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DOE OSTI2021

Neural Density Estimation and Uncertainty Quantification for ChemCam Spectra [Slides]

The ChemCam instrument of Curiosity uses laser-induced breakdown spectroscopy (LIBS). It fires a laser at target and vaporizes rock surfaces, creating a plasma. Three spectrographs divide the plasma light into wavelengths for chemical analysis: ultraviolet, violet, and visible near-infrared. Regression methods (SVR, PCR, CNN) have been employed for calibration (prediction of the elemental composition of samples); however, labeled ChemCam samples are limited. Here, we focus on unsupervised learning and employ generative models from ChemCam analysis. Further, we use labels (supervised) in combination to the generative model to compute uncertainties related to predictions. We report generative modeling can be successfully applied to model real-world data. Normalizing flow models can be efficiently constructed on latent spaces for fast downstream inference. Unsupervised and supervised learning can be combined to form an uncertainty quantification framework.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Auto-Curation of Seismic Event Data for Signal Denoising

Denoising contaminated seismic signals for later processing is a fundamental problem in seismic signals analysis. Neural network approaches have shown success denoising local signals when trained on short-time Fourier transform spectrograms. One challenge of this approach is the onerous process of hand-labeling event signals for training. By leveraging the SCALODEEP seismic event detector, we develop an automated set of techniques for labeling event data. Despite region specific challenges, training the neural network denoiser on machine curated events shows comparable performance to the neural network trained on hand curated events. We showcase our technique with two experiments, one using Utah regional data and one using regional data from the Korean peninsula.

58 GEOSCIENCES↗

DOE OSTI2021

Semi-supervised Bayesian Low-shot Learning

Deep neural networks (NNs) typically outperform traditional machine learning (ML) approaches for complicated, non-linear tasks. It is expected that deep learning (DL) should offer superior performance for the important non-proliferation task of predicting explosive device configuration based upon observed optical signature, a task which human experts struggle with. However, supervised machine learning is difficult to apply in this mission space because most recorded signatures are not associated with the corresponding device description, or “truth labels.” This is challenging for NNs, which traditionally require many samples for strong performance. Semi-supervised learning (SSL), low-shot learning (LSL), and uncertainty quantification (UQ) for NNs are emerging approaches that could bridge the mission gaps of few labels and rare samples of importance. NN explainability techniques are important in gaining insight into the inferential feature importance of such a complex model. In this work, SSL, LSL, and UQ are merged into a single framework, a significant technical hurdle not previously demonstrated. Exponential Average Adversarial Training (EAAT) and Pairwise Neural Networks (PNNs) are chosen as the SSL and LSL methods of choice. Permutation feature importance (PFI) for functional data is used to provide explainability via the Variable importance Explainable Elastic Shape Analysis (VEESA) pipeline. A variety of uncertainty quantification approaches are explored: Bayesian Neural Networks (BNNs), ensemble methods, concrete dropout, and evidential deep learning. Two final approaches, one utilizing ensemble methods and one utilizing evidential learning, are constructed and compared using a well-quantified synthetic 2D dataset along with the DIRSIG Megascene.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Integrating static PRA information with risk informed safety margin characterization (RISMC) simulation methods

The overall objective of the project was to develop a computationally feasible and user-friendly mechanized process to integrate traditional probabilistic risk assessment (PRA) and dynamic PRA (DPRA) results. Starting with the systematic identification of items in an existing PRA that need dynamic augmentation, the project used a generic 4-loop pressurized reactor (PWR) and 3-loop PWR as example plants. Station blackout (SBO) and large break loss of coolant accident SBLOCA) were selected as the example initiating events. Using the traditional event-tree (ET)/fault-tree (FT) methodology augmented by dynamic evet tree approach, the potential consequences of the initiating events were simulated with RELAP-3D and MELCOR/RASCAL codes to cover Level 1 through Level 3 of PRA. RAVEN and ADAPT software were used to generate Level 1 simulations with RELAP-3D and Level 2/3 simulations with MELCOR (Level 2)/RASCAL (Level 3), respectively. Example branching conditions (BCs) for SBO included AC power recovery time, valve repair failure time, reactor coolant pump leak time/break size and emergency power supply duration to a total of 9. Example BCs for LOCA included off-site power recovery time, diesel generator power recovery time, auxiliary feed water system operation time, safety relief valve failure to open upon demand, reactor coolant pump seal break time and size to a total of 21. Each RELAP-3D simulation (9,587 scenarios) was labelled OK or Core Damage based on the maximum allowed peak clad temperature (2,100oF). Each MELCOR simulation (4610 scenarios) was labeled as Bin over 10rem or Bin 0-10rem based on the dose at the site boundary. The scenarios were clustered based on the criteria above using the mean shift methodology. Classical PRA (CPRA) and DPRA results were compared to identify the ET sequences that need DPRA augmentation. Several approaches were proposed for the incorporation of these sequences into CPRA using clustering with the mean shift methodology, restructuring the CPRA ETs by adding new BCs/sequences, and using the concept of a limit surface. Procedures for decision making regarding the possible consequences of an initiating event (e.g. core damage or not, site evacuation or not) were developed using a convolutional neural network (CNN), a recurrent neural network (RNN) and a transformer neural network (TNN). The project has led to two PhD degrees, three archival journal papers and five refereed conference proceedings.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

Big Data Synchrophasor Monitoring and Analytics for Resiliency Tracking (BDSMART)

This report contains key findings from a project titled Big Data Synchrophasor Monitoring and Analytics for Resiliency Tracking (BDSMART), which was carried out through a collaborative effort of a team of researchers from Texas A&M Engineering Experiment Station, Temple University, and Quanta Technology, LLC. The in-kind support came from OSIsoft (acquired by AVEVA), which provided their PI Historian software to demonstrate the use case of streaming PMU data. The first section of the report describes the project goals and objectives related to the development of Machine Learning (ML) models capable of detecting and classifying events by processing phasor measurements captured in the field by Phasor Measurement Units (PMUs). The data for this study was contributed by the utilities/ISOs from the Western and Eastern interconnects and ERCOT, further referred to as Interconnect B (IC B), Interconnect A (IC A), and Interconnect C (IC C), respectively. The approach that the BDSMART Research Team proposed and the key research tasks defined by the team are outlined in this section. The next section describes the technical approach. We first discuss the data constraints related to the PMU measurements and data interpretation constraints imposed by the data contributors. They provided neither the topological information of the grid nor PMU placement locations and captured recorded data at very few locations in the system with the reporting rate of either 30 or 60 fps. The recordings are mostly positive sequence voltage, frequency, and ROCOF, and in some limited cases, three-phase voltages and currents. We then reflect on the bad data issues that stem from poor recording practices and vague definitions of the PMU status bits to supposedly be used for bad data identification. Finally, the data discovery points to imprecise time stamps with incomplete event start/end time, as well as inconsistent and incomplete event labeling, which combined make the implementation of the data models using supervising learning quite challenging. Following the data discovery study, we hypothesize that because the IC B data has the most complete labels, we should focus our model development on that data and then test it on data from other interconnects. We also define the common metrics used to evaluate the results from the ML algorithm tests. We concluded this section by summarizing the common ML models we used and explaining how we implemented and tested them. The issues from this section are expanded in the Training Dataset Report from this project. The final section of this report deals with the accomplishments and conclusions. As the accomplishments, we formulate the problem we are solving and what is achieved by solving the problem. We then reflect on each of the analytics tools we developed and point out the performance of each tool when applied to solving the mentioned problems. We reference this work for further details to the papers we published on each tool. In the conclusions, we give recommendations on how to improve future PMU recording practices to facilitate the ML algorithm implementation and guidance for the future standardization work aimed at clarifying the ambiguities associated with the PMU status bits. We finally list future tasks that can bring about further improvements in the proposed algorithms. The issues from this section are expanded in the Training, and Test Dataset Report filed at the project completion date.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Rays for Roots - Integrating Backscatter X-Ray Phenotyping, Modeling and Genetics to Increase Carbon Sequestration and Switchgrass Resource Use (Final Report)

To increase carbon (C) deposition in the soil and enhance crop resource use efficiency, characterizing root form and function is essential. Several root and soil traits have been linked to increased root-to-soil C transfer. Technology that could provide high-resolution characterization of many of these traits in field conditions would revolutionize our ability to study and understand how to increase C sequestration. In this effort, we developed an initial early prototype backscatter X-ray system for non-destructive imaging of root traits. We collected initial backscatter X-ray data in field and lab settings and carried out early analysis of these data. Along with this prototype, we also developed a suite of root phenotyping approaches including advanced minirhizotron image analysis, soil core imaging, and mesocosm imaging. Minirhizotron (MR) tubes are clear tubes inserted into the soil in the field and used to image roots and the surrounding soil. Our team has developed deep learning-based methods that can segment roots from soil that can learn from imprecise image-level labels. The ability to learn or fine-tune our deep learning algorithms from image-level labels allows easier and faster application of these approaches to new locations and new plant species. We have successfully implemented and applied our MR analysis approaches to thousands of switchgrass MR images collected across geographical regions. An advantage of MR imaging is the ability to collect root and soil images over time. Our soil core analysis included collecting hundreds of soil core samples from harvested switchgrass fields and imaging these cores with both X-ray CT and backscatter X-ray imaging. Initial segmentation approaches for the X-ray CT images of these cores have been developed and applied. An advantage of soil core analysis is that it preserves the three-dimensional structures of the roots and soil in the core collected. Our group also developed photogrammetry-based mesocosm root imaging and phenotyping approaches. In this approach, a plant was grown in a large mesocosm with a three-dimensional grid of thin supporting lines inserted throughout the mesocosm. After the plant (and, correspondingly, the root architecture is grown and established) the soil media was removed and the supporting lines approximately preserved the three-dimensional root architecture. Then, we applied photogrammetry techniques to create a three-dimensional digital representation of the root architecture for which we developed analysis algorithms including skeletonization. We carried out our phenotyping development with powerful switchgrass resources and physiological and agroecosystem modeling to deliver novel technology. This project contributes to multiple ARPA-E missions including reduction of foreign imports of energy, reduction of energy-related emissions including greenhouse gases, and ensuring that the United States maintains a technological lead in developing and deploying advanced energy technology. Furthermore, the developed tools could transform public and private plant breeding and could be broadly applicable to other crops and, potentially, other application areas. Our team of engineers, plant and soil scientists, and modelers i) developed an early prototype backscatter X-ray platform that can operate in field conditions; ii) developed a suite of root phenotyping and characterization approaches as described above; iii) developed and carried out plant biology and physiology roots studies and; iv) developed and implemented mechanistic physiological modeling.

42 ENGINEERING↗

DOE OSTI2023

Development and implementation of an in situ high-resolution isotopic microscope for measuring metabolic interactions in soil mesocosms (Final Report)

Many of our planet’s ecosystems rely on the activities of soil microbial communities. These microbes have significant and wide-ranging effects: they metabolize carbon and other nutrients, interact with plants and fungi, and perform other processes important to soil health. However, our ability to directly observe the enzymatic and metabolic activities of microbes within soil is currently limited, not only by the complexity of soil microbial communities themselves, but also by the lack of experimental tools to study them and their molecular interactions in situ. These challenges hinder our understanding of the life-sustaining processes of biomass decomposition and the manner in which it contributes to the movement of freed carbon within soil ecosystems. Here we aimed to develop a novel ultrahigh-resolution isotopic microscope that combines complementary imaging modalities to gain insights into metabolic cycling in soil. This final report covers both the portion of this work that was initially completed at the University of North Carolina at Chapel Hill from 2018 to 2019 (as award DE-SC0019012) and then from 2020 to 2022 (2023 in NCE) at the University of Massachusetts Chan Medical School. This goal was to build an integrated platform consisting of fluorescence microscopy, Raman microspectroscopy, and nanospray desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (nanoDESI-FTICR-MS) to directly investigate microbial activities and molecular transformations occurring in soil by exploiting the use of both fluorescent labels and stable isotope probing. Specifically, our instrument was conceived as integrating: (A) fluorescence detection to localize soil microbes, identify bacteria taking up polysaccharides, and monitor gene expression of enzymes involved in decomposition; (B) Raman microspectroscopy to determine which microbes incorporate decomposition products into their biomass, as well as which decomposers are metabolically active; and (C) nanoDESI-FTICR-MS imaging to spatially probe, in real-time, the metabolites in the surrounding area, which we expect will reveal the distributions of the products of the enzymatic breakdown of polysaccharides, as well as specialized metabolites acting as cell-cell signals between decomposers. To enable these measurements, we exploited fluorescence-based probes to map the microbes that are enzymatically active (per A) and utilized stable isotope-labeled substrates to visualize both the microbial and molecular fate of decomposed biomass (B and C, respectively). To accomplish our goal, we combined the expertise of a multidisciplinary group of scientists to pursue the construction of this microscope and to investigate scientific questions that would be facilitated by such a capability. We aimed to employ this spatially informative, high-resolution isotopic microscope to visualize the critical steps of biomass degradation and the molecular fate of other environmentally relevant substrates within soil mesocosms. Accordingly, this technology will enhance our understanding of the microbial and metabolic interactions occurring within soil communities that are relevant to carbon degradation and other soil processes. The instrument has been developed and housed at EMSL, where it will be available to the entire EMSL User Base, enabling a variety of related DOE-relevant systems to be interrogated in the future by diverse scientific research groups.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

National User Resource for Biological Accelerator Mass Spectrometry Annual Report

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

AI Data Quality Monitoring with Hydra

Hydra is an extensible framework for training and managing AI for near real time monitoring that aims to replace the tedious and repetitive data quality monitoring activities the shift crew and online monitoring coordinator typically perform. It continuously scans incoming data in the form of monitoring plots for signs of problems, flagging them for human review. A web app was developed such that experts can efficiently label images for training. Labels are stored in a database for use in training and model validation. Backed up by a comprehensive database, it utilizes an additional web based front-end for viewing the current monitoring status from anywhere in the world. The system has been in production use for the GlueX experiment at Jefferson Lab for more than 2 years with new features still under active development.

Britton, Thomas↗

DOE OSTI2023

Powder Characterization Inter-Comparison

We performed qualitative and quantitative image analysis on SEM images for 5 uranium samples. Qualitative assessment was completed using the lexicon of Tamasi et al. 2017 on a subset of images from each sample to provide an overall morphological profile of each material. Quantitative analysis of the particles was done using the Morphological Analysis for Materials Attribution, or MAMA, software. We performed particle analysis primarily on samples labeled U Mo, U Si, and UO 2 . Samples labeled ADU and DU Ox were not prioritized for quantitative analysis due to staffing and time it took to segment these images. Two lab analysts worked on this effort, one focusing on the qualitative assessment and the other focusing on the quantitative assessment.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Data Steward Team Wall-to-Wall Inventory Status Update October - December 2023 [Slides]

7 Wall-to-wall inventories were completed between October 2 – December 11, 2023. The team viewed 12 technical areas. A total of 280 containers were verified against current WCATS data. We worked with WMCs team to schedule for all waste throughout WFO FOD. WMCs are doing an incredible job with keeping up with all their locations; The team only found one discrepancy that was resolved the same day, and The WMC also took the time to explain their process on how containers are labeled with closure days and why it was labeled as such.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

National User Resource for Biological Accelerator Mass Spectrometry

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Hydra: Computer Vision for Data Quality Monitoring

Hydra: Computer Vision for Data Quality Monitoring Mar 13, 2024, 4:15 PM 30m Charles B. Wang Center, Stony Brook University Poster Track 1: Computing Technology for Physics Research Poster session with coffee break Speaker Ayan Roy Description Hydra is an extensible framework for training, managing, and deploying machine learning models for near real-time data quality monitoring. It is designed to take some of the burden off of shift crews by providing ‘round-the-clock’ monitoring of plots representing the data being collected. The Hydra system is backed by a database which is leveraged for near push button training and is primarily controlled and viewed through a set of web interfaces. This web interface contains a simple-to-use web based GUI for labeling of the datasets used in training; making it possible to label thousands of images quickly and efficiently. To aid in the analysis of Hydra inferences gradCAM, a method of interpretability, is performed and overlaid on the target image, highlighting regions of interest, making diagnosis of problems much faster. Development began in 2019 for the GlueX Experiment in Hall-D, the Hydra system has grown to encompass all of the experimental halls at Jefferson Laboratory. This talk will focus on the features of Hydra as well as provide details of the challenges present with deploying to disparate experimental halls. With a roadmap of development established, Hydra aims to continue to grow in richness of feature set and expand to encompass other monitoring tasks in differing communities.

Roy, Ayan↗

DOE OSTI2024

Identifying a novel pathway for extracellular electron uptake in Methanosarcina barkeri using shotgun

The overarching goal of this project was to identify the genetic and/or enzymatic basis for extracellular electron uptake in Methanosarcina barkeri—an organism we previously characterized to be capable of this process using poised potential electrodes and a range of electrochemical techniques. In our first aim, we will utilized proteomic techniques that labels extracellular proteins with free amine groups with biotin and perform a selective purification of these proteins from the rest of the proteome. These were identified using mass spectrometry, providing us insight into the identity of the cell surface proteins, including redox active proteins present during extracellular electron uptake. We will also used an isobaric tagging technique (iTRAQ labeling) of proteomes from different experiment conditions to look at differential proteins expression and better understand the total pathway involved in extracellular electron uptake coupled to methanogenesis. In our final aim, we will investigated the electrochemical nature of electron uptake in co-cultures, compared to our pure culture data sets. We predict the process of electron uptake from electrodes replicates what goes on in nature when these organisms for co-cultures with electrogenic microbes such as Geobacter, and to test this hypothesis we have begun to probe co-cultures electrochemically during direct interspecies electron transfer. Our final aim took much longer than expected due to challenges replicating co-cultures between Geobacter metallireducens and Methanosarcina barkeri. We found the major problem with this work was the inability of the M. barkeri strain we used (and we tried strains from three different labs) to successfully grow on acetate in the absence of hydrogen. As such, we began to use the strain Methanosarcina acetivorans—another close relative that specializes on acetate growth. We are currently in the process of comparing electrochemical observations of this microorganism between pure and co-culture experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Testing mechanisms of how mycorrhizal associations affect forest soil carbon and nitrogen cycling (Final Technical Report)

Trees are in a symbiotic partnership with mycorrhizal fungi in which they provide the fungi with carbon from photosynthesis and the fungi provide the trees with nutrients and water. In temperate forests, the vast majority of trees form symbioses with one of two types of mycorrhizal fungi—arbuscular mycorrhizal (AM) fungi or ectomycorrhizal (EcM) fungi. These fungi differ in their morphology, hyphal length, and nutrient acquisition strategies. Many studies have found systematic differences in soil organic matter and nitrogen availability between forest stands dominated by AM-associating trees versus EcM-associating trees. For instance, there is a larger proportion of organic matter that is mineral-associated, more available nitrogen, and lower soil carbon to nitrogen ratios in AM forest stands relative to EcM forests stands. However, the mechanisms driving these patterns are not known, which complicates our ability to model soil organic matter dynamics in forested ecosystems. The main objective of this research was to understand the degree to which the observed differences in soil C and N dynamics between AM and EcM dominated forests are driven by tree traits like litter decomposability and root exudation versus mycorrhizal fungal nutrient acquisition strategies. We investigated these mechanisms using observations and targeted experiments and incorporated this knowledge into a process-based soil organic matter model. The observational studies compared the importance of leaf litter decomposability versus fungal identity on soil organic matter processes. We found that often fungal identity and traits were more important drivers of soil organic matter patterns than leaf litter decomposability. We ran two novel experiments: 1) a growth chamber experiment across four EcM and four AM tree species using a 13 C-labeled atmosphere to trace seedling-derived C into hyphae, the rhizosphere, and soil; and 2) an in situ decomposition experiment of six different 13 C and 15 N labeled litters that ranged in decomposability incubated across a gradient of EcM dominance at three sites that capture important variation in climate, soils, and forest species composition. In the first experiment, we found no significant differences of seedling mycorrhizal association on soil carbon sequestration over a growing season, but we did find that mycorrhizal association affected rhizodeposition with EcM-associating seedlings depositing more carbon in response to increased nitrogen availability. The decomposition experiment is still ongoing, but thus far, we have found slower litter decomposition in only one of three EcM-dominated forests which suggests that differences between AM- and EcM-dominated forests depend on the environmental context and identity of the EcM fungi. Lastly, we explicitly incorporated mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model creating Myco-CORPSE. By including the different nutrient acquisition strategies of AM and EcM fungi, we explored the conditions under which EcM fungi can slow decomposition rates and lead to greater soil organic carbon accumulation compared to AM fungi. We found that the effect of EcM fungi was highly context dependent and that EcM fungi decreased decomposition in colder forests with recalcitrant litter inputs and when they produced oxidases and necromass-degrading enzymes. Our research highlights the importance of fungal nutrient acquisition in driving soil organic matter patterns and the need to move beyond the AM-EcM dichotomy to consider the identity and traits of the specific fungi participating in the symbiosis. Overall, this research has resulted in six, peer-reviewed published papers in journals such as Global Change Biology, Ecology (2), Soil Biology and Biochemistry, and Ecosystems (2). There are at least two more papers in progress on this research including one that was recently submitted to Global Change Biology.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

TRACKING LIGNOCELLULOSIC BREAKDOWN BY ANAEROBIC FUNGI AND FUNGAL CELLULOSOMES

Anaerobic fungi degrade plant biomass through invasive, filamentous growth, and the secretion of multi-protein biomass-degrading complexes called fungal cellulosomes. This project developed new tools for anaerobic, non-destructive, real-time imaging of cellulosomes across spatial and temporal scales. Novel nanobody tools were synthesized and deployed to image native fungal cellulosomes. Antibodies raised against key fungal cellulosome components were also used to define the localization patterns of cellulosomes in mature fungal mats vs. fungal zoospores, and revealed direct connections between cellular life stage progression and the regulation of cellulosome production. New procedures were developed to purify native cellulosomes and study their morphology and sub-structures, and genetic engineering tools were also developed and applied to anaerobic fungi to advance in vivo labeling capabilities. A cryoEM structure of a native fungal cellulosome was achieved, as well as a proof of concept for transformation of fungi with flavin-based anaerobic reporter proteins for in vivo labeling of cellulosome components.

09 BIOMASS FUELS↗

DOE OSTI2025

Replace Human Intelligence with Fast and Smart Geometric Reasoning and Graph Neural Network to Accelerate Next Gen ModSim Workflows

We present an agent-guided approach to CAD geometry decomposition that automates hex/hybrid meshing with graph neural networks (GNNs) to accelerate next-generation ModSim workflows. Our end-to-end pipeline (i) reduces 3D boundary-representation (B-Rep) models to a 2D chordal axis skeleton (CAT) and then to a 1D bipartite graph of surface and curve nodes, (ii) assigns per node labels as Cubit® WebCut actions, (iii) trains a multi-action GNN under supervised learning, and (iv) predicts five surface-node and three curve-node actions on out-of-distribution test geometries. Each graph node carries geometric, topological, and meshing attributes drawn from the B-Rep “skin” and CAT “skeleton,” with two-way mappings across 3D↔2D↔1D representations to maintain traceability back to 3D CAD. The supervised learning model exhibits stable convergence of the binary cross-entropy loss and achieves 98.7% accuracy on unseen lattice models. To operationalize decision-making, we rank predicted commands by geometric significance and prototyped the agent-guided workflow through the Cubit® Meshing PowerTool GUI. As a stretch goal, we explore reinforcement learning (RL) to reduce or remove label requirements and to learn policies for action sequences that maximize total reward (e.g., size of hex-meshable regions and resulting hex mesh quality). When all-hex meshing is not feasible, the agent assists in producing hybrid meshes—prioritizing hex in critical regions and transitioning to tetrahedral elements (tets) elsewhere—maintaining fidelity while ensuring robustness. The overarching objective is to replace manual, heuristics-based decomposition with data-driven, reproducible automation, cutting meshing turnaround time by orders of magnitude. We anticipate direct impact on simulation workflows through intelligent, scalable decomposition of complex CAD models into hex-meshable subdomains.

97 MATHEMATICS AND COMPUTING↗