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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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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quantitative imaging and automated fuel pin identification for passive gamma emission tomography

Compliance of member States to the Treaty on the Non-Proliferation of Nuclear Weapons is monitored through nuclear safeguards. The Passive Gamma Emission Tomography (PGET) system is a novel instrument developed within the framework of the International Atomic Energy Agency (IAEA) project JNT 1510, which included the European Commission, Finland, Hungary and Sweden. The PGET is used for the verification of spent nuclear fuel stored in water pools. Advanced image reconstruction techniques are crucial for obtaining high-quality cross-sectional images of the spent-fuel bundle to allow inspectors of the IAEA to monitor nuclear material and promptly identify its diversion. In this work, we have developed a software suite to accurately reconstruct the spent-fuel cross sectional image, automatically identify present fuel rods, and estimate their activity. Unique image reconstruction challenges are posed by the measurement of spent fuel, due to its high activity and the self-attenuation. While the former is mitigated by detector physical collimation, we implemented a linear forward model to model the detector responses to the fuel rods inside the PGET, to account for the latter. The image reconstruction is performed by solving a regularized linear inverse problem using the fast-iterative shrinkage-thresholding algorithm. We have also implemented the traditional filtered back projection (FBP) method based on the inverse Radon transform for comparison and applied both methods to reconstruct images of simulated mockup fuel assemblies. Higher image resolution and fewer reconstruction artifacts were obtained with the inverse-problem approach, with the mean-square-error reduced by 50%, and the structural-similarity improved by 200%. We then used a convolutional neural network (CNN) to automatically identify the bundle type and extract the pin locations from the images; the estimated activity levels finally being compared with the ground truth. The proposed computational methods accurately estimated the activity levels of the present pins, with an associated uncertainty of approximately 5%.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Genome-wide identification of novel flagellar motility genes in Pseudomonas syringae pv. tomato DC3000

Pseudomonas syringaepv.tomatoDC3000 (PstDC3000) is a plant pathogenic bacterium that possesses complicated motility regulation pathways including a typical chemotaxis system. A significant portion of our understanding about the genes functioning inPstDC3000 motility is based on comparison to other bacteria. This leaves uncertainty about whether gene functions are conserved, especially since specific regulatory modules can have opposite functions in sets ofPseudomonas. In this study, we used a competitive selection to enrich for mutants with altered swimming motility and used random barcode transposon-site sequencing (RB-TnSeq) to identify genes with significant roles in swimming motility. Besides many of the known or predicted chemotaxis and motility genes, our method identified PSPTO_0406 (dipA), PSPTO_1042 (chrR) and PSPTO_4229 (hypothetical protein) as novel motility regulators. PSPTO_0406 is a homolog ofdipA, a known cyclic di-GMP degrading enzyme inP. aeruginosa. PSPTO_1042 is part of an extracytoplasmic sensing system that controls gene expression in response to reactive oxygen species, suggesting that PSPTO_1042 may function as part of a mechanism that enablesPstDC3000 to alter motility when encountering oxidative stressors. PSPTO_4229 encodes a protein containing an HD-related output domain (HDOD), but with no previously identified functions. We found that deletion and overexpression of PSPTO_4229 both reduce swimming motility, suggesting that its function is sensitive to expression level. We used the overexpression phenotype to screen for nonsense and missense mutants of PSPTO_4229 that no longer reduce swimming motility and found a pair of conserved arginine residues that are necessary for motility suppression. Together these results provide a global perspective on regulatory and structural genes controlling flagellar motility inPstDC3000.

Microbiology↗
DOE OSTI2020

Benchmark Dose Analysis of DNA Damage Biomarker Responses Provides Compound Potency and Adverse Outcome Pathway Information for the Topoisomerase II Inhibitor Class of Compounds

Genetic toxicology data have traditionally been utilized for hazard identification to provide a binary call for a compound's risk. Recent advances in the scientific field, especially with the development of high‐throughput methods to quantify DNA damage, have influenced a change of approach in genotoxicity assessment. The in vitro MultiFlow® DNA Damage Assay is one such method which multiplexes γH2AX, p53, phospho‐histone H3 biomarkers into a single‐flow cytometric analysis (Bryce et al., [2016]: Environ Mol Mutagen 57:546–558). This assay was used to study human TK6 cells exposed to each of eight topoisomerase II poisons for 4 and 24 hr. Using PROAST v65.5, the Benchmark Dose approach was applied to the resulting flow cytometric datasets. With “compound” serving as covariate, all eight compounds were combined into a single analysis, per time point and endpoint. The resulting 90% confidence intervals, plotted in Log scale, were considered as the potency rank for the eight compounds. The in vitro MultiFlow data showed a maximum confidence interval span of 1Log, which indicates data of good quality. Patterns observed in the compound potency rank were scrutinized by using the expert rule‐based software program Derek Nexus, developed by Lhasa Limited. Compound sub‐classification and structural alerts were considered contributory to the potencies observed for the topoisomerase II poisons studied herein. The Topo II poison Adverse Outcome Pathway was evaluated with MultiFlow endpoints serving as Key Events. The step‐wise approach described herein can be considered as a foundation for risk assessment of compounds within a specific mode of action of interest. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.

Wheeldon, Ryan P.↗
DOE OSTI2023

Partial Wave Analysis of Strange Mesons Decaying to K+p+p- in the Reaction ¿p ¿ K+p+p-¿(1520) and the Commissioning of the GlueX DIRC Detector

Hadron spectroscopy is a cornerstone of our understanding of the strong nuclear interactions. Studying the hadron spectrum led to the postulation of quarks and gluons, and the development of Quantum Chromodynamics (QCD), the theory of the strong nuclear force. Today hadron spectroscopy provides an important test of QCD, particularly in the non-perturbative energy regime. One such test is the existence of hybrid hadrons that have gluonic degrees of freedom, e.g. q ?qg states, that are allowed by QCD but have remained elusive in experimental searches. The GlueX experiment located at Thomas Jefferson National Accelerator Facility, is designed to map the light meson spectrum, including hybrid mesons, produced by a linearly polarized photon beam that is scattered off of a liquid hydrogen target. This dissertation concerns the installation and commissioning of the GlueX DIRC upgrade and the analysis of three reactions measured by the GlueX experiment. The GlueX DIRC is a particle identification detector installed as an upgrade to the GlueX experiment in 2019 to improve the experiment?s ability to distinguish pions and kaons. The DIRC uses Cherenkov photons radiated by charged particles that travel faster than the speed of light in the detector medium to determine the velocity of said particles. The velocity measurement is used in conjunction with momentum measurements from other detectors to determine the mass of the particle. The DIRC will be essential to the future of strange meson spectroscopy in GlueX. The reactions ?p ? K+K??+??p, ?p ? K+K??0?0p, ?p ? K+K??0?p were initially chosen for this analysis to search for the hybrid meson candidate ?(2170) and related resonances. The ?(2170) has been observed in e+e? collider experiments decaying to K+K??+?? and K+K??0?0, among other final states. The ?(2170) was not observed in this analysis. The reaction ?p ? K+?+???(1520), a subset of the ?p ? K+K??+??p reaction, was analyzed with a Partial Wave Analysis (PWA) in order to study strange mesons that decay to K+?+??. In the PWA, a useful model for the angular distributions was found but no significant structures could be observed due to statistical limitations.

Hurley, Andrew↗
DOE OSTI2020

Hubble constant difference between CMB lensing and BAO measurements

We apply a tension metric QUDM, the update difference in mean parameters, to understand the source of the difference in the measured Hubble constant H0 inferred with cosmic microwave background lensing measurements from the Planck satellite (H 0 = $67.9$ $^{+1.1}_{–1.3}$ km/s/Mpc) and from the South Pole Telescope (H 0 = $72.0$ $^{+2.1}_{–2.5}$ km/s/Mpc) when both are combined with baryon acoustic oscillation (BAO) measurements with priors on the baryon density (BBN). Q UDM isolates the relevant parameter directions for tension or concordance where the two data sets are both informative, and aids in the identification of subsets of data that source the observed tension. With Q UDM , we uncover that the difference in H 0 is driven by the tension between Planck lensing and BAO+BBN, at probability-to-exceed of 6.6%. Most of this mild tension comes from the galaxy BAO measurements parallel to the line of sight in the redshift range 0.2 < z < 0.75. Here, the redshift dependence of the parallel BAOs pulls both the matter density Ω m and H 0 high in Λ CDM, but these parameter anomalies are usually hidden when the BAO measurements are combined with other cosmological data sets with much stronger Ω m constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils

The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP’s propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Interpretable machine learning models classify minerals via spectroscopy

Developing methods to identify mineral species confidently and rapidly from Raman spectral analysis is critical to numerous fields. Traditionally, analysis relies on pattern matching the Raman spectrum of an unknown dataset with a supporting library of well-characterized spectral data, which may prove difficult for environmental samples that are poorly crystalline or phase mixtures. Here, we developed interpretable machine learning models that can classify uranium minerals by secondary oxyanion chemistry and other physicochemical properties based solely on Raman spectra. This new ML method produces a mineral profile of physical and chemical properties for an unknown sample and can rapidly classify or identify unknown minerals from Raman data, without the need for an exact pattern match in a spectral library. Training models are validated by 1. Strong correlation of high confidence model regions with published spectroscopic assignments and 2. Correct classification of a mineral not present in training data. Training data are from the Compendium of Uranium Raman and Infrared Experimental Spectra and available crystallographic information files within the open-source Smart Spectral Matching scientific framework. Physically meaningful classifier models can rapidly identify key structural and chemical information about unknown uranium minerals and the overall methodology is broadly applicable for mineral phases.

Machine learning↗
DOE OSTI2020

Surface and bulk characterization of reservoir and cap-rocks: Past, present, and future

Geologic formations provide potentially some of the largest volume capacities for CO 2 storage or sequestration. Potential storage sites can be deep saline aquifers, depleted oil reservoirs, and coal seams, surrounded by sealing layers to prevent CO 2 from leaking. It is therefore critical to understand mechanisms contributing to CO 2 trapping and CO 2 leaks. Both phenomena are governed by reactions at the interfaces of the reservoir and cap-rocks and are controlled by the complex chemistry and pore structures of rocks. Mechanisms at the macroscale are affected by the processes occurring at the nanoscale. This review highlights the necessity of multitechnique, multiscale characterization of rocks and points to the importance of surface analysis and surface science studies. Two shale rocks (seals) from Niobrara and Agardhfjellet formations with complex surface chemistry are used as examples throughout the paper. Typically, evaluation of rocks with x-ray diffraction, thermogravimetric analysis, Rock-Eval pyrolysis, gas adsorption, and electron microscopy combined with energy dispersive x-ray spectroscopy is conducted to provide valuable information about the bulk mineralogy, elemental composition, pore volume, and adsorbed species on the sample surface. These studies are necessary prior to designing surface sensitive experiments with x-ray photoelectron spectroscopy (XPS), guiding both sample preparation and sample analysis. XPS has been widely used to study the surface composition of rocks during the investigations of their fine-scale wettability, and the main findings are highlighted here. This paper also reviews the existing literature on ambient-pressure XPS, which provides new opportunities to study in situ chemical alteration due to interactions with CO 2 and offers recommendations for adapting this technique to study rock-fluid interactions, allowing for the identification of fundamental interactions during CO 2 sequestration and guide selection of formation sites for improved storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

COMPASS-FME Synoptic Sites Level 2 Sensor Data v2-1

This is the version 2-1 Level 2 (L2) data release for COMPASS-FME environmental sensors located at our synoptic field sites. COMPASS-FME is studying sites in two distinct regions, the Chesapeake Bay and the Western Lake Erie Basin. We established the network at seven "synoptic" (observational) sites along the Chesapeake Bay and Lake Erie coastlines, collectively generating over three million observations per month, to track and comprehend environmental changes where land and water intersect. Additionally, the two regions provide an interesting contrast of saltwater and freshwater coasts that allow us to differentiate the impacts of inundation and coastal water chemistries in two nationally important coastal systems. Level 2 (L2) data consist of sensor observations from the COMPASS-FME synoptic sites, TEMPEST, and DELUGE. Compared to the L1 data, these are more consistent (always 15-minute timestamps for the entire year); better QA/QC’d (out of bounds, out of service, and extreme outlier values are removed); and more complete, with a gap-filled time series available alongside the main observations, and additional derived (calculated) variables. L2 data are intended to be rapidly and easily usable in analyses and simulations. However, algorithmic outlier identification always carries the risk of removing valid data, and Level 1 data may be more suitable for analyses that focus on variability or extreme events. This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific Parquet (a high performance, space efficient format; see https://parquet.apache.org) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are reported every 15 minutes. Data files are in Apache Parquet, a high performance, space efficient format for tabular data. These files can be read using R's `arrow` package (https://arrow.apache.org/docs/r/), with similar tools available in other languages. Please see v2-1 L2 Sensor Package QStart.pdf for detailed information on data package structure, temporal coverage, and versioning.

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗
DOE OSTI2020

Application of Koopman operator for model-based control of fracture propagation and proppant transport in hydraulic fracturing operation

This work explores the application of the recently developed Koopman operator approach for model identification and feedback control of a hydraulic fracturing process. Controlling fracture propagation and proppant transport with precision is a challenge due in large part to the difficulty of constructing approximate models that accurately capture the characteristic moving boundary and highly-coupled dynamics exhibited by the process. Koopman operator theory is particularly attractive here as it offers a way to explicitly construct linear representations for even highly nonlinear dynamics. The method is data-driven and relies on lifting the states to an infinite-dimensional space of functions called observables where the dynamics are governed by a linear Koopman operator. Here this work considers two problems: (a) fracture geometry control, and (b) proppant concentration control. In both cases, an approximate linear model of the corresponding dynamics is constructed and used to design a model predictive controller (MPC). The manuscript shows that in the case of highly nonlinear dynamics, as observed in the proppant concentration, use of canonical functions in the observable basis fails. In such cases, a priori system knowledge can be leveraged to choose the required basis. The numerical experiments demonstrate that the Koopman linear model shows excellent agreement with the real system and successfully achieves the desired target values maximizing the oil and gas productivity. Additionally, due to its linear structure, the Koopman models allow convex MPC formulations that avoid any issues associated with nonlinear optimization.

42 ENGINEERING↗
DOE OSTI2024

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗
DOE OSTI2023

Single-Filament Imaging Mass Spectrometry Lipidomics in Arthrospira platensis

Elucidating intra-organismal biochemical and lipid organization in photosynthetic biological cell factories of filamentous cyanobacteria, i.e., Arthrospira platensis (Spirulina), is important to track physiological response mechanisms during growth. Little is known about the filaments' biochemical organization and cellular structure and no label-free imaging techniques exist that provide molecular mapping. We applied ultra-high resolution mass spectrometry (7T FT-ICR-MS) matrix-assisted laser desorption ionization (MALDI) imaging to immobilized Spirulina filaments to investigate the localization of lipids across distinct physiological regions. We optimized matrix selection and deposition methods with the goal of facilitating high spatial, and intra-filament, resolution using untargeted multivariate statistical spectral deconvolution across MS pixels. Our results demonstrate an improved two step application with an optimized procedure for intra-organismal lipid profiling to improve analyte sensitivity and achieve higher spatial resolution, whereby we evaluate three conventional matrices 2,5-dihydroxybenzoic acid (DHB), a 9:1 ratio of DHB:superDHB (sDHB), 1,5- diaminonaphthalene (DAN) and a 50:50 mix of DHB:sDHB and compare delineation and pixel-based elucidation of intra-filament lipidomics. We identified a total of 1,626 features that could be putatively assigned a lipid-like formula based on database query and 46 unique features, with associated lipid assignments that were significantly distinct in their intra-filament location. MALDI- imaging MS with untargeted statistical spectral deconvolution was used to visualize intra-filament lipidomics organization in Spirulina filaments. Improvements in matrix deposition, including sequential sublimation and pneumatic spraying, increased signal abundance at high spatial resolution and allowed for identification of distinct lipid composition regions. Here in this work outlines a methodology that may be used for micro-ecological untargeted molecular phenotyping.

09 BIOMASS FUELS↗
DOE OSTI2022

A thermochemical database from high-throughput first-principles calculations and its application to analyzing phase evolution in AM-fabricated IN718

A comprehensive thermochemical database is constructed based on high–throughput first-principles phonon calculations of over 3000 atomic structures in limited concentrations in Ni, Fe, and Co alloys involving a total of 26 elements including Al, B, C, Cr, Cu, Hf, La, Mn, Mo, N, Nb, O, P, Re, Ru, S, Si, Ta, Ti, V, W, Y, and Zr, providing thermochemical data largely unavailable from existing experiments. Here, the database can be employed to predict the equilibrium phase compositions and fractions directly from first-principles by minimizing the chemical potential of a multicomponent system with a fixed overall chemical composition and a fixed temperature. It is applied to the additively manufactured nickel-based IN718 superalloy to analyze the phase evolution with temperature. IN718 is known for its great performance in tensile, fatigue, creep, and rupture strength, combined with easy fabrication and corrosion resistance. In particular, we successfully predicted the formation of L1 0 -FeNi, γ’-Ni 3 (Fe,Al), α-Cr, δ-Ni 3 (Nb,Mo), γ”-Ni 3 Nb, and η-Ni 3 Ti at low temperatures (below 680 K), γ’-Ni 3 Al, δ-Ni 3 Nb, γ”-Ni 3 Nb, α-Cr, and γ-Ni(Fe,Cr,Mo) at intermediate temperatures (between 680 and 1140 K), and δ-Ni 3 Nb and γ-Ni(Fe,Cr,Mo) at high temperatures (above 1140 K) in IN718. These predictions are validated by EDS mapping of compositional distributions and corresponding identifications of phase distributions. The database is expected to be a valuable source for future thermodynamic analysis and microstructure prediction of alloys involving the 26 elements.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Evaluation of an in vitro three-dimensional HepaRG spheroid model for genotoxicity testing using the high-throughput CometChip platform

Three-dimensional (3D) culture systems are increasingly being used for genotoxicity studies due to improved cell-to-cell interactions and tissue-like structures that are limited or lacking in 2D cultures. The present study optimized a 3D culture system using metabolically competent HepaRG cells for in vitro genotoxicity testing. 3D HepaRG spheroids, formed in 96- or 384-well ultra-low attachment plates, were exposed to various concentrations of 34 test articles, including 8 direct-acting and 11 indirect-acting genotoxicants/carcinogens as well as 15 compounds that show different genotoxic responses in vitro and in vivo. DNA damage was evaluated using the high-throughput CometChip assay with concurrent cytotoxicity assessment by the ATP assay in both 2D and 3D cultures. 3D HepaRG spheroids maintained a stable phenotype for up to 30 days with higher levels of albumin secretion, cytochrome P450 gene expression, and enzyme activities compared to 2D cultures. 3D spheroids also demonstrated a higher sensitivity than 2D cultures for detecting both direct- and indirect-acting genotoxicants/carcinogens, indicating a better prediction of in vivo genotoxicity responses. When DNA damage dose-response data were quantified using PROAST software, 3D spheroids generally had lower or similar benchmark dose values compared to 2D HepaRG cells and were more comparable with primary human hepatocytes. These results demonstrate that 3D models can be adapted to the CometChip technology for high-throughput genotoxicity testing and that 3D HepaRG spheroids may be used as a reliable and pragmatic in vitro approach to better support the hazard identification and risk assessment of potential human genotoxic carcinogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Performance of Embedded Sensors in 3D Printed SiC

This report summarizes recent advances in embedding sensors in 3D printed silicon carbide (SiC) ceramic components under the Transformational Challenge Reactor (TCR) program. The additive manufacturing technologies developed under this program will enable fabrication of complex structures with embedded fuels and sensors. The sensors will be capable of characterizing fuel performance using spatially distributed measurements at the most strategic locations that would be otherwise inaccessible using conventional manufacturing techniques. While previous programmatic updates describe initial concepts for embedding sensors, materials selection, and initial characterization of the embedded sensors, the technology requires further demonstration, and quality-significant procedures must be established before the embedding technology is ready for adoption by industry. To this end, this report describes the most effective techniques that have been used to embed functional sensors in 3D printed components using a combination of binder-jet additive manufacturing and chemical vapor infiltration (CVI). A detailed procedure describes each step in the process and is available upon request. Molybdenum (Mo)-sheathed thermocouples have been successfully embedded in complex SiC components, and temperatures were monitored in situ during the embedding process. Post-embedding measurements showed no significant hysteresis, and characterization of the interface revealed qualitatively strong bonding around the entire perimeter of the sensor sheath. Distributed fiber-optic temperature sensors were able to briefly measure temperature profiles during CVI, but they ultimately failed prior to completion of the CVI run. The failure appears to be related to the fiber coating at temperatures close to 1,000°C. Future work will focus on irradiation testing of embedded thermocouples and other sheathed electrical sensors, as well as the identification of fiber-optic sensor coatings that can survive CVI.

42 ENGINEERING↗
DOE OSTI2022

Understanding the Physics Representation of Deep Learning Models in Environmental Applications

Deep learning (DL) models have been popular in earth and environmental modeling and analysis, which exhibit huge potential in capturing and reconstructing the non-linearity of relevant environmental processes. They are extensively used as analytical tools or emulators for multiple domains (atmosphere, land surface, ocean, and biogeochemistry). Despite their success, their internal working mechanism remains largely unknown. Such a lack of knowledge hinders the identification of physically consistent models that are fully adaptive to non-stationary climate, as well as the development of physics-informed machine learning such as physics-informed neural network (PINN). To establish preliminary knowledge and framework of such physics representation evaluation, this project focuses on an improved understanding of DL models in the environmental applications. DL models are increasingly applied to environmental modeling and prediction. However, they have been evaluated mostly from a performance perspective, and there is a gap in understanding how they represent the known physics internally. Such knowledge is especially critical when applying DL models under climate change conditions, where new inputs are likely outside the ranges of the training datasets. In this project, we reveal how the known physical processes are represented within DL models from both statistical and mechanistic perspectives. Leveraging the traditional model evaluations that focus more on the accuracies of predictions, we establish a framework that examines both the accuracy and physics representation of DL models. This analysis framework can identify DL models that make the correct predictions based on correct physics, thus enhancing the existing explainable artificial intelligence (explainable-AI) portfolio. It lays a foundation for developing novel metrics to evaluate the emerging DL models in environmental applications. This knowledge also informs the development of physics-informed DL models by revealing the direct connections between the known physical processes and specific model components or structures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Identification and Classification of Fungal GPCR Gene Families

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eukaryotes, responding to diverse extracellular signals. Researchers have found and systematically summarized 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Additionally, three families of mammalian homologs (Rhodopsin, Glutamate, and Frizzled) have been found in previous studies, but they are not included in the systematic classification of fungal GPCRs. Our study establishes a unified classification of 17 GPCR classes in fungi, combining 14 fungal and 3 mammalian previously recognized groups, and classifies 28,294 GPCRs across 1357 fungal species, significantly expanding the scale of GPCRs in fungi and demonstrating their broader distribution. We found that mammalian homologs are notably more prevalent in Early Diverging Fungi (EDF), whereas the previous 14 classes are predominantly found in Ascomycota and Basidiomycota. The most abundant class detected in fungi was Pth11-like GPCRs, exclusively found in Pezizomycotina and involved in fungal pathogenicity. Our analysis suggested that Pezizomycotina ancestor possessed an extensive array of Pth11-like GPCRs, but over time, some species underwent considerable reductions in these GPCRs in conjunction with genome contractions. Utilizing a custom-built convolutional neural network (CNN) for the identification of fungal GPCRs, we identified several putative novel fungal GPCRs. Predicted interactions between these prospective new GPCRs and G-alpha proteins, as simulated by AlphaFold Multimer, provided additional support for their functional relevance. In conclusion, our work defines the first large-scale, unified classification of fungal GPCRs, reveals lineage-specific expansions and contractions, and uncovers previously unrecognized GPCR candidates with potential functional roles in fungal signaling.

G protein-coupled receptors↗
DOE OSTI2023

Atomic-scale identification of defects in alite

Crystallographic defects play a crucial role in cement hydration, with initial dissolution being dominated by the formation of etch pits that rely on the intersection of defects on surfaces. However, the defects present in cement particles have remained a mystery due to the lack of detailed direct observation at the atomic scale. In this study, we used scanning transmission electron microscopy to unravel the defects in alite particles at the single-atom level. Our observations identified different types of defects, including vacancies, doping, dislocations, rough surfaces, and grain boundaries. Atomic ordering in the alite crystal was further examined based on our single-atom recognition method. Our findings indicate that defects in cement particles may serve as reactive sites during the early hydration stage, facilitating the initial dissolution and providing nucleation sites for hydration products. Finally, this work provides insights into cement defect formation at the single-atom level and offers new opportunities in tuning the hydration process through defect engineering of cement particles.

36 MATERIALS SCIENCE↗