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DOE OSTI2025

Accurate segmentation of localized corrosion in structural alloys via deep learning

This study presents a deep learning-based approach for the automated segmentation of corrosion damage in scanning electron microscopy (SEM) images. The proposed method enables rapid and accurate segmentation of corrosion features in these SEM images, making it highly suitable for real-time applications such as automated microscopy. Specifically, a dedicated corrosion segmentation database tailored for this task is constructed. The newly constructed dataset, alongside data from two public databases, are employed to jointly train a deep learning-based model modified with a texture refinement module. Compared to the same model without the texture refinement module, the refined model substantially enhances the efficacy and efficiency of corrosion segmentation. Furthermore, the methodology developed here is extendable to segmentation tasks for other materials with similar resolution, texture, and contrast characteristics, thereby paving the way for accelerated and automated analysis in corrosion science and beyond.

Artificial Intelligence↗

DOE OSTI2021

Contributions to the BeEST sterile neutrino search

Sterile neutrinos are hypothetical right-handed leptons that have been postulated as extensions to the Standard Model to help explain the origin of neutrino masses and the matter-antimatter asymmetry in the Universe. Sterile neutrinos with keV-scale masses are also a promising candidate for dark matter. LLNL and the Colorado School of Mines are developing an experiment to search for sterile neutrinos by measuring the \Beryllium-7 Electron capture in Superconducting Tunnel junctions (STJs)" (the \BeEST" Experiment). When 7 Be implanted into STJ radiation detectors decays by electron capture, the neutrino escapes and the energy of the recoiling 7 Li nucleus can be measured with high accuracy. Using conservation of energy and momentum, the mass of the emitted neutrino can then be found. Sterile keV neutrinos would generate additional peaks in the spectrum, and the experiment uses high-resolution STJs to observe such a potential signal. During my internship, I contributed to different aspects of the BeEST experiment. I designed a UHV setup for X-ray spectroscopy analysis with STJs. It will allow high-resolution X-ray spectroscopy of different materials to examine the broadening in the BeEST spectra, the origins of which are unknown but may be related to material effects inside the STJ detectors. The design accounts for the specific demands of the BeEST project, but provides a degree of flexibility that makes it useful for other potential STJ projects. Additionally, to test the accuracy of the electronics and data analysis routine, an arbitrary waveform generator (AWG) will be used to generate simulated spectra that contain sterile neutrino signals of a specified mass and admixture. For this I programmed an AWG to output random STJ signals whose amplitudes follow the appropriate user-de ned probability distribution. The AWG signals can be input into the 32-channel preamplifier to simulate any spectrum of interest and test the uniformity of the amplifier chain, as well as the sensitivity of the data analysis.

42 ENGINEERING↗

DOE OSTI2020

EXPERIMENTAL INVESTIGATION OF IMPACT AND ABRASION EROSIONS AT LOW VELOCITIES AND COMPARISON TO CFD SIMULATIONS

Wear and erosion damage of materials due to interaction of the surface with solid particles is a major issue in various industries. This phenomenon is common in mining, and oil and gas production, causing damages worth millions of dollars annually. Erosion is becoming a critical issue in renewable technologies as well such as concentrated solar thermal power (CSP) systems. In some CSP systems, solid particles can be used to absorb solar energy and enhance the heat storage. However, these particles may cause significant amount of wear to system components while falling down the power tower at high temperatures. This damage can be costly, and therefore, investigating solid particle erosion in CSP systems is of utmost importance. In collaboration with Sandia National Laboratories, the erosion durability of particle-based Generation 3 (GEN3) CSP system are being investigated both experimentally and numerically. In order to develop models to predict the life time of such systems, erosion under low temperature and low particle impact velocity conditions are investigated. Impact erosion and abrasion erosion experiments are conducted for low velocity and low temperature conditions for various candidate particles and containment materials. The impact erosion testing is conducted for three different containment material including Stainless Steel 316, special refractory material, and Inconel 740H with CARBOBEAD HSP 40/70 ceramic particles and UNIWEST 430 silica quartz erodent particles. All this data will enable us to better model the erosion behavior of these materials and provides a data base to investigate erosion at high temperatures experienced in CSP systems. At low temperatures and low velocities the softer refractory material exhibited greater erosion by an order-of-magnitude when compared to the harder Inconel 740H and Stainless Steel 316 materials. The overall erosion ratio for all the candidate materials was of the order of 10 -7 kg/kg. We also investigated wear in containment materials from sliding of particles over the surfaces at very low angles, also referred to as abrasion. For the velocities expected in a typical 1MW CSP plant, visible surface wear was noted, but the overall mass loss per unit surface area was found to be dependent on the hardness of the containment material tested. In this manuscript, we also present Computational Fluid Dynamics (CFD) simulations and erosion prediction of low velocity impact erosion. These results are compared with the experimental data to evaluate the ability of available erosion models for predicting erosion under these conditions.

14 SOLAR ENERGY↗

DOE OSTI2026

Kinetics Modeling and Reactor Design Study of Glucose-to-Terpenes Cell-Free Conversion

Cell-free systems offer many advantages over traditional biological conversion by eliminating biological growth constraints. It also offers easy manipulation and finetuning of the reaction conditions for each individual enzyme. The conversion of cellulosic glucose to Limonene, a terpene, is a promising pathway for producing fuels and chemicals. Recent advances in developing cell-free systems focuses on bench scale optimization of terpene yield and to demonstrate its feasibility towards commercialization [1,2]. There is significant knowledge gap regarding reaction kinetics of these cell-free systems to further study how it will perform at larger scale. We present here, our studies on reaction kinetics and reactor design implications of cell-free glucose to Limonene conversion to facilitate the further development and commercialization of this process. We developed a novel kinetic model based on the metabolic-network structure of the cell-free system with multi-substrate reversible Michaelis-Menten rate law. To estimate kinetic parameters for this system of rate equations, we employed Bayesian optimization to perform global search with the assistance of gaussian processes to balance exploration and exploitation. The model parameters estimated showed good results compared with experimental data. The estimated parameters were used to perform sensitivity analysis. We found that Hexokinase is one of the most critical enzymes that affect the conversion of the glucose. We also observed that abundance of co-factors is also critical to the conversion of glucose to limonene. We investigated packed bed reactors with enzymes immobilized on the surface of particles to convert glucose stream into Limonene for larger scale production. The reactor design such as particle size, enzyme loading, and flow rate are found to be critical for improving yields. [1] Dudley, Q.M., Nash, C.J. and Jewett, M.C., 2019. Synthetic Biology, 4(1), p.ysz003. [2] Korman, T.P., Opgenorth, P.H. and Bowie, J.U., 2017. Nature communications, 8(1), p.15526.

09 BIOMASS FUELS↗

DOE OSTI2025

First Joint Oscillation Analysis of Super-Kamiokande Atmospheric and T2K Accelerator Neutrino Data

The Super-Kamiokande and T2K Collaborations present a joint measurement of neutrino oscillation parameters from their atmospheric and beam neutrino data. It uses a common interaction model for events overlapping in neutrino energy and correlated detector systematic uncertainties between the two datasets, which are found to be compatible. Using 3244.4 days of atmospheric data and a beam exposure of 19.7⁢(16.3) × 10 20 protons on target in (anti)neutrino mode, the analysis finds a 1.9⁢𝜎 exclusion of 𝐶⁢𝑃 conservation (defined as 𝐽 𝐶⁢𝑃 = 0) and a 1.2⁢𝜎 exclusion of the inverted mass ordering.

Neutrino detection↗

DOE OSTI2024

Deep Learning-enhanced Block-Diagram Modeling of Solar Power Systems

Data-driven models of power system inverter-based resources are desired to run simulations faster than with detailed electromagnetic transient models, to hide proprietary design details, to support control system design applications, and to aggregate the effects of distributed energy resources. This paper applies a customized Hammerstein Wiener framework to train block diagram models from thousands of electromagnetic transient simulations or experimental test records. The block diagram models integrate with larger grid simulations as voltagecontrolled current sources or current-controlled voltage sources for several simulators. Guidelines for block architecture and training are presented. Three-phase balanced, three-phase unbalanced, and single-phase examples all achieve an acceptable root mean square error of no more than 0.05 per-unit.

Mcdermott, Thomas E. [Private consulting company]↗

DOE OSTI2025

Predicting Initial Trans-Membrane Pressure for Optimized Operations in UF Unit Using Random Forest

With the growing scarcity of freshwater, innovative process design mechanisms like Ultra-filtration(UF) units are increasingly gaining attention among water treatment utilities to address the rising demand. Ensuring reliable water production necessitates efficient resource utilization, minimizing downtime in UF systems. Recent advancements in machine learning (ML) have enabled the development of accurate data-driven models for Model Predictive Control (MPC), often requiring minimal prior knowledge of underlying physical processes. In this study, we present predictive regression models based on Random Forest (RF) and Auto-Regressive (AR) approaches to forecast the initial Trans-Membrane Pressure (TMP) for each filtration cycle in data generated by Direct Potable Reuse (DPR) systems. The proposed RF-based model demonstrates superior performance compared to baseline methods, including historical mean, Last Observation Carried Forward (LOCF), and naïve AR models, across various forecasting horizons in terms of root mean square (RMSE) metric. Accurate prediction of initial TMP is critical for optimizing CCRO operations, as it enables the development of robust modelling frameworks that enhance process efficiency and reliability. The demonstrated efficacy of the RF-based approach highlights its potential as a tool for real-time decision-making in water treatment systems, paving the way for advanced process optimization and sustainable water resource management.

Mukherjee, Subrata [ORNL] (ORCID:0000000309930338)↗

DOE OSTI2025

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape

The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Fractal Scaling of Explosively Driven Product Gases

ABSTRACT Characterization of the interface between explosive product gases and ambient air in an explosion is a complicated task due to the turbulent mixing and inherently three‐dimensional expansion of the interface. This study aims to quantify the evolution of the interface as a temporally varying Hausdorff dimension. Two test series were conducted with Composition C‐4 charges with masses of 105 and 880 g. Imaging data were collected from the time of detonation until shock wave detachment using ultra‐high‐speed cameras. Gas cloud profiles were extracted using automated image processing algorithms, and the Hausdorff dimension of these two‐dimensional slices of the gas cloud was then estimated using boxcounting algorithms. When scaled with standard gas dynamic nondimensional scalings, the Hausdorff dimension of all explosive events appears to collapse towards a single curve. The fireball was initially nonfractal and began to develop fractal properties as the shock wave separated from the detonation products. Artificial perturbation of the charged surface had no detectable impact on the evolution of the Hausdorff dimension in the early development of the fireball outside of error, despite visible phenomenological differences in the early development of mixing on the fireball surface.

42 ENGINEERING↗

DOE OSTI2025

Structural Evolution of the Hogback Monocline and Its Tectonic Significance in the San Juan Basin

The San Juan Basin is recognized as a Laramide foreland basin. It is located within the Colorado Plateau, a broad tectonic province characterized by a thick sedimentary sequence that was segmented into smaller sub basins during the Late Cretaceous to Paleogene Laramide orogeny. The Hogback Monocline lies along the northwestern margin of the San Juan Basin and is considered a Laramide-age structure formed in response to compressional stress. In this study, we interpret surface and subsurface datasets to construct a structural geological model and evaluate its tectonic significance. Through seismic data, we identify key fault and fold geometries at depth. The seismic dataset used in this study was reprocessed in depth and constrained with well log velocity data to enhance seismic imaging quality. Additionally, we performed well log correlations to identify formation tops and assess variations in basin infill and thickness geometry. A series of structural cross-sections, constructed using seismic data and a high density of boreholes, are presented to evaluate geometric variations along the structure and its evolution during basin development. Furthermore, kinematic restoration and forward modeling analyses were conducted to validate our structural interpretation. This work suggests that the Hogback Monocline formed through fault-propagation folding and flexural slip affecting the pre-Laramide sedimentary sequence under compressional stresses associated with the Laramide orogeny. This structure is interpreted as a high-angle reverse fault that influenced the geometry of the late basin infill. Additionally, monocline bending along the structure may have been controlled by fault relay systems and, in some cases, influenced by strike-slip faulting.

Reyes, Martin [New Mexico Bureau o fGeology and Mi↗

DOE OSTI2026

Location Identifiers, Metadata, and Map for Field Measurements at the East-Taylor Watershed Community Observatory, Colorado, USA (Version 3.3)

This dataset contains identifiers, metadata, and a map of the locations where field measurements have been conducted at the East-Taylor Watershed Community Observatory located in the Upper Colorado River Basin, United States. This is version 3.3 of the dataset and replaces the prior version 3.2 (see below for details on changes between the versions). Dataset description: The East River-Taylor Watershed is the primary field site of the Watershed Function Scientific Focus Area (WFSFA) and the Rocky Mountain Biological Laboratory. Researchers from several institutions generate highly diverse hydrological, biogeochemical, climate, vegetation, geological, remote sensing, and model data at the East-Taylor Watershed in collaboration with the WFSFA. Thus, the purpose of this dataset is to maintain an inventory of the field locations and instrumentation to provide information on the field activities in the East-Taylor Watershed and coordinate data collected across different locations, researchers, and institutions. The dataset contains (1) a README file with information on the various files, (2) three csv files describing the metadata collected for each surface point location, plot and region registered with the WFSFA, (3) csv files with metadata and contact information for each surface point location registered with the WFSFA, (4) a csv file with with metadata and contact information for plots, (5) a csv file with metadata for geographic regions and sub-regions within the watershed, (6) a compiled xlsx file with all the data and metadata which can be opened in Microsoft Excel, (7) a kml map of the locations plotted in the watershed which can be opened in Google Earth, (8) a jpg image of the kml map which can be viewed in any photo viewer, and (9) a zipped file with the registration templates used by the SFA team to collect location metadata. The zipped template file contains two csv files with the blank templates (point and plot), two csv files with instructions for filling out the location templates, and one compiled xlsx file with the instructions and blank templates together. Additionally, the templates in the xlsx include drop down validation for any controlled metadata fields. Persistent location identifiers (Location_ID) are determined by the WFSFA data management team and are used to track data and samples across locations. Dataset uses: This location metadata is used to update the Watershed SFA’s publicly accessible Field Information Portal (an interactive field sampling metadata exploration tool; https://wfsfa-data.lbl.gov/watershed/), the kml map file included in this dataset, and other data management tools internal to the Watershed SFA team. Version Information: The latest version of this dataset publication is version 3.3. This version contains 167 new point locations, 1 new plot, and 2 new geographic regions. Overall, there are a total of 1439 point locations, 75 plots, and 54 geographic regions. Additionally, the kml map of locations and image now includes two boundaries (Upper Ohio Creek (UO) and Carbon Creek (CA)) outside of the East River watershed (USGS HUC-10) and accompanying stream network that represents areas of focus. Refer to methods for further details on the version history. This dataset will be updated on a periodic basis with new measurement location information. Researchers interested in having their East-Taylor Watershed measurement locations added to this list should reach out to the WFSFA data management team at wfsfa-data@googlegroups.com. Acknowledgments: Please cite this dataset if using any of the location metadata in other publications or derived products. If using the location metadata for the 2018 NEON hyperspectral campaign, additionally cite Chadwick et al. (2020). doi:10.15485/1618130. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

2018 NEON and 2025 CHESS Campaigns↗

DOE OSTI2025

Intercomparison of Three Continuous Monitoring Systems on Operating Oil and Gas Sites

We compare continuous monitoring systems (CMS) from three different vendors on six operating oil and gas sites in the Appalachian Basin using several months of data. We highlight similarities and differences between the three CMS solutions when deployed in the field and compare their output to concurrent top-down aerial measurements and to site-level bottom-up inventories. Furthermore, we compare vendor-provided emission rate estimates to estimates from an open-source quantification algorithm applied to the raw CMS concentration data. This experimental setup allows us to separate the effect of the sensor platform (i.e., sensor type and arrangement) from the quantification algorithm. We find that 1) localization and quantification estimates rarely agree between the three CMS solutions on short time scales (i.e., 30 min), but temporally aggregated emission rate distributions are similar between solutions, 2) differences in emission rate distributions are generally driven by the quantification algorithm, rather than the sensor platform, 3) agreement between CMS and aerial rate estimates varies by CMS solution but is close to parity when CMS estimates are averaged across solutions, and 4) similar sites with similar bottom-up inventories do not necessarily have similar emission characteristics. These results have important implications for developing measurement-informed inventories and for incorporating CMS-inferred emission characteristics into emission mitigation efforts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Simulations of muon imaging with the LANL GMT detector for spent nuclear fuel cask content verification

Atmospheric muons are typically high energy, highly penetrating charged particles. They interact with matter primarily through multiple Coulomb scatterings. Muon scattering intensities can be used to characterize the density and atomic number of the matter that they pass through. Previously, the Los Alamos National Laboratory (LANL) muon tomography team performed muon imaging of the partially filled MC-10 spent nuclear fuel (SNF) cask at Idaho National Laboratory (INL). This experiment demonstrated the feasibility of muon imaging for the verification of spent fuel container contents. That original effort used the mini muon tracker array, consisting of two arrays of drift tubes on either side of the SNF cask. The reconstructed image quality was limited by statistics, largely due to low muon flux at high zenith angles. A LANL led team will perform new measurements with a larger array, the Giant Muon Tracker (GMT), to improve data collection rates and statistics. In this work, simulations were performed with the GMT near the partially filled INL MC-10 cask. For more general fuel diversion detection, a full MC-10 cask and casks with a singular missing fuel bundle were also simulated. To understand minimum measurement times needed for missing bundle identification, 100 000 to millions of tracked muons (corresponding to 1.4 days to several weeks measurement time) were analyzed. Simulated images were then analyzed visually and numerically to explore techniques designed to minimize the collection time needed to identify the diversion of fuel in each scenario.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Zinc isotope constraints on the cycling of carbon in the Bermuda mantle source

Volatile recycling and storage in the mantle transition zone (MTZ) is important for the refertilization of the upper mantle and is associated with the generation of high-µ (HIMU, where µ is 238 U/ 204 Pb) mantle. One way to probe the MTZ and the processes associated with mantle convection is to sample lavas that originate from the shallow mantle and were contaminated by upwelling from the MTZ, such as at the previously proposed shallow plume of Bermuda. Here we present the first δ 66 Zn isotopic compositions of Bermuda silica-undersaturated and silica-saturated lavas to explore the origin of the carbon-rich lithologies and the genesis of the large seamount found in the western North Atlantic Ocean. Contrasting with global δ 66 Zn data sets, our results (δ 66 Zn between 0.24 ± 0.04 and 0.41 ± 0.04) do not support direct sampling of recycled marine carbonates in the Bermuda HIMU mantle. Instead, we show that δ 66 Zn fractionation toward higher values is associated with magmatic processes and incorporation of carbon sourced from deep fluids associated with the formation of carbonatites. These carbon-rich fluids are likely sourced from the metasomatic reactions between the subducted cold slab of the Iapetus oceanic lithosphere ca. 500 Ma and the thickened continental lithospheric mantle of Pangea. Melting of this metasomatized mantle was triggered by the arrival of the Farallon slab to the eastern North American margin in the late Cenozoic via shallow convection.

Mazza, Sarah E. [Smith College, Northampton, MA (U↗

DOE OSTI2025

NdPO 4 solubility and aqueous Neodymium speciation in supercritical fluids: An experimental study at 500–700 °C and 1.7 kbar

A key aspect in the formation of rare earth elements (REE) deposits is the role of REE transport as aqueous REE complexes in supercritical hydrothermal solutions, where the nature of the aqueous complex is controlled by solution composition, temperature and pressure. Despite chloride being considered as one of the most abundant transporting ligands in magmatic-hydrothermal fluids, experimental investigations on the stability of aqueous REE chloride complexes are scarce above 300 °C. In this study, synthetic NdPO 4 crystals were reacted with non-saline and saline (0, 0.05 and 0.5 mNaCl), acidic (0.01 mHCl) aqueous solutions in a series of solubility experiments conducted at 500–700 °C and 1.7 kbar, where the solubilities were determined using a stable Nd isotope ( 145 Nd isotope spike) dilution technique. NdPO 4 solubility ranges between 28 ppm and 10,858 ppm, where solubility increases with both temperature and salinity. At 500 °C, log mNdPO 4 increases from –3.93 to –1.60 and there is a strong correlation between NdPO 4 solubility and NaCl concentrations (slope of 1.2 ± 0.3), indicating stabilization of the Nd chloride aqueous complexes with a stoichiometry corresponding to NdCl 2+ . At 600 °C, this correlation is weaker (slope of 0.4, log mNdPO 4 increases from –2.63 to –1.88) indicating the stabilization of both Nd chloride and hydroxyl species controlling solubility. At 700 °C, NdPO 4 solubility is largely independent of NaCl concentration indicating that solubility is controlled by Nd hydroxyl complexes, where stoichiometry suggests the neutral Nd(OH) 3 0 species is dominant. The solubility product (Ksp) of NdPO4 is derived from experimental data with the relation: log K sp = -41.81 – 0.057T – 20987/T, with T temperature in Kelvin. Comparison of the measured Nd phosphate solubility to thermodynamic predictions using the available Helgeson-Kirkham-Flowers equation of state parameters for aqueous Nd complexes indicate that predictions are up to three orders of magnitude lower compared to experimental observations. This discrepancy is most pronounced in saline solutions, suggesting that thermodynamic properties of the REE chloride species in supercritical fluids require revision. Numerical simulations of fluid-rock interaction between acidic, saline fluids and a Strange Lake felsic mineral assemblage demonstrates that NdPO 4 solubility predictions from models are four to six orders of magnitude lower than those calculated based on empirical fits from experiments, which suggests that acidic, saline fluids may play an important role in mobilizing large amounts of light REE from 450 to 700 °C.

58 GEOSCIENCES↗

DOE OSTI2025

Combining Theory and Experiment to Map the Atomic-Level Structure–Energy Pathways of Adsorbate-Mediated Phase Changes in a Cooperatively Flexible Metal–Organic Framework

An important subclass of metal–organic frameworks (MOFs) exhibits cooperative flexibility, wherein individual crystallites undergo global structural phase changes in response to external stimuli. Where cooperative flexibility results in reversible changes between crystalline states of distinct accessible porosity, these frameworks can exhibit rare yet desirable behaviors that cannot be explained by local dynamics alone. Yet, the chemical and structural origins of cooperative flexibility and how frameworks undergo these reversible phase changes at the atomic level remain poorly understood. Deliberate design for specific applications is therefore exceedingly difficult, and there is great impetus to develop a fundamental understanding of this phenomenon. Here, an effective and widely accessible computational approach is developed, which is designed to provide microscopic resolution via direct comparison to experimental data along the desorption-guided pathway. The strategy is applied to explain the desorption-induced phase change in an experimentally well-characterized framework, CdIF-13 (sod-Cd(benzimidazolate)2), where experiment alone was unable to resolve the atomistically detailed phase change landscape. Our findings reveal that the cooperative phase change pathways are adsorbate dependent with thermodynamics of intermediate structural states dictated by a nuanced interplay of ligand orientation, skeletal symmetry, and modes of surface adsorption. The results reveal that this isotropically flexible framework is “chaperoned” through a complex energy landscape by specific adsorbates, revealed by the reported computational approach with atomic-level insight and validated by experimentally determined structures. Thus, this work facilitates both understanding and future design of flexible materials for applications in gas storage, transport, delivery, and separation technologies.

03 NATURAL GAS↗

DOE OSTI2022

Uranium sorption to organic matter and long-term accumulation in a pristine alpine wetland

Understanding the controls on uranium (U) mobility in the environment is key to improve the management of sites contaminated by U mining activities. Previous research has shown that natural or engineered wetlands are particularly able to scavenge high amounts of U(VI) and U(IV) under noncrystalline forms. However, questions remain on the respective roles of sorption and reduction processes in the removal of U from running waters in wetlands, as well as on the long-term stability of U storage. Here, we performed a series of geochemical, isotopic ($δ$ 238 U, ( 234 U/ 238 U)), microscopic (SEM-EDXS, EPMA) and spectroscopic (µ-XRF, µ-XAS, XANES and EXAFS at the U L 3 and M 4 -edges and Fe K-edge) investigations to determine the modes of U accumulation and assess U mobility in a natural exceptionally U-enriched (up to 5000 µg/g) wetland on the shore of Lake Nègre (Mediterranean Alps, France). Uranium (VI) was largely dominant in the two studied soil cores, except a few samples containing as much as ~50 % U(IV). At the particle scale, U is associated to a variety of organic constituents of the soil matrix with a homogenous oxidation state. Bulk EXAFS spectroscopy at the U L 3 -edge shows that U is mostly mononuclear, with dominant monodentate binding to organic moieties (C neighbors at ~3.45 Å). An additional minor fraction of U under polymeric forms is inferred from wavelet (CCWT) analysis of the EXAFS data. These observations are reinforced by 1 M bicarbonate extractions that result in the dissolution of 82–96 % of total U, including putative polymeric species. At the wetland scale, similar or slightly fractionated isotopic ratios ($δ$ 238 U) between the wetland-feeding creek waters and the wetland soils are observed, supporting the idea that U(VI) sorption on organic matter is the primary U scavenging mechanism. Furthermore, it indicates that partial U(VI) reduction to U(IV) occurs as a second step, after sorption. Analysis of U decay chain disequilibria in the cores as a function of depth suggests that U accumulation in this wetland has lasted for several thousand years. In conclusion, we propose that the wetland acts as an active reactor where U has been massively accumulating for ~14500 years, especially as U(VI) forms associated to organic matter and is further partly exported to the lake through soil erosion.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2023

Pickaxe: a Python library for the prediction of novel metabolic reactions

Abstract Background Biochemical reaction prediction tools leverage enzymatic promiscuity rules to generate reaction networks containing novel compounds and reactions. The resulting reaction networks can be used for multiple applications such as designing novel biosynthetic pathways and annotating untargeted metabolomics data. It is vital for these tools to provide a robust, user-friendly method to generate networks for a given application. However, existing tools lack the flexibility to easily generate networks that are tailor-fit for a user’s application due to lack of exhaustive reaction rules, restriction to pre-computed networks, and difficulty in using the software due to lack of documentation. Results Here we present Pickaxe, an open-source, flexible software that provides a user-friendly method to generate novel reaction networks. This software iteratively applies reaction rules to a set of metabolites to generate novel reactions. Users can select rules from the prepackaged JN1224min ruleset, derived from MetaCyc, or define their own custom rules. Additionally, filters are provided which allow for the pruning of a network on-the-fly based on compound and reaction properties. The filters include chemical similarity to target molecules, metabolomics, thermodynamics, and reaction feasibility filters. Example applications are given to highlight the capabilities of Pickaxe: the expansion of common biological databases with novel reactions, the generation of industrially useful chemicals from a yeast metabolome database, and the annotation of untargeted metabolomics peaks from an E. coli dataset. Conclusion Pickaxe predicts novel metabolic reactions and compounds, which can be used for a variety of applications. This software is open-source and available as part of the MINE Database python package ( https://pypi.org/project/minedatabase/ ) or on GitHub ( https://github.com/tyo-nu/MINE-Database ). Documentation and examples can be found on Read the Docs ( https://mine-database.readthedocs.io/en/latest/ ). Through its documentation, pre-packaged features, and customizable nature, Pickaxe allows users to generate novel reaction networks tailored to their application.

59 BASIC BIOLOGICAL SCIENCES↗