differentiation frameworks, scale efficiently when run on graphics processing units (GPUs), and maintain high accuracy for a large range of input parameters. We have designed the jaxhps package with these use-cases in mind by implementing a highly efficient and accurate solver for elliptic problems with native hardware acceleration and automatic differentiation support.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗

DOE OSTI2025

SQuaD: Smart Quantum Detection for Photon Recognition and Dark Count Elimination

Quantum detectors of single photons are an essential component for quantum information processing across computing, communication and networking. Today's quantum detection system, which consists of single photon detectors, timing electronics, control and data processing software, is primarily used for counting the number of single photon detection events. However, it is largely incapable of extracting other rich physical characteristics of the detected photons, such as their wavelengths, polarization states, photon numbers, or temporal waveforms. This work, for the first time, demonstrates a smart quantum detection system, SQuaD, which integrates a field programmable gate array (FPGA) with a neural network model, and is designed to recognize the features of photons and to eliminate detector dark-count. The SQuaD is a fully integrated quantum system with high timing-resolution data acquisition, onboard multi-scale data analysis, intelligent feature recognition and extraction, and feedback-driven system control. Our \name experimentally demonstrates 1) reliable photon counting on par with the state-of-the art commercial systems; 2) high-throughput data processing for each individual detection events; 3) efficient dark count recognition and elimination; 4) up to 100% accurate feature recognition of photon wavelength and polarization. Additionally, we deploy the SQuaD to an atomic (erbium ion) photon emitter source to realize noise-free control and readout of a spin qubit in the telecom band, enabling critical advances in quantum networks and distributed quantum information processing.

Linne, Karl C. [U. Chicago (main)] (ORCID:00090009↗