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DOE OSTI2024

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

VitroJet: new features and case studies

Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tick-borne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Arjun Shankar: Advancing National Missions through Smart Data

Computer scientist Arjun Shankar is director of the Compute and Data Environment for Science (CADES), ORNL’s multidisciplinary big data computing center. CADES offers computing, networking and data analytics to facilitate workflows for both ORNL and external research projects.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Teaching Freight Mode Choice Models New Tricks Using Interpretable Machine Learning Methods

Understanding and forecasting the intricate freight mode choice behavior under various industry, policy, and technology contexts is essential in freight planning and policymaking. Numerous models have been developed in prior studies to provide insights into freight mode selection, the majority of which use discrete choice models such as multinomial logit (MNL) models. However, logit models often rely on linear specifications of independent variables, despite potential nonlinear relationships in the data. Moreover, there often lacks a heuristic and efficient approach to identify such complex relationships to define the logit model specifications. To fill this gap, we developed an MNL model for freight mode choice using the insights from state-of-the- art machine learning (ML) models. ML models can capture the nonlinear nature of the complex decision-making process, and recent advances in 'explainable AI' have greatly improved their interpretability. The interpretable ML methods help enhance the performance of MNL models and advance knowledge of freight mode choice. Specifically, the influential factors and their relationship with individual modes are identified using SHapley Additive exPlanations (SHAP) to improve the MNL's performance. The workflow is demonstrated in a case study of Austin, Texas, and the SHAP results reveal multiple nonlinear relationships predicted by ML models. Incorporating those relationships into MNL model specifications improves the interpretability and accuracy of the MNL model compared to a conventional MNL model. Findings from this study can be used to guide freight planning and inform policymakers and practitioners on how key factors affect freight decision-making.

ADVANCED PROPULSION SYSTEMS,MATHEMATICS AND COMPUT↗

DOE OSTI2014

MURMoT. Design and Application of Microbial Uranium Reduction Monitoring Tools

Uranium (U) contamination in the subsurface is a major remediation challenge at many DOE sites. Traditional site remedies present enormous costs to DOE; hence, enhanced bioremediation technologies (i.e., biostimulation and bioaugmentation) combined with monitoring efforts are being considered as cost-effective corrective actions to address subsurface contamination. This research effort improved understanding of the microbial U reduction process and developed new tools for monitoring microbial activities. Application of these tools will promote science-based site management decisions that achieve contaminant detoxification, plume control, and long-term stewardship in the most efficient manner. The overarching hypothesis was that the design, validation and application of a suite of new molecular and biogeochemical tools advance process understanding, and improve environmental monitoring regimes to assess and predict in situ U immobilization. Accomplishments: This project (i) advanced nucleic acid-based approaches to elucidate the presence, abundance, dynamics, spatial distribution, and activity of metal- and radionuclide-detoxifying bacteria; (ii) developed proteomics workflows for detection of metal reduction biomarker proteins in laboratory cultures and contaminated site groundwater; (iii) developed and demonstrated the utility of U isotopic fractionation using high precision mass spectrometry to quantify U(VI) reduction for a range of reduction mechanisms and environmental conditions; and (iv) validated the new tools using field samples from U-contaminated IFRC sites, and demonstrated their prognostic and diagnostic capabilities in guiding decision making for environmental remediation and long-term site stewardship.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Future SDN-HPON Control Plane Architecture and Protocol for On-Demand Terabit End-to-End Extreme-Scale Science Applications

The UC Davis team conducted architecture, algorithm and experimental studies for next generation ultra-high-bandwidth optical networks in support of extreme-scale science applications. In particular, over the course of this 3-year project, the UC Davis team achieved the following main accomplishments: Designed a network architecture for automated multi-domain service provisioning: Designed information exchange schemes between autonomous systems (domains) Designed application programming interfaces to orchestrate resource reservation in data centers, high performance computation facilities, and communication networks belonging to different autonomous systems Experimentally assessed the multi-domain network architecture in a distributed field trial set-up connecting premises in three continents Designed a broker-based orchestrated multi-domain optical networking framework supporting observe-analyze-act cycle based cognitive inter-domain service provisioning: Designed an inter-domain operation mechanism, e.g., topology abstraction, for the broker plane and domain managers to collaboratively accomplish inter-domain service provisioning while respecting the autonomy of each administrative domain Designed an alien wavelength monitoring scheme and an artificial neural network based optical signal-to-noise ratio estimator for quality-of-transmission aware inter-domain service provisioning Developed a deep neural network based multi-domain traffic predictor and a cognitive routing and spectrum assignment algorithm to realize knowledge-based autonomous traffic engineering in multi-domain networks Implemented an optical signal-to-noise ratio estimator and traffic predictor with Google’s Tensor flow and assessed their performance using experimental and synthetic data Demonstrated the benefits of the proposed cognitive schemes with experiments ona two-domain elastic optical network testbed and evaluations on a six-domain simulation framework Built a two-domain software-defined networking control plane testbed using the ONOS platform and demonstrated the workflow of broker and domain manager cooperation, including hierarchical performance monitoring, topology abstraction and cognitive resource allocation. Designed self-learning cognitive service provisioning schemes using advanced machine learning technologies: Designed a self-taught anomaly detection framework for optical networks, including an unsupervised data clustering module for pattern recognition, a supervised data regression and classification module for online anomaly detection, and the system operation principle Experimentally validated the effectiveness of the self-taught anomaly detection framework with various failure/anomaly scenarios. Designed a self-learning autonomic routing, modulation and spectrum assignment (RMSA) provisioning framework for elastic optical networks with deep reinforcement learning. Designed effective modeling and training mechanisms for the self-learning RMSA framework Conducted extensive numerical simulations with various traffic patterns and topologies to verify the advantage of the self-learning RMSA framework.

42 ENGINEERING↗

DOE OSTI2025

An open-source hybrid unstructured mesh - CAD fusion multiphysics analysis workflow in SALAMANDER

Plasma facing components in fusion devices will endure extreme neutron and heat fluxes. To facilitate their design using simulation tools, the open-source Fusion Module, Fusion ENergy Integrated multiphys-X (FENIX) framework is being developed to model these components with a high-fidelity multi-physics multi-dimensional approach. It can iteratively resolve couplings between all the physics at play, from neutron radiation, to thermomechanics, to near-wall plasma dynamics. This framework is based on the Multiphysics Object Oriented Simulation Environment (MOOSE), which is developed by a collaboration of US National Laboratories since 2008, for advanced nuclear, geomechanics simulations and other applications. FENIX couples numerous simulation tools, including OpenMC, the Tritium Migration Analysis Program v8, the NekRS CFD software, and most MOOSE modules. For the coupling of radiation transport and other physics, FENIX supports a hybrid workflow between Computer Assisted Design (CAD) and unstructured mesh geometries. The CAD can be generated from skinning the unstructured mesh, to enable a coarse geometry for efficient particle transport, but still resolving the local material compositions and temperature gradients. Neutron transport is performed using DAGMC on the CAD, and Cardinal, integrated in FENIX, maps tallied quantities, such as the heat deposition or the tritium generation rates, from a tally volumetric mesh to the other physics’ unstructured mesh. This coupling was exercised on a simplified tokamak geometry, coupling neutron transport with the heat conduction equation, and on a monoblock divertor problem, coupling additionally with tritium migration. Mesh convergence studies highlight the importance of the mapping conservativeness. Coupling with thermo-mechanics is further enabled by the generalization of the approach to moving meshes. The presentation will include these coupled analysis as well as an update on status of the FENIX framework.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Hybrid learning techniques for scientific data reduction with performance guarantees

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Final report- UFL - RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Invertible Temper Modeling using Normalizing Flows and the Effects of Structure Preserving Loss

Advanced manufacturing research and development is typically small-scale, owing to costly experiments associated with these novel processes. Deep learning techniques could help accelerate this development cycle but frequently struggle in small-data regimes like the advanced manufacturing space. While prior work has applied deep learning to modeling visually plausible advanced manufacturing microstructures, little work has been done on data-driven modeling of how microstructures are affected by heat treatment, or assessing the degree to which synthetic microstructures are able to support existing workflows. We propose to address this gap by using invertible neural networks (normalizing flows) to model the effects of heat treatment, e.g., tempering. The model is developed using scanning electron microscope imagery from samples produced using shear-assisted processing and extrusion (ShAPE) manufacturing. This approach not only produces visually and topologically plausible samples, but also captures information related to a sample’s material properties or experimental process parameters. We also demonstrate that topological data analysis, used in prior work to characterize microstructures, can also be used to stabilize model training, preserve structure, and improve downstream results. We assess directions for future work and identify our approach as an important step towards end-to-end deep learning system for accelerating advanced manufacturing research and development.

Howland, Sylvia↗

DOE OSTI2025

Position Papers for Inverse Methods for Complex Systems under Uncertainty Workshop

The ability to solve inverse problems – inferring unknown parameters, structures, or states of a system from observed data – is essential for advancing scientific discovery and innovation capabilities for the DOE mission. Basic research needs and challenges are particularly acute in emerging areas such as the interactive, data-driven, modeling and simulation of digital twins; decision support for experiments at DOE scientific user facilities; and for other complex systems and workflows. Inverse problems are at the heart of understanding and controlling complex systems due to factors such as observational data with varying modalities and fidelities, inherent uncertainties in physical measurements and numerical models, and the computational demands of rapid and high-fidelity simulations. The convergence of recent scientific computing trends – scientific machine learning, artificial intelligence, and computing advances such as exascale computing – is creating unprecedented opportunities. These advancements offer the potential to revolutionize how we approach inverse problems to extract actionable insights with the required level of accuracy and computational efficiency. This workshop and the Call for Position Papers are vital steps in bringing together experts to collectively explore and identify the new computational and mathematical directions needed in inverse methods for complex systems under uncertainty.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Advances in Multimodal Characterization of Structural Materials

The myriad detectors and instruments now available for materials characterization provide researchers with an ever-growing suite of tools to probe material behavior. Progress in the development of instrumentation and workflows that enable the collection, and leverage the potential, of various data modalities have provided novel insights into material behavior. Using data across multiple length scales, or performing complementary analyses of in situ and ex situ data, can help reveal a more complete picture of dynamic processes or material structure. However, the accurate combination, or fusion, of these disparate data modalities presents new challenges. Differences in resolution, as well as the varying length scales at which physical phenomena are exploited to generate these data, necessitate novel approaches to accurately interpret and combine these data. Furthermore, the papers within this special topic focus on the collection and fusion of multimodal data to better understand structural materials. From new frameworks and workflows for data segmentation and analysis, process monitoring, enhancing simulations, or interrogating mechanical response, these papers reveal the potential benefits of utilizing multimodal data.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Methods development towards automated, physics-informed, quantitative quality control of TRISO-SiC

Tristructural-isotropic (TRISO) fuel particles have been developed as a high-performance fuel for use in high-temperature gas-cooled reactor (HTGR) systems due to their high efficiency and stability under both normal and off-normal conditions. Broader deployment of this technology in advanced nuclear applications may benefit from quantitative quality assurance and quality control (QA/QC) methods that directly link TRISO properties to downstream performance. A key TRISO property is the SiC layer microstructure, which influences fission product retention during irradiation. However, existing QA/QC for the TRISO-SiC microstructure comprises only a qualitative visual inspection; therefore, there is a clear opportunity for the development of quantitative methods for TRISO QA/QC. Here, to this end, previous work has demonstrated an image processing approach to grain boundary (GB) identification and subsequent extraction of microstructural metrics; however, extensive twinning within the SiC layer complicates such analyses because twin GBs significantly influence microstructural metrics but are not expected to contribute to fission product transport. This study presents the initial development, training, and testing of an ML-based image segmentation algorithm designed to identify and remove twin GBs from standard backscattered electron micrographs, providing an industrially applicable, quantitative, and physically meaningful QA/QC approach for the TRISO-SiC microstructure. Although pixel-wise performance metrics for the twin predictions are low, the change in grain area and the number of GB pixels after twin removal predicted by the ML workflow are within 1% of the true values calculated using crystallographic data. This suggests that the model is well capable of predicting overall twin boundary structures and grain morphology, and continued advancement of this approach could enable automated, scalable, and physics-informed QA/QC for TRISO-SiC microstructures, supporting the reliable qualification of coated particle fuels for next-generation reactor systems.

Computer vision↗

DOE OSTI2023

Comprehensive Analysis of Streaming and Shutdown Dose Rate Experiments at JET with ORNL Fusion Neutronics Workflows

Current experimental fusion systems and conceptual designs of fusion pilot plants (FPPs) are growing in complexity and size. Several radiation metrics are crucial to the safe operation of fusion machines, including neutron flux streaming through openings and the shutdown dose rate (SDDR). Most current designs of advanced experimental fusion systems—and the most probable candidates for FPPs—are based on the tokamak concept, which is prone to neutron streaming through the myriad openings needed for diagnostic and support systems. SDDR is caused by decay gamma rays from radionuclides that become activated by neutrons during the operation of a fusion system that use deuterium-deuterium (DD), tritium-tritium, or deuterium-tritium plasma. Because computational tools have become essential for determining these radiation metrics, they must be validated against reliable and applicable experimental data. Experiments at the Joint European Torus (JET) provide a unique source of experimental data for validating computational tools and nuclear data used to determine SDDR and neutron fluxes in streaming-dominated geometries. Here, this paper presents the comprehensive analysis of the high-performance DD JET SDDR, and streaming experiments performed using Oak Ridge National Laboratory (ORNL) fusion workflows. The computational results were compared with experimental results that consist of online SDDR measurements with ionization chambers and neutron fluence streaming measurements using thermoluminescent detectors. The ratio of calculated-to-experimental SDDR values ranges from 0.6 to 2.5, and the streaming results range from 0.5 to 8.0. Future work will include analyzing the JET 2021 DTE2 campaign alongside the integration of the Shift Monte Carlo transport code into all ORNL fusion neutronics workflows.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

High-throughput physiochemical and biogeochemical characterization for coastal soils and waters

Coastal environments span large biogeochemical gradients and provide critical ecosystem services worldwide, thereby having a disproportionately larger influence on global biogeochemical cycles and greenhouse gas fluxes than their geographical extent suggests. Despite this, cohesive quantitative tools to understand and describe these environments, including scalable, standardized field and laboratory methodologies are lacking. In this work, we advanced the streamlining and standardizing of quantitative approaches to measure and understand coastal physiochemical properties and biogeochemical processes across systems and scales. Outcomes of this work includes workflows for multiple complementary and in-line analyses, from basic physiochemical datasets to targeted molecular approaches and proof of concept through manipulation and analysis of coastal soils and waters with varying salinity, minerology, and biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

Climate Science Performance, Data and Productivity on Titan

Climate Science models are flagship codes for the largest of high performance computing (HPC) resources, both in visibility, with the newly launched Department of Energy (DOE) Accelerated Climate Model for Energy (ACME) effort, and in terms of significant fractions of system usage. The performance of the DOE ACME model is captured with application level timers and examined through a sizeable run archive. Performance and variability of compute, queue time and ancillary services are examined. As Climate Science advances in the use of HPC resources there has been an increase in the required human and data systems to achieve programs goals. A description of current workflow processes (hardware, software, human) and planned automation of the workflow, along with historical and projected data in motion and at rest data usage, are detailed. The combination of these two topics motivates a description of future systems requirements for DOE Climate Modeling efforts, focusing on the growth of data storage and network and disk bandwidth required to handle data at an acceptable rate.

Mayer, Benjamin W↗

DOE OSTI2020

Improving climate model coupling through a complete mesh representation: a case study with E3SM (v1) and MOAB (v5.x)

One of the fundamental factors contributing to the spatiotemporal inaccuracy in climate modeling is the mapping of solution field data between different discretizations and numerical grids used in the coupled component models. The typical climate computational workflow involves evaluation and serialization of the remapping weights during the preprocessing step, which is then consumed by the coupled driver infrastructure during simulation to compute field projections. Tools like Earth System Modeling Framework (ESMF) and TempestRemap offer capability to generate conservative remapping weights, while the Model Coupling Toolkit (MCT) that is utilized in many production climate models exposes functionality to make use of the operators to solve the coupled problem. However, such multistep processes present several hurdles in terms of the scientific workflow and impede research productivity. In order to overcome these limitations, we present a fully integrated infrastructure based on the Mesh Oriented datABase (MOAB) library, which allows for a complete description of the numerical grids and solution data used in each submodel. Through a scalable advancing-front intersection algorithm, the supermesh of the source and target grids are computed, which is then used to assemble the high-order, conservative, and monotonicity-preserving remapping weights between discretization specifications. The Fortran-compatible interfaces in MOAB are utilized to directly link the submodels in the Energy Exascale Earth System Model (E3SM) to enable online remapping strategies in order to simplify the coupled workflow process. We demonstrate the superior computational efficiency of the remapping algorithms in comparison with other state-of-the-science tools and present strong scaling results on large-scale machines for computing remapping weights between the spectral element atmosphere and finite volume discretizations on the polygonal ocean grids.

58 GEOSCIENCES↗

DOE OSTI2026

Interactions Between Climate Policy and Technology-influenced Travel Behavior: Mitigating Induced Demand from CACC

Advances in vehicle technology have influenced the development of automated vehicle systems, where vehicles that do not require human intervention are already deployed in the roadway networks. While these advances are proved to increase roadway safety and highway capacity, more research is needed to understand the long-term and regional-level impacts on mobility, land use, energy consumption, and emissions. This study proposes a multi-model approach to analyze the effect of vehicle automation and deep decarbonization policies over a period from 2020 to 2040 in Austin, Texas. We use the Global Change Analysis Model (GCAM) to develop internally the scenarios that are then passed to the SMART Mobility modeling workflow, a large-scale simulation framework combining the POLARIS activity-based travel demand model and mesoscopic traffic simulator with the Autonomie vehicle energy consumption model and the UrbanSim land use simulator. Results suggest that the introduction of vehicles with advanced automation could increase fuel consumption when no decarbonization policies are implemented. Also, advances in vehicle technology research and development could lead to a decline in energy use in the long-term. Energy pricing and vehicle electrification incentives could help reduce the impact of vehicle automation. Finally, our analysis indicates the relevance of introducing land use processes in longterm vehicle automation studies.

land use↗