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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2023

Reconstructing PM 2.5 Data Record for the Kathmandu Valley Using a Machine Learning Model

This paper presents a method for reconstructing the historical hourly concentrations of particulate matter 2.5 (PM2.5) over the Kathmandu Valley from 1980 to the present. The method uses a machine learning model that is trained using PM2.5 readings from US Embassy (Phora Durbar) as a ground truth, and the meteorological data from Modern-Era Retrospective Analysis for Research and Applications v2 (MERRA2) as input. The Extreme Gradient Boosting (XGBoost) model acquires a credible 10-fold cross-validation (CV) score of ~83.4%, an r2-score of ~84%, a Root Mean Square Error (RMSE) of ~15.82 µg/m3, and a Mean Absolute Error (MAE) of ~10.27 µg/m3. Further demonstrating the model's applicability to years other than those for which truth values are unavailable, the multiple cross-test with an unseen data set offered r2-scores for 2018, 2019, and 2020 ranging from 56% to 67%. The model-predicted data agrees with true values and indicates that MERRA2 underestimates PM2.5 over the region. It strongly agrees with ground-based evidence showing substantially higher mass concentrations in the dry pre- and post-monsoon seasons than in the monsoon months. It also shows a strong anti-correlation between PM2.5 concentration and humidity. The results also demonstrate that none of the years fulfilled the annual mean air quality index (AQI) standards set by the World Health Organization (WHO).

machine learning↗
DOE OSTI2020

Experimental validation of solid oxide fuel cell polarization modeling: An LSM-YSZ/YSZ/Ni-YSZ case study

Polarization modeling based on the measured I-V curves is a useful tool for analyzing SOFC performance and diagnosing performance limitations. Using the polarization model, the overpotential of a cell is usually separated into different polarization contributions, including area specific ohmic polarization, activation polarization, and anodic and cathodic concentration polarizations. In this study, we aim to experimentally validate the accuracy of the polarization model. As a case study, anode-supported cells with LSM-YSZ/YSZ/Ni-YSZ configuration are used. By curve-fitting the I-V curves of a cell tested under different cathode oxygen partial pressures into the polarization model, the contributions of different polarization losses are quantified. To validate the polarization model, independent experiments/studies including electrochemical impedance spectroscopy, cathode kinetics study, ex-situ diffusivity measurement, and tortuosity measurement using 3D reconstructed anode are conducted. The results from polarization modeling and from validation studies are in good agreement, thereby validating the polarization model for SOFC performance analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Highly Crystalline and Porous Borocarbonitrides as Metal‐Free Catalysts for Boosted N‐Heterocycle Dehydrogenation

Safe and efficient hydrogen storage is pivotal for enabling a clean hydrogen economy. Liquid organic hydrogen carriers (LOHCs) offer a practical solution, but their deployment is hindered by the lack of highly active and economical dehydrogenation catalysts. In this work, we report a metal‐free catalyst design that overcomes the long‐standing trade‐off between crystallinity and surface area in two‐dimensional frameworks for highly efficient dehydrogenation of LOHCs. A flux‐assisted reconstruction strategy transforms amorphous borocarbonitrides (AM‐BCN) into highly crystalline, defect‐rich BCN nanosheets (C‐BCN) with large surface area and accessible porosity, as confirmed by complementary spectroscopic, x‐ray, and neutron analyses. C‐BCN catalyzes the acceptor‐less dehydrogenation of aza‐fused LOHCs with quantitative hydrogen release under mild conditions, outperforming AM‐BCN and previously reported metal‐free scaffolds. Mechanistic insights from x‐ray, neutron scattering, and theoretical calculations identify open C‐B‐N and N‐B‐N defect motifs as the primary active sites. This work establishes a generalizable strategy to engineer crystalline, porous, defect‐rich two‐dimensional lattices and demonstrates a highly active metal‐free platform for LOHC dehydrogenation with high‐purity H 2 generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Isotopic compositions and probable origins of organic molecules in the Eocene Messel shale

It is shown here that the carbon isotopic compositions of biomarkers from the Eocene Messel shale, accumulated 47 + or - 2 million years ago in anaerobic waters at the bottom of a lake, allow identification of specific sources for some materials and reconstruction of carbon flows within the lake and its sediments. The C-13 content of organic matter synthesized by lacustrine primary producers can be estimated from the observed C-13 content of the geoporphyrins derived from their chlorophylls. Total organic material in the shale is depleted in C-13 by six parts per thousand relative to that input. This difference cannot be explained by selective loss of components enriched in C-13, nor, as shown by isotopic compositions of other biomarkers, by inputs from land plants surrounding the lake or from methanogenic bacteria.

Hayes, J. M.↗
DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Abstract Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

Langwig, Marguerite V. (ORCID:0000000202472816)↗
NASA NTRS1975

Holographic recording materials development

The area of organic cis-trans photoisomerization systems for holographic memory applications was examined. Photochemical studies were made of stilbene, indigo, and thioindigo derivatives in solution and in a variety of polymer matrix materials, to optimize the photorefractive behavior of the chemical system as a whole. Lithium niobate was used to study the writing and reading efficiencies of thick phase holograms. Both phase-wave holograms and Fourier-transform holograms were employed, and a number of reconstruction techniques are discussed. The possibility of using cis-trans photoisomerization of appropriate organic chemicals as the basis for a holographic recording system is confirmed.

Source record↗
DOE OSTI2020

Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models

Mathematical modeling of plant metabolism allows the plant science community to understand the organization of plant metabolism, obtain quantitative insights into metabolic functions, and derive engineering strategies for manipulation of metabolism. Among the various modeling approaches, metabolic pathway analysis can dissect the basic functional modes of subsections of core metabolism, such as photorespiration, and reveal how classical definitions of metabolic pathways have overlapping functionality. In current research using constraint-based modeling in plants, numerous computational tools are currently available to analyze large-scale and genome-scale metabolic networks. For 13 C-metabolic flux analysis, principles of isotopic steady state have been used to study heterotrophic plant tissues, while nonstationary isotope labeling approaches are amenable to the study of photoautotrophic and secondary metabolism. Enzyme kinetic models explore pathways in mechanistic detail, and we discuss different approaches to determine or estimate kinetic parameters. In this review, we describe recent advances and challenges in modeling plant metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for FUN-PROSE: A Deep Learning Approach to Predict Condition-Specific Gene Expression in Fungi

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

Genomics↗
NASA NTRS1976

Computer simulation and evaluation of edge detection algorithms and their application to automatic path selection

The construction of an autonomous roving vehicle requires the development of complex data-acquisition and processing systems, which determine the path along which the vehicle travels. Thus, a vehicle must possess algorithms which can (1) reliably detect obstacles by processing sensor data, (2) maintain a constantly updated model of its surroundings, and (3) direct its immediate actions to further a long range plan. The first function consisted of obstacle recognition. Obstacles may be identified by the use of edge detection techniques. Therefore, the Kalman Filter was implemented as part of a large scale computer simulation of the Mars Rover. The second function consisted of modeling the environment. The obstacle must be reconstructed from its edges, and the vast amount of data must be organized in a readily retrievable form. Therefore, a Terrain Modeller was developed which assembled and maintained a rectangular grid map of the planet. The third function consisted of directing the vehicle's actions.

Longendorfer, B. A.↗
NASA NTRS2026

Advances in Entry Systems Modeling: Modeling Summer Visit 2025 Technical Reports

This NASA Technical Memorandum presents the collective work carried out during the Modeling Summer Visit (MSV) 2025, a collaborative research program between NASA Ames Research Center and three leading European research institutions: the University of Bordeaux, the von Karman Institute (VKI), and Ecole Polytechnique. Held from July 7th to August 1st, 2025, the NASA ARC MSV program brought together 42 researchers from Europe to work alongside NASA staff on 22 projects in entry systems modeling. The program was organized by Bruno Dias, Sergio Fraile-Izquierdo, and Jeremie Meurisse from Analytical Mechanics Associates, Inc., in collaboration with Marc Massot (Ecole Polytechnique), Jean Lachaud (University of Bordeaux), and Thierry Magin (VKI). The MSV program traces its origins to an initiative started by Nagi N. Mansour in 2018, with this 2025 edition representing a consolidation and expansion of that original vision. The projects were organized into six thematic groups: Porous Media, Numerical Methods, Plasma/Rarefied Methods, Experimental Reconstruction, Flow and Material Coupling Methods, and Transition and High-Speed Flows. Throughout the four-week program, participants presented their work in three public presentations (July 7th, July 21st, and August 1st), allowing for continuous feedback and discussion of their evolving research.

Plasmas↗
DOE OSTI2022

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers

Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Spatially resolved X-ray imaging and molecular characterisation of sulfur and iron in organic- and sulfur-rich hydrocarbon source mudstones

Sulfurisation of organic matter (OM) is a prominent preservation mechanism, however iron sulfide precipitation, particularly pyrite (FeS2), can counteract this mechanism. There is a dearth of high-resolution, spatially-resolved spectroscopic (redox) information on sulfur and iron inventories within organic-rich rocks that would improve our understanding of prevailing environmental conditions during deposition. Here, state-of-the-art synchrotron-based X-ray absorption and fluorescence analyses of key organic- and sulfur-rich mudstones demonstrate the potential of these techniques to non-destructively map and produce detailed spectroscopic information. Detailed high-resolution analyses (μm- to mm-scale) reveal the presence of widespread sulfurised OM in the Blackstone Band of the Kimmeridge Clay Formation, in line with a persistence of euxinia over a long temporal span and low reactive iron input, facilitating the preservation of OM through sulfurisation. In contrast, the presence of sulfurised OM was transitional in the Monterey Formation, consistent with fluctuating water column redox conditions, and is less significant in the Whitby Mudstone Formation, likely due to the high reactive iron concentrations outcompeting sulfurised OM formation. Analyses of sulfur species using model compounds further indicate that the Whitby Formation is strongly enriched in inorganic reduced sulfur minerals, while both the Kimmeridge Clay and Monterey Formations are dominated by organic sulfur species. These synchrotron-based observations improve our understanding of environmental conditions during the time of deposition of these mudstones and thus show great promise in the study of organic-rich sediments, especially in allowing their depositional settings to be more accurately reconstructed.

Kimmeridge Clay Formation↗
DOE OSTI2024

KBase Narrative - Metabolic_reconstruction_ETDI_mangrove

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

Laux, Marcele↗
DOE OSTI2026

Branched-chain amino acid specialization drove diversification within Calditenuaceae ( Caldarchaeia ) and enables their cultivation

Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 6 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.

Biological and medical sciences↗
DOE OSTI2023

Robust Interfacial Effect in Multi-interface Environment through Hybrid Reconstruction Chemistry for Enhanced Energy Storage

Electrochemical-oxidation-driven reconstruction has emerged as an efficient approach for developing advanced materials, but the reconstructed microstructure still faces challenges including inferior conductivity, unsatisfying intrinsic activity, and active-species dissolution. In this report we present hybrid reconstruction chemistry that synergistically couples electrochemical oxidation with electrochemical polymerization (EOEP) to overcome these constraints. During the EOEP process, the metal hydroxides undergo rapid reconstruction and dynamically couple with polypyrrole (PPy), resulting in an interface-enriched microenvironment. We observe that the interaction between PPy and the reconstructed metal center (i.e., Mn > Ni, Co) is strongly correlated. Theoretical calculation results demonstrate that the strong interaction between Mn sites and PPy breaks the intrinsic limitation of MnO 2 , rendering MnO 2 with a metallic property for fast charge transfer and enhancing the ion-adsorption dynamics. Operando Raman measurement confirms the promise of EOEP-treated Mn(OH) 2 (E-MO/PPy) to stably work under a 1.2 V potential window. The tailored E-MO/PPy exhibits a high capacitance of 296 F g –1 at a large current density of 100 A g –1 . Here our strategy presents breakthroughs in upgrading the electrochemical reconstruction technique, which enables both activity and kinetics engineering of electrode materials for better performance in energy-related fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗