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DOE OSTI2023

Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype

The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2013

File Specification for GEOS-5 FP (Forward Processing)

The GEOS-5 FP Atmospheric Data Assimilation System (GEOS-5 ADAS) uses an analysis developed jointly with NOAA's National Centers for Environmental Prediction (NCEP), which allows the Global Modeling and Assimilation Office (GMAO) to take advantage of the developments at NCEP and the Joint Center for Satellite Data Assimilation (JCSDA). The GEOS-5 AGCM uses the finite-volume dynamics (Lin, 2004) integrated with various physics packages (e.g, Bacmeister et al., 2006), under the Earth System Modeling Framework (ESMF) including the Catchment Land Surface Model (CLSM) (e.g., Koster et al., 2000). The GSI analysis is a three-dimensional variational (3DVar) analysis applied in grid-point space to facilitate the implementation of anisotropic, inhomogeneous covariances (e.g., Wu et al., 2002; Derber et al., 2003). The GSI implementation for GEOS-5 FP incorporates a set of recursive filters that produce approximately Gaussian smoothing kernels and isotropic correlation functions. The GEOS-5 ADAS is documented in Rienecker et al. (2008). More recent updates to the model are presented in Molod et al. (2011). The GEOS-5 system actively assimilates roughly 2 × 10(exp 6) observations for each analysis, including about 7.5 × 10(exp 5) AIRS radiance data. The input stream is roughly twice this volume, but because of the large volume, the data are thinned commensurate with the analysis grid to reduce the computational burden. Data are also rejected from the analysis through quality control procedures designed to detect, for example, the presence of cloud. To minimize the spurious periodic perturbations of the analysis, GEOS-5 FP uses the Incremental Analysis Update (IAU) technique developed by Bloom et al. (1996). More details of this procedure are given in Appendix A. The assimilation is performed at a horizontal resolution of 0.3125-degree longitude by 0.25- degree latitude and at 72 levels, extending to 0.01 hPa. All products are generated at the native resolution of the horizontal grid. The majority of data products are time-averaged, but four instantaneous products are also available. Hourly data intervals are used for two-dimensional products, while 3-hourly intervals are used for three-dimensional products. These may be on the model's native 72-layer vertical grid or at 42 pressure surfaces extending to 0.1 hPa. This document describes the gridded output files produced by the GMAO near real-time operational FP, using the most recent version of the GEOS-5 assimilation system. Additional details about variables listed in this file specification can be found in a separate document, the GEOS-5 File Specification Variable Definition Glossary. Documentation about the current access methods for products described in this document can be found on the GMAO products page: http://gmao.gsfc.nasa.gov/products/.

GSI↗

DOE OSTI2023

Pilot Business Case Analysis for Digital Infrastructure

The Inflation Reduction Act Has Provided an Opening to Dramatically Change and Improve the Economics of Nuclear Power Until recently, the commercial nuclear sector has faced unprecedented financial challenges driven by low natural gas prices and subsidized renewables, in a marketplace that did not reward carbon-free baseload capacity. The industry is also plagued by labor shortages, increasingly obsolete labor-centric operating models and antiquated analog technology that threaten the viability of the long-term operations of domestic nuclear facilities. In this context, the economic survival of nuclear power plants requires an efficient and technology-centric operating model that harvests the native efficiencies of advanced technology. Such transformations have been made in many other industries – notably, oil and gas. The passage by Congress of the Inflation Reduction Act (IRA) in 2022 provides nuclear operators with unprecedented economic incentives to pursue these upgrades. To realize the benefits of these incentives and achieve the necessary transformations in the nuclear operating model, the nuclear industry must overcome both the continuing unease about licensing pathways and uncertainty related to implementation costs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis

Abstract Background Recent engineering efforts have targeted the ethanologenic bacterium Zymomonas mobilis for isobutanol production. However, significant hurdles remain due this organism’s vulnerability to isobutanol toxicity, adversely affecting its growth and productivity. The limited understanding of the physiological impacts of isobutanol on Z. mobilis constrains our ability to overcome these production barriers. Results We utilized a systems-level approach comprising LC–MS/MS-based lipidomics, metabolomics, and shotgun proteomics, to investigate how exposure to ethanol and isobutanol impact the lipid membrane composition and overall physiology of Z. mobilis . Our analysis revealed significant and distinct alterations in membrane phospholipid and fatty acid composition resulting from ethanol and isobutanol exposure. Notably, ethanol exposure increased membrane cyclopropane fatty acid content and expression of cyclopropane fatty acid (CFA) synthase. Surprisingly, isobutanol decreased cyclopropane fatty acid content despite robust upregulation of CFA synthase. Overexpression of the native Z. mobilis’ CFA synthase increased cyclopropane fatty acid content in all phospholipid classes and was associated with a significant improvement in growth rates in the presence of added ethanol and isobutanol. Heterologous expression of CFA synthase from Clostridium acetobutylicum resulted in a near complete replacement of unsaturated fatty acids with cyclopropane fatty acids, affecting all lipid classes. However, this did not translate to improved growth rates under isobutanol exposure. Correlating with its greater susceptibility to isobutanol, Z. mobilis exhibited more pronounced alterations in its proteome, metabolome, and overall cell morphology—including cell swelling and formation of intracellular protein aggregates —when exposed to isobutanol compared to ethanol. Isobutanol triggered a broad stress response marked by the upregulation of heat shock proteins, efflux transporters, DNA repair systems, and the downregulation of cell motility proteins. Isobutanol also elicited widespread dysregulation of Z. mobilis ’ primary metabolism evidenced by increased levels of nucleotide degradation intermediates and the depletion of biosynthetic and glycolytic intermediates. Conclusions This study provides a comprehensive, systems-level evaluation of the impact of ethanol and isobutanol exposure on the lipid membrane composition and overall physiology of Z. mobilis . These findings will guide engineering of Z. mobilis towards the creation of isobutanol-tolerant strains that can serve as robust platforms for the industrial production of isobutanol from lignocellulosic sugars.

09 BIOMASS FUELS↗

DOE OSTI2026

Collision Tracking in OpenMC: Methods and Applications in Neutron Noise, Neutron Imaging, Time-of-Flight, and Multiplicity Counting

We present the development and application of a collision tracking feature within the OpenMC Monte Carlo particle transport code, designed for diverse applications such as neutron spectroscopy, scatter camera system, neutron noise, and multiplicity counting simulations. This feature enables the tracking of individual particle collisions, with potential applications in nuclear nonproliferation, reactor physics, and nuclear security. Additionally, the feature holds potential for the calibration of neutron detectors, specifically in converting light output into energy deposited within the detectors. The implementation consists of a set of filters—such as reaction type, energy, cell, and material—that constrain the set of collisions that are tracked, extensions to the Python API to enable simple input specification, and support for writing either OpenMC’s native HDF5-based format or the Monte Carlo particle list format. This feature was added to the official OpenMC release in version 0.15.3. In this work, the feature will be applied to showcase scenarios such as time-of-flight simulations, scatter-camera imaging for neutron source localization, neutron-noise analysis to extract integral kinetic parameters such as the prompt decay constant α, and multiplicity counting to estimate the mass of special nuclear materials. Ultimately, this feature aims to expand the application scope of open-source Monte Carlo particle transport codes such as OpenMC.

Monte Carlo code↗

DOE OSTI2025

Data Agnostic Feature-Target Analysis & Ranking Machine Learning Pipeline (DAFTAR-ML) v0.1.0

DAFTAR-ML is a specialized machine-learning pipeline that identifies relevant features based on their relationship to a target variable. Many ML pipelines focus solely on prediction, and feature ranking is often absent or lacks robust statistical methods. DAFTAR-ML performs its tasks with this outcome in mind. Model training is robust, using nested cross-validation and hyperparameter tuning. Instead of relying on native feature-importance scores, it employs SHAP (SHapley Additive exPlanations) to quantify feature importance. The pipeline also produces comprehensive results, including publication-quality visualizations.

Melie, Tina [Lawrence Berkeley National Laboratory↗

DOE OSTI2024

Storage and persistence of organic carbon in the upper three meters of soil under arable and native prairie land use

Aims: Land use change from native grasslands to arable lands globally impacts soil ecosystem functions, including the storage of soil organic carbon (SOC). Understanding the factors affecting SOC changes in topsoil and subsoil due to land use is crucial for effective mitigation strategies. We determined SOC storage and persistence as affected by land use change from native prairies to arable lands. Methods: Here we examined SOC stocks, soil δ 13 C and Δ 14 C signatures, microbial communities (bacteria and fungi), and soil mineral characteristics under native prairies and long-term arable lands (i.e., > 40 years) down to 3 m in the U.S. Midwest. Results: Native prairie soils had higher SOC stocks in the A horizon and 0–50 cm depth increment than arable soils. For both land use types, the δ 13 C and Δ 14 C values significantly decreased with depth, with the latter pointing towards highly stabilized SOC, especially in the B- and C-horizons. Analysis of the microbial communities indicated that the diversity of bacteria and fungi decreased with increasing soil depth. The content of oxalate soluble Al appeared to be the single most important predictor of SOC across horizons and land use types. Conclusion: Our data suggest that most SOC gains and losses and transformation and translocation processes seem to be restricted to the uppermost 50 cm. Increasing SOC retention in the A and B horizons within the 0–50 cm depth would enhance organic material serving as substrate and nutrients for microbes and plants (A horizon) and facilitate long-term SOC storage in the subsoil (B horizon).

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1982

Ellipsometric studies of sputtered silicon nitride on n-GaAs

Ellipsometry, which is the study of optical systems through their effect on polarized light, is a nondestructive technique offering extremely high sensitivity and in situ operation. One of the intriguing possibilities is to make use of the high sensitivity of ellipsometry for studying the very thin interface between an insulating film and a semiconductor substrate. Researchers have been especially interested in native or anodic oxides. In a recent study, Aspnes and Theeten used ellipsometry to study the interface between silicon and its thermally grown oxide, SiO2. These authors were able to conclude that the interface consisted of a 7 +/- 2 A graded region of atomically mixed silicon and oxygen. In this paper we report both analysis and experimental results for the system: sputtered silicon nitride on (100) n-type gallium arsenide.

Peng, Y. K.↗

NASA NTRS1990

Energy balance components from six sites in a native prairie

The surface-flux stations investigated are of similar design and operation, but are located on different slopes and aspects and provided data with significant variations. The largest difference between sites is noticed in the data for soil heat-flux density, and the general variability is theorized to be related to treatment and locations. The number of surface-flux stations required for the prairie topography can be inferred from the results of the data analysis.

Fritschen, Leo J.↗

NASA NTRS2017

Metadata Evaluation and Improvement: Evolving Analysis and Reporting

ESIP Community members create and manage a large collection of environmental datasets that span multiple decades, the entire globe, and many parts of the solar system. Metadata are critical for discovering, accessing, using and understanding these data effectively and ESIP community members have successfully created large collections of metadata describing these data. As part of the White House Big Earth Data Initiative (BEDI), ESDIS has developed a suite of tools for evaluating these metadata in native dialects with respect to recommendations from many organizations. We will describe those tools and demonstrate evolving techniques for sharing results with data providers.

metadata recommendations↗

DOE OSTI2025

Financial Analysis of the Smallmouth Bass Flows implemented at the Glen Canyon Dam during Water Year 2024

The Glen Canyon Dam (GCD) is a Colorado River Storage Project (CRSP) power resource that is a component of the Salt Lake City Area Integrated Projects (SLCA/IP). The 2016 record of decision (ROD) for the GCD long-term experimental and management plan (LTEMP) final Environmental Impact Statement (EIS) specifies criteria for GCD monthly water releases, daily and hourly operating limits, and experimental releases. This report presents a financial analysis of the Smallmouth bass (Micropterus dolomieu) (SMB) flows implemented at GCD during Water Year (WY) 2024. These bypass flows were introduced by the U.S. Bureau of Reclamation (USBR) as an emergency response to the growing threat posed by invasive SMB in the Colorado River ecosystem downstream of the dam. SMB are a non-native predatory species that pose a significant threat to native fish populations, including the endangered humpback chub (Gila cypha). The thermal regime below GCD, typically cold due to hypolimnetic releases from Lake Powell, has historically served as a thermal barrier limiting SMB establishment. However, persistently low reservoir levels in recent years have reduced stratification in Lake Powell, allowing warmer water to be released downstream. This has enabled SMB to spawn successfully below the dam, prompting urgent ecological concerns. To mitigate the risk of SMB proliferation, the USBR implemented a series of bypass flows in WY 2024. Drawn from a lower elevation than the penstocks, the bypass structures released cooler water downstream. These short-duration bypass flows aimed to keep temperatures cool enough to prevent SMB from spawning, thereby reducing the ecological threat posed by this invasive species. Although motivated by ecological objectives, these bypass flows came with financial tradeoffs. Releasing water through the bypass structures instead of the turbines at GCD reduced hydropower generation, resulting in a significantly lower financial position for Western Area Power Administration (WAPA), which is responsible for marketing the electricity produced by the GCD Powerplant. This report analyzes the financial impact of the SMB flows implemented from July to November 2024. These experimental releases led to an estimated financial cost of approximately $18.9 million, primarily driven by the substantial volume of water diverted through the bypass structures. This study applies an integrated set of tools to estimate WAPA financial impacts by simulating GCD under two types of cases; namely, (1) a “With Experiment” case that mimics the water operations that actually occurred, including the SMB bypass flows, and (2) a “Without Experiment” case that simulates operations under the assumption that the SMB flows did not occur. Both cases comply with LTEMP hourly and daily operating criteria, and the monthly water release volumes are assumed to be identical under both cases. The Colorado River Storage Project Python-based model (CRiSPPy) model was the main modeling tool used to simulate the dispatch of the GCD hydropower plant and associated water releases from Lake Powell. In the modeling process, the research team used extensive data sets and historical information on SLCA/IP power plant characteristics, hydrologic conditions, and WAPA’s power purchases and sales prices.

13 HYDRO ENERGY↗

DOE OSTI2025

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

An Examination of Issues Related to a Europa Subsurface Component for the JIMO Mission

The Galileo Europa data set served to revolutionize our view of Europa. In particular the strong evidence of a large, cold, salty Ocean beneath 5-30 km of ice has profoundly altered the significance of Europa in our thinking, especially of context of habitability in the solar system. While much remains to be learned from spacecraft observations of several sorts, there are significant questions answerable only by in-situ techniques; these relate to the formation of Europa, the nature of its ocean, and the prospects for life in its ocean, sediments, and ice. We feel that wide-ranging discussion of an in-situ subsurface mission to Europa, as part of JIMO, should proceed. The science objective of the mission is to characterize the icy shell of Europa to resolve its provenance, estimate the composition of brine of the Europa ocean, and search for evidence of Earth-like life. Probably anyone would agree that an in-situ mission to Europa would be of great value, but he or she would also immediately take the position that such a mission is utterly impractical. We take the position here of defining the least complex mission that can nonetheless justify its cost and to argue that such a mission is realistic enough that it should be seriously considered. Our mission thinking has been: 1) Soft landing. A soft lander is required on a site sufficiently flat to offer a stable platform; no further site selectivity is required. 2) Subsurface exploration. The Europa subsurface must be examined. Surficial processes on Europa arguably have exposed the upper 200 m of shell to chemical effects from the Jovian radiation belts as well as cometary infall, etc; to examine native ice we must descend below that point to, for discussion, 300 m. At that depth we argue that the ice is characteristic of ice at depth and possibly is effectively sea ice. 3) Science data. A few simple measurements at various depths and at 300 m constitute a scientifically successful mission. Measurements would include analysis of meltwater for a few inorganic ions and amino acids and an optical examination of the borehole wall. 4) Communication. Transmission of data to an orbiter is essential, but we will constrain the landed mission to a daily communication over a few days. 5) Subsurface access. Drilling to 300 m is a significant challenge; it can be addressed by several means: Thermal Probe (Cryobot) which permits water to refreeze above the vehicle. This is our tentative choice with plutonium as the fuel to generate thermal energy for drilling and electrical power for operations. Open Hole Drill, a thermal system in which the meltwater is removed for greater thermal efficiency. Meltwater removal on Europa is both a complexity and a risk, but analysis is improved. Mechanical Drilling in which cutting or grinding generates ice chips which are removed. This is too complex at Europa temperatures. The measurement objectives for the mission will be: Obj. 1: Determine the concentration of simple inorganic salts in the Europa Ice Shell and, by extrapolation, of the ocean. These data will also validate spaceborne sensors. Obj. 2: Determine the nature and abundance of amino acids in the ice such that cometary infall material in the upper ice can be compared to material at depth. Obj. 3: Optically examine the ice to resolve inclusion structure, particulate content, and stratification. Access to 300 m depth is a significant if not audacious plan; we are aware that this has not been done on any planetary body. Our approach is the use of a plutonium heat source; to overcome Europa's surface temperature and to melt ice a significant amount of plutonium is needed, and significant shielding and other protective steps will be required. The quantity of plutonium is a key concern. The mission will require subsurface collection and processing of samples for in situ analysis, calling for a miniature, high pressure micro-sampling system designed to meet needs of instruments that require low presses for operation. The inlet system itself collects a micro-sample in the external high pressure environment, then transfers it into a protected low pressure environment for analysis.

Carsey, F. D.↗

DOE OSTI2024

Boundary spanning increases knowledge and action on invasive species in a changing climate

Abstract Challenges associated with global change stressors on ecosystems have prompted calls to improve actionable science, including through boundary‐spanning activities, which aim to build connections and communication between researchers and natural resource practitioners. By synthesizing and translating research and practitioner knowledge, boundary‐spanning activities could support proactive, research‐informed conservation practice, but the success of these efforts is rarely evaluated. Using repeat survey data from the Northeast Regional Invasive Species and Climate Change (NE RISCC) Management Network, a boundary‐spanning organization, we evaluate whether participating in NE RISCC affected practitioners' knowledge, actions and priorities related to invasive species management under a changing climate. Our survey results suggest that practitioners who participate in NE RISCC have greater knowledge about invasive species and climate change and are incorporating climate change in more ways into their invasive species management. We also found NE RISCC membership affected the perceived usefulness of informational resources, with NE RISCC members more frequently identifying research syntheses and targeted workshops (both are common products used by NE RISCC to translate science into practice and share manager knowledge) as useful compared to non‐members. Practitioners who participate in NE RISCC also identified somewhat different research priorities, with non‐members and short‐term members more frequently identifying range‐shifting neonative species and their impacts on native communities as higher priorities compared to long‐term NE RISCC members. NE RISCC research activities and outreach materials have consistently framed range‐shifting neonative species as comparatively low risk, suggesting that this information has influenced practitioner's perception of risk. Practical implication : Although real‐world impacts of applied ecology are notoriously difficult to quantify, this analysis illustrates that if research results are actively translated, they can affect the knowledge and actions of natural resource practitioners. These impacts illustrate the potential for boundary‐spanning efforts to address other global change challenges to conservation.

Evans, Annette E.↗

DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Polymer Coatings on Virus-like Particle Nanoreactors at Low Ionic Strength—Charge Reversal and Substrate Access

Virus-like particles (VLPs) are a class of biomaterials which serve as platforms for achieving the desired functionality through interior and exterior modifications. Through ionic strength-mediated electrostatic interactions, VLPs have been assembled into hierarchically ordered materials. This work builds on predictive models to prepare polymer-coated VLP dusters at very low ionic strength. Zeta potential measurements showed that the clusters carried a strongly positive charge, a complete charge reversal from the VLP building block. SAXS analysis confirmed polymer adsorption onto the VLP exterior. Furthermore, we then studied the activity of an encapsulated enzyme toward small molecular and macromolecular substrates to determine the effect of each component of the hierarchically assembled material. We found that while encapsulation and polymer coating did not have a large effect on access to the enzyme by its native, small molecular substrate, substrate modification with a macromolecule caused the polymer coating and encapsulation to affect the access to the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

MOOSE Framework Meshing Enhancements to Support Reactor Analysis

MOOSE-based physics codes require an input finite element mesh on which the physics solution is calculated, reported, and transferred to other physics codes. The use of difficult-touse, external licensed software is often required to generate high quality meshes for reactor geometries. High-fidelity geometry modeling also requires elaborate tracking of groups of elements for material property assignment and output reporting which can be considerably complex for the user to identify and maintain. Under the U.S. Department of Energy Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, several meshingrelated enhancements have been developed for the MOOSE framework to address user challenges in creating finite element meshes for advanced reactor geometries. MOOSE mesh generators have been developed to mesh hexagonal geometries (pins, ducted assemblies, and cores) commonly found in liquid-metal cooled fast reactor concepts. The mesh generator used for hexagonal pin cells is generic for regular polygons and therefore may also be used for Cartesian pin cells. Hexagonal pin cells can be stitched into ducted assemblies, and assemblies can be stitched together into a core. The user may specify region ids, region names, and other preferences on the mesh. This control is useful for later material mapping in the MOOSE-based physics codes input. A capability was also developed for meshing rotating control drums including determination of material volume fractions in each mesh element as a function of time. Control drum meshes may be stitched to other hexagonal assemblies to create a core configuration. Additional mesh generators were developed that wrap around the hexagonal meshing capabilities and utilize “extra element integer” ID values on each element. In regular Cartesian or hexagonal assemblies or cores, the bookkeeping of element groups for both material assignment and output reporting can now be automated through assignment of pin, assembly, core, axial and depletion id values stored as extra element integers. The extra element tags on the mesh greatly speed the reactor analyst’s efforts to map materials to meshes, track depletion zones, and parse output such as axial pin power distributions. At the highest level, pin, assembly, and core mesh generators (with this reactor terminology) have also been developed to easily generate regular Cartesian and hexagonal cores, including axial extrusion. These reactor geometry builders call upon the previously mentioned capabilities to produce analysis-ready 3D meshes including material assignments. Open source mesh triangulation capabilities were also investigated for integration into the MOOSE framework to address the need for meshing the core periphery region which extends from the irregular outer assembly border to a cylindrical boundary. Options are limited due to licensing constraints, and the recommendation is pursue building a native MOOSE Delaunay triangulator routine with full functionality. Finally, a series of verification problems were performed with NEAMS physics tools. All developed capabilities will be available in the new open-source “Reactor” module of the MOOSE framework, which is accessible to any MOOSE-based NEAMS physics tool.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Matrix Metalloproteinases as Candidate Antigenic Determinants for Anti‐Tumor Autoantibodies in Human Ovarian Cancer: A Post Hoc Analysis

Circulating antibodies in patients with cancer can facilitate the identification of accessible epitopes on autoantigens expressed by tumors. To identify previously unrecognized protein targets in ovarian cancer, we computationally assessed a heptapeptide consensus motif (VPELGHE, flanked by two cysteine residues yielding a cyclic nonapeptide under oxidizing conditions) previously discovered via phage display-based epitope mapping of autoantibodies in patients. Eight proteins associated with ovarian cancer encompass amino acid sequences similar to the consensus motif and were, therefore, considered as candidate native autoantigens. Among these candidate targets, however, matrix metalloproteinase 14 (MMP14) demonstrates gene expression that is both high and negatively correlated with survival in ovarian cancer patient cohorts. MMP14 protein levels are also stable in tumor versus non-tumor tissues. Moreover, the corresponding heptapeptide mimic in MMP14 occurs within an α-helical secondary structural element observed in its catalytic domain. These findings demonstrate that a subset of patient-derived autoantibodies may interact with a previously unknown antigenic epitope found in MMP14 and other MMPs, thereby providing opportunities for the development of new targeted agents.

Biochemistry & Molecular Biology↗