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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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431 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mg-Ion Conduction in Antiperovskite Solid Electrolytes Revealed by 25 Mg Ultrahigh Field NMR and First-Principles Calculations

Magnesium-ion batteries hold the potential to outperform the energy density of lithium-ion batteries, given the divalent charge carried by each Mg 2+ cation, but remain in an early stage of development. Here, in this study, 25 Mg solid-state nuclear magnetic resonance (ssNMR) is used to gain insight into the local structure and Mg-ion dynamics of candidate Mg-ion solid electrolytes, the antiperovskites Mg 3 SbN and Mg 3 AsN. Using the highest available magnetic field (35.2 T) for high-resolution solid-state NMR, the largest 25 Mg quadrupole coupling constants (C Q ) yet measured of up to 22 MHz are reported and corroborated by first-principles calculations. Predicted C Q values are shown to correlate with the antiperovskite’s tolerance factor; thus, 25 Mg NMR linewidths can report on lattice distortions and phase stability of these antiperovskites. Variable-temperature 25 Mg NMR spectra demonstrate changes at elevated temperatures, ascribed to Mg-ion motional effects. 25 Mg T 1 relaxometry measurements at ultrahigh field reveal a lower activation energy for the more distorted Mg 3 AsN phase, matching computational predictions of a lower energy barrier for Mg 2+ ion migration and suggesting that additional scrutiny of antiperovskites as Mg-ion conductors is warranted. Given the inherent challenges of 25 Mg NMR, this work demonstrates the benefits of combining ultrahigh field NMR spectroscopy, advanced pulse sequences, modern signal processing, and first-principles calculations to facilitate NMR of quadrupolar nuclei as a tool to probe the local structure and ion dynamics in beyond-Li battery materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Population Genomics of Pseudocercospora griseola Reveals New Groups in the Middle American Clade and the Presence of the Endophytic Bacterium Achromobacter xylosoxidans

Angular leaf spot (ALS), caused by Pseudocercospora griseola is an important disease of common beans. P. griseola, is highly variable and has co-evolved with its host. In this study, 48 isolates of P. griseola from Puerto Rico, Guatemala, Honduras and Tanzania were sequenced (3RADseq), resulting in the de novo assembly of 42,214 contigs. Phylogenomic, population genetic structure and principal component analyses using 1,260 SNPs divided these isolates into two populations, Andean and Middle American, while the Middle American population was further divided into three sub-populations. There were moderate to high levels of differentiation between P. griseola populations, with pairwise Fst values ranging from 0.11 to 0.95. The Andean population was composed of isolates from Tanzania, and was separated from the Middle American population (Fst = 0.95). The Middle American population was separated into 3 subpopulations including isolates from: 1. Guatemala and Honduras, 2. Tanzania, and 3. Puerto Rico. Pathogenicity testing of 27 isolates from Puerto Rico, using 12 common bean differential lines, identified ten races, but these races were not associated with SNPs found in virulence genes. DNA of an endophytic bacterium (Achromobacter xylosoxidans) was found in seven mildly virulent isolates suggesting a possible role of the bacterium in the observed virulence patterns. To understand the evolution and diversity of P. griseola, further study of the virulence genes and the interactions among the endophytic bacterium, the fungus, and the host plant is required. Such information is critical to inform breeding strategies for the development of resistant germplasm and cultivars.

Serrato-Diaz, Luz M. [U.S. Department of Agricultu↗
DOE OSTI2024

Bioblendstocks to Optimize Mixing Controlled Compression Ignition (MCCI) Engines

In this project, a team of researchers from the University of Massachusetts Lowell, the University of Maine, and Mainstream Engineering developed an integrated process for the product of bioblendstocks to optimize mixing controlled compression ignition (MCCI) engines. The objective was to improve the energy density, sooting propensity, and cetane number of base diesel fuel while maintaining cold weather behavior. The process converts woody biomass (e.g. sawmill residues) into bio-oil through selective fast pyrolysis; the bio-oil is then selectively upgraded to form selectively oxygenated, minimally-branched hydrocarbons using non-noble metal catalysts in combination with metal-catalyzed hydrogenation. Advanced predictive models, in conjunction with existing property databases, and experimental testing are used to evaluate overall bioblendstock properties and their impact on base diesel fuel. An iterative, targeted upgrading approach was implemented to optimize the proposed bioblendstock’s properties. Assessment methodologies included techno-economic analysis, life-cycle assessment, property testing, and engine testing. Ultimately, the project team successfully produced a viable bioblendstock while identifying critical process points related to scale-up efforts. It was found that producing pyrolysis oils at 500 degrees C and with pine particle sizes of 1-2 mm led to bio-oil with a higher yield (of approximately 45 wt%) and rich amounts of aromatic alcohols. The resultant pyrolysis oil was then upgraded using a sequence of mild hydrotreating, followed by catalytic etherification and esterification, followed by another final mild hydrotreating to produce a blendstock containing saturated species with a limited, but non-zero, amount of oxygen. The aromatic alcohols produced by pyrolysis were especially helpful in this regard, as the resulting bicycloethers and derivatives exhibited high cetane numbers. While most bulk properties of the bioblendstock met or exceeded targeted thresholds, viscosity and cloud point notably fell outside the expected range; this could be addressed by blending limits and/or through the use of additives that are commonplace in current refinding practices. Identification of a bioblendstock that can be produced economically at scale while improving the performance and emissions characteristics of internal combustion engines positively affects the economy by boosting domestic fuel production and the environment by decreasing harmful emissions and increasing efficiency.

09 BIOMASS FUELS↗
DOE OSTI2025

Surface intermediates identified using IR spectroscopy during the catalytic oxidation of C 2 H 6 on IrO 2 (1 1 0) at near-ambient pressures

Characterizing surface intermediates during catalysis is essential for developing mechanistic models of catalytic reactions and for identifying rate-controlling steps. Here, in this work, we used polarization-dependent reflection absorption infrared spectroscopy (PD-RAIRS) to investigate surface intermediates that form on IrO 2 (1 1 0) during the catalytic oxidation of C 2 H 6 at pressures near 0.5 Torr. Our results show that adsorbed CO and HCO 2 are the only intermediates detectable with PD-RAIRS across a wide range of temperatures and reactant compositions during complete C 2 H 6 oxidation, giving rise to dominant peaks at about 2093 and 1310 cm −1 , respectively. These assignments were corroborated by RAIRS measurements following CO and HCOOH adsorption in ultrahigh vacuum, RAIRS with C 2 H 6 – 18 O 2 mixtures during catalysis and vibrational frequencies and IR intensities computed using density functional theory. We find that increasing the C 2 H 6 mole fraction in the reaction mixture raises the CO surface coverage relative to HCO 2 , correlating with increasing catalytic oxidation rates. The formation of CO and HCO 2 surface species at temperatures well below catalytic ignition indicates that the overall rate of C 2 H 6 oxidation on IrO 2 (1 1 0) is governed by steps late in the reaction sequence, such as H 2 O formation, CO oxidation and HCO 2 dehydrogenation. These findings provide key insight into the mechanism of alkane oxidation on IrO 2 (1 1 0) and valuable input for first-principles microkinetic modeling.

Pope, Connor [Univ. of Florida, Gainesville, FL (U↗
DOE OSTI2025

Assessing the potential of deep learning for protein–ligand docking

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.

Morehead, Alex [Lawrence Berkeley National Laborat↗
DOE OSTI2024

Availability of Critical Benchmark Experiments for the Pebble Tanker Transportation Model for Nuclear Criticality Safety Validation of TRISO Pebbles

This study addresses the need for comprehensive investigations into TRi-structural ISOtropic (TRISO) fuel pebble transportation validation. In this work, an exploratory model, the pebble tanker(PT), was developed with the aim of facilitating the validation of nuclear criticality safety calculations in the context of industrial-scale transportation of TRISO fuel. The PT model was designed to investigate the availability and applicability of critical benchmark experiments crucial for assessing the transportation of these pebbles. This work incorporated sensitivity/uncertainty (S/U) similarity studies to quantify the applicability of critical benchmark experiments and to address nuclear data uncertainties in the context of TRISO transportation. Two container models were investigated: one for the Hermes-type pebble and one for the Pebble Bed Modular Reactor (PBMR)–type pebble. The models were simplified, considering fuel, containment, and either water or air, to enable a focus on the underlying physics of applications involving TRISO fuel pebbles using the PT model. A crucial aspect under consideration was the capacity of the transport package to hold pebbles while ensuring subcriticality in the flooded state. An approach in the criticality validation process involves assessing the similarity between systems through an integral index parameter evaluation. This involves calculating a correlation coefficient (referred to as c k ) based on shared nuclear data–induced uncertainty between a benchmark experiment and the application of the PT model. To facilitate this analysis, the SCALE tools, particularly the CSAS6-Shift, TSUNAMI-3D-Shift, and TSUNAMI-IP sequences, were employed for comprehensive studies in neutronics and S/U analysis. Our findings showed that there are sufficient critical experimental benchmarks to perform this validation of the PT model in the most reactive state, i.e. when the tanker is flooded. This paper provides valuable insights into validating a transport package for Generation IV TRISO fuel pebbles.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Investigating biological nitrogen fixation via single-cell transcriptomics

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

Lotus japonicus↗
DOE OSTI2026

Methyl formate oxidation kinetics up to 100 atm

Methyl formate (MF, CH3OCHO), the simplest ester, is a representative oxygenated fuel with high oxygen content, and low sooting tendency. However, its oxidation behavior under high-pressure and intermediate-temperature conditions remains insufficiently understood, especially where low-temperature peroxy radical chemistry, methanol chemistry, and pressure-dependent reaction pathways play a critical role. In this study, MF oxidation experiments were conducted in the Princeton supercritical-pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm over the temperature range of 400–950 K under both fuel-lean and fuel-rich conditions. Based on the experimental results, an updated HP-Mech was developed by incorporating previous MF sub-mechanisms, expanded low-temperature peroxy pathways, and evaluated pressure-dependent decomposition kinetics. The newly updated HP-Mech shows greatly improved performance in predicting the onset temperature, the key intermediate species fractions, methanol formation, and the progression of MF oxidation across all the experimental conditions. Path flux analysis indicates that MF consumption at the onset stage is dominated by H-abstraction at the methyl site, forming CH2OCHO radicals that lead to the formation and isomerization of O2CH2OCHO, driving low-temperature chain propagation. Moreover, H-abstraction at the formate site forms CH3OCO radicals that preferentially decompose to CH3, initiating the methanol formation pathway linked to CH3O2 and HO2 chemistry. At the same time, HO2 formation is strongly coupled to MF oxidation through multiple MF-derived radical pathways. HCO originates from MF oxidation and acts as a key coupling species linking fuel consumption to HO2 buildup, especially under high-pressure and intermediate-temperature conditions. In addition to this dominant channel, supplementary HO2 formation pathways involving CH3, CH3O, CH2OH, and CH3O2 reacting with O2 further connect methanol chemistry and oxygenated radical chemistry to the HO2 pool, indicating the central role of HO2 in governing MF oxidation. Sensitivity analysis identifies MF with OH/HO2/CH3O2 reactions and the HO2/H2O2/OH sequence as the key factors controlling reactivity in the high-pressure and intermediate-temperature regime. MF directly reacts with OH/HO2/CH3O2 to consume the fuel and produce reactive radicals like CH2OCHO and CH3OCO that undergo subsequent oxidation pathways. Moreover, HO2 recombination suppresses oxidation at lower temperatures, while thermal decomposition of H2O2 accelerates OH production and promotes fuel consumption as temperature increases. The direct formation of active OH from HO2 radicals further completes the mechanism, improving its prediction especially during the oxidation onset stage.

Low-temperature Chemistry↗
DOE OSTI2024

Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola

In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen Colletotrichum sublineola , the causal agent of anthracnose, a problematic disease of sorghum ( Sorghum bicolor (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum− C. sublineola interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and C. sublineola can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with C. sublineola . Approximately 0.3% and 93% of the reads mapped to the genomes of C. sublineola and Sorghum bicolor , respectively. Expression profiling of in vitro versus in planta C. sublineola at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by C. sublineola were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of C. sublineola but also supports the long-term goal of developing resistant sorghum cultivars.

Vela, Saddie↗
DOE OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 2. Evaluating Controls on Flow Persistence in an Urbanized Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in an urbanized catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, distributed temperature sensing (DTS), continuous self-potential (SP) monitoring, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Field_Application subfolder contains the ATS XML input scripts, data files, output data for the SP site. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. The flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.m can only be used with COMSOL with MATLAB) is executed using the ATS output data to simulate the potential field. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) DTS Contains collated DTS data including raw Stokes and anti-Stokes measurement (provided as .h5 file). It also includes DTS processing.ipynb, a Jupyter notebook for calibrating the DTS data using dts_calibration Python package. cooler_calibration.csv is the DTS calibration CSV used in the calibration sequence. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion. 6) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 7) SP Contains the SP data collected in field at the SP sites (provided as CSV files). 8) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). Note: Code files (.ipynb, .py, .xml) can be opened in any standard code editor, .exo file can be viewed using Paraview, .h5 files can be opened using HDFView software and h5py Python package, and .resipy file can be opened with the open-source ResIPy software.

ATS↗
DOE OSTI2026

Evaluation of a Reduced-Order Model for IBR Fault Response Representation via OEM Blackbox Models: Preprint

Driven by the need to capture the electromagnetic transients of transmission lines, inverter switching behavior, and detailed control systems, electromagnetic transient (EMT) studies have become increasingly important in industry, such as IBR interconnection study and fault study. However, original equipment manufacturer (OEM) inverter models typically include extensive parameters and proprietary settings that are unavailable to protection engineers. This paper introduces a data-driven, reduced-order model (ROM) developed as a PSCAD library component for use in EMT-based fault studies. The ROM replicates key OEM model behaviors without requiring detailed knowledge of control design or parameterization. The accompanying Python automation scripts streamline data generation, parameter fitting, and validation. The ROM's performance is demonstrated through comparison with both IEEE 2800-compliant and non-compliant OEM models in a real-world power system. Relay responses show nearly identical results, while simulation runtime is reduced by an average of 32.8\%, highlighting the ROM's practicality for protection engineers.

14 SOLAR ENERGY↗
DOE OSTI2024

Hydropower Black Start: A Guidebook for Retrofitting Grid Dependent Hydropower

Not all United States (US) hydropower plants were designed to provide black start, but they are increasingly needed to uphold resilience in the evolving electric grid. This guidance is designed to help understand the minimal retrofits required for grid dependent hydropower (GDH) plants behind the point of interconnection (POI). For distribution connected hydropower plants or those with dedicated cranking paths, such upgrades can be sufficient for the plant to provide black start. For others, more coordination with the transmission system operator will be needed. This guidebook answers a number of questions relevant to retrofitting hydropower plants with black start capabilities. For example, the guidebook answers: • How flexible do the wicket gate controls need to be? • Who needs to do hydro governor model validation, why, and how? • How robust and flexible do the excitation and AVR controls need to be? • What protection settings need to be adjusted? • What relay(s) will need to be bypassed or overridden and at what risk? • What is the electrical energy demand of the station load or auxiliary power systems? • What should the strategy to energize transformer(s) along cranking path to address inrush currents be? • How should the critical load restoration be sequenced? In addition to outlining the specifications that hydropower plants need to meet for each component to be able to perform black start, this guidebook provides a set of case studies for specific upgrades needed at actual plants. Between the case studies of plants that have already performed black start retrofits and the examples of how this guidebook can be applied to scope future retrofits, five key themes have been identified for retrofit needs. 1. Protection needs “black start” mode: hydropower plants that are not designed with black start capabilities will have protections that prevent them from interconnecting to a “dead bus.” These protections will need to be overridden in every retrofit case and a separate black start mode should be established so that operators can safely switch between black start and grid connected modes, minimizing the risk to the plant. 2. Wicket gates need modern controls: digital governors accelerate the parameter tuning process and gate position sensors improve controllability, so plants with mechanical governors should be upgraded. Furthermore, a black start and islanding mode should be established for controls to maximize plant performance. 3. Robust excitation support: the DC system or excitation generator needs to be reliable enough to form and sustain the rotor electromagnetic field. These systems are typically undersized in plants that were not designed for black start, so they will need to be upgraded. 4. Turbine-governor model validation and operator training: validation of a standard hydro governor model is needed to characterize the dynamic response (i.e., inertial and primary frequency response) of the GDH. This is required for control development and old hydropower plants often have outdated or incorrect models. Operator training is also typically required to ensure the hardware retrofits are utilized correctly during the black start process. 5. Transformer and cranking path energization: any upgradation and control adjustment in front of the POI will depend upon the existing interconnection. Coordination with the transmission or distribution operator may be required.

13 HYDRO ENERGY↗
DOE OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 1. Evaluating Above- and Below-ground Controls of Flow Persistence in a Forested Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in a forested catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, ground penetrating radar (GPR), continuous self-potential (SP) monitoring, electromagnetic (EM) imaging, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Contains two subfolders: Synthetic and Field_Application subfolder. Synthetic subfolder contains the ATS XML input script (can be opened using any code editor) for the four synthetic hydrological cases tested (Connected and gaining, Connected and losing, Disconnected and losing, and dry stream). It also includes other experimental cases to test the influence of precipitation and concentration gradient. For each synthetic case, the flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.mph can be opened with the commercial software COMSOL and requires a license) is executed using the ATS output data to simulate the potential field. It also includes the Synthetic_model_plot.ipynb (can be opened using any code editor) to visualize the SP result and generate manuscript figures. The data subfolder contains mesh files to run both the ATS (.exo and .stl files can be viewed using Paraview; .h5 files can be opened using HDFView software and h5py Python package) and COMSOL models. Field_Application subfolder contains two subfolders: ES_MDA_inversion and Final_Model. ES_MDA_inversion contains the Python script (.py can be opened using any code editor) and SP observation data used to run the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) inversion sequence to get the optimal model parameters. The Final_model subfolder contains the ATS XML input scripts, data files, output data for the two SP sites. The same workflow steps outlined for the Synthetic subfolder apply here. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) EM Contains the CSV file of the EM data from the DUALEM-42, including spatial coordinates (x, y, z), apparent conductivity, and in-phase measurements at 2 m coil separations for horizontal coplanar (HCP) and perpendicular (PRP) geometries. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion (.resipy can be opened with the open-source ResIPy software). 6) GPR Includes GPR field datasets collected at 100 MHz and 250 MHz antenna frequencies, along with the processing/interpretation project file (GPR_process.gpz can be viewed using EKKO_Project 6, a commercial software by Sensors & Software that requires a license). 7) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 8) SP Contains the SP data collected in field at the two SP sites (one in the perennial reach and the other in the intermittent reach), provided as DAT files. 9) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). It also includes DTW.ipynb, a Jupyter notebook containing the code for the dynamic time warping (DTW) with sliding window to evaluate SP signal synchronicity.

ATS↗
DOE OSTI2025

Semi-supervised permutation invariant particle-level anomaly detection

The development of analysis methods to distinguish potential beyond the Standard Model phenomena in a model-agnostic way can significantly enhance the discovery reach in collider experiments. However, the typical machine learning (ML) algorithms employed for this task require fixed length and ordered inputs that break the natural permutation invariance in collision events. To address this, a semi-supervised anomaly detection tool is presented that takes a variable number of particle-level inputs and leverages a signal model to encode this information into a permutation invariant, event-level representation via supervised training with a Particle Flow Network (PFN). Data events are then encoded into this representation and given as input to an autoencoder for unsupervised ANomaly deTEction on particLe flOw latent sPacE (ANTELOPE), classifying anomalous events based on a low-level and permutation invariant input modeling. Performance of the ANTELOPE architecture is evaluated on simulated samples of hadronic processes in a high energy collider experiment, showing good capability to distinguish disparate models of new physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics

General proteomics research for fundamental science typically addresses laboratory- or patient-derived samples of known origin and composition. However, in a few research areas, such as environmental proteomics, clinical identification of infectious organisms, archeology, art/cultural history, and forensics, attributing the origin of a protein-containing sample to the organisms that produced it is a central focus. A small number of groups have approached this problem and developed software tools for taxonomic characterization and/or identification using bottom-up proteomics. Most such tools identify peptides via database search, and many rely on organism-specific peptides as markers. Our group recently introduced MARLOWE, a software tool for taxonomic characterization of unknown samples based on de novo peptide identification and signal-erosion-resistant strong peptides, which are shared peptides distributed in a taxonomy-dependent manner. In the current work, we further characterize the utility of MARLOWE using publicly available proteomics data from forensically-relevant samples. MARLOWE characterizes samples based on their protein profile, and returns ranked organism lists of potential contributors and taxonomic scores based on shared strong peptides between organisms. Overall, the correct characterization rate ranges between 44 and 100%, depending on the sample type and data acquisition parameters (with lower numbers associated with lower-quality data sets). MARLOWE demonstrates successful characterization of true contributors and close relatives, and provides sufficient specificity to distinguish certain microbial species. MARLOWE demonstrates its ability to provide insight into potential taxonomic sources for a wide range of sample types without prior assumptions about sample contents. As a result, this approach can find utility in forensic science and also broadly in bioanalytical applications that utilize proteomics approaches for taxonomic characterization.

Bacteria↗
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

Metabolomic and transcriptomic remodeling of bone marrow myeloid cells in response to maternal obesity

Maternal obesity puts the offspring at high risk of developing obesity and cardiometabolic diseases in adulthood. Here, we utilized a mouse model of maternal high-fat diet (HFD)-induced obesity that recapitulates metabolic perturbations seen in humans. We show increased adiposity in the offspring of HFD-fed mothers (Off-HFD) when compared with the offspring of regular diet-fed mothers (Off-RD). We have previously reported significant immune perturbations in the bone marrow of newly weaned Off-HFD. Here, we hypothesized that lipid metabolism is altered in the bone marrow of Off-HFD versus Off-RD. To test this hypothesis, we investigated the lipidomic profile of bone marrow cells collected from 3-week-old Off-RD and Off-HFD. Diacylglycerols (DAGs), triacylglycerols (TAGs), sphingolipids, and phospholipids were remarkably different between the groups, independent of fetal sex. Levels of cholesteryl esters were significantly decreased in Off-HFD, suggesting reduced delivery of cholesterol. These were accompanied by age-dependent progression of mitochondrial dysfunction in bone marrow cells. We subsequently isolated CD11b+ myeloid cells from 3-wk-old mice and conducted metabolomic, lipidomic, and transcriptomic analyses. The lipidomic profiles of myeloid cells were similar to those of bone marrow cells and included increases in DAGs and decreased TAGs. Transcriptomics revealed altered expression of genes related to immune pathways, including macrophage alternative activation, B-cell receptors, and transforming growth factor-β signaling. All told, this study revealed lipidomic, metabolomic, and gene expression abnormalities in bone marrow cells broadly, and in bone marrow myeloid cells particularly, in the newly weaned offspring of mothers with obesity, which might at least partially explain the progression of metabolic and cardiovascular diseases in their adulthood.

RNA sequencing↗