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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate

Abstract Microbial predators such as choanoflagellates are key players in ocean food webs. Choanoflagellates, which are the closest unicellular relatives of animals, consume bacteria and also exhibit marked biological transitions triggered by bacterial compounds, yet their native microbiomes remain uncharacterized. Here we report the discovery of a ubiquitous, uncultured bacterial lineage we name Candidatus Comchoanobacterales ord. nov., related to the human pathogen Coxiella and physically associated with the uncultured marine choanoflagellate Bicosta minor . We analyse complete ‘Comchoano’ genomes acquired after sorting single Bicosta cells, finding signatures of obligate host-dependence, including reduction of pathways encoding glycolysis, membrane components, amino acids and B-vitamins. Comchoano encode the necessary apparatus to import energy and other compounds from the host, proteins for host-cell associations and a type IV secretion system closest to Coxiella’s that is expressed in Pacific Ocean metatranscriptomes. Interactions between choanoflagellates and their microbiota could reshape the direction of energy and resource flow attributed to microbial predators, adding complexity and nuance to marine food webs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multireference diffusion Monte Carlo reaches 2D materials

Abstract Quantum confinement in 2D materials strongly enhances electronic correlation effects. Therefore, predicting the properties of these unique materials, with both a high level of accuracy and computational efficiency, without relying on adjustable parameters or functionals, remains an outstanding theoretical challenge. The majority of theoretical studies are based on the approximations of density functional theory (DFT). The reliability of DFT predictions are heavily dependent on the choice of an approximated exchange-correlation functional. Here, we estimate the magnitude of impact of correlation on the total energy for the quintessential 2D material, graphene, by performing and comparing state-of-the-art selected CI and quantum Monte Carlo extrapolated calculations for a single unit cell at the$$\Gamma$$point. We demonstrate that Self-Healing Diffusion Monte Carlo (SHDMC) obtains a very compact, but high-quality wavefunction for this system that lacks the strong basis set dependence displayed by state of the art quantum chemistry methods. The SHDMC wavefunction is of higher quality compared to that obtained from sCI, in the same orbital basis, while being$$\sim$$ 1000 times smaller in terms of determinant count compared to sCI. We also demonstrate that extrapolating SHDMC results to the infinite determinant limit compares extremely well with complete basis set extrapolated sCI. Our work paves the way for future validation of SHDMC applied to challenging 2D materials.

Science & Technology - Other Topics↗
DOE OSTI2025

Synthesis, structure, and stability of a novel 2 H -azirine under pressure

We have synthesized 2,3-diphenyl-2H-azirine, a strained unsaturated heterocyclic compound, and examined its high-pressure behavior to above 10 GPa using diamond anvil cell techniques. Single crystal X-ray diffraction at ambient conditions reveals that the crystal structure is hexagonal and consists of interesting helices surrounding voids in the structure. A continuous shift of the Raman and infrared vibrational spectra with increasing pressure is observed, indicating that the molecular structure is preserved to at least 8 GPa at room temperature. High-pressure synchrotron powder X-ray diffraction shows that the hexagonal structure persists, with a smooth compression of the a and c parameters to 10 GPa. The structural stability under pressure is attributed to the reduction in void size within the helical framework despite the inherent strain and reactivity of the molecule. The channels in the structure could encapsulate small molecules for gas or energy storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗
DOE OSTI2024

Spatial Proteomics towards cellular Resolution

Introduction: Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g. genetic mutations and epigenetic marks), multiplexed immunofluorescence, and spatial metabolomics/lipidomics have enabled high-resolution spatial profiling of gene expression, genetic variation, protein expression, and metabolites/lipids profiles in tissue. These developments contribute to a deeper understanding of the spatial organization within tissue microenvironments at the molecular level. Areas covered: This report provides an overview of the untargeted, bottom-up mass spectrometry (MS)-based spatial proteomics workflow. It highlights recent progress in tissue dissection, sample processing, bioinformatics, and liquid chromatography (LC)-MS technologies that are advancing spatial proteomics toward cellular resolution. Expert opinion: The field of untargeted MS-based spatial proteomics is rapidly evolving and holds great promise. To fully realize the potential of spatial proteomics, it is critical to advance data analysis and develop automated and intelligent tissue dissection at the cellular or subcellular level, along with high-throughput LC-MS analyses of thousands of samples. In conclusion, achieving these goals will necessitate significant advancements in tissue dissection technologies, LC-MS instrumentation, and computational tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multiferroic ground states in free standing perovskite-based nanodots: a density functional theory study

In this work, we use density functional theory to investigate the possibility of polar and multiferroic states in free-standing, perovskite-based nanodots at the atomic limit of miniaturization: single unit cells with terminations which allow centro-symmetry. We consider both A-O and B-O 2 terminations for three families of nanodots: (i) A = Ba with B = Ti, Zr, and Hf; (ii) A = Ca and Sr with B = Ti; and (iii) A = Na and K with B = Nb. We find all A–O terminated dots to be non-polar and to exhibit cubic symmetry (except for K 8 NbO 6 ), regardless of the presence of ferroelectricity in the bulk. In contrast, all the B–O 2 terminated nanodots considered relax to a non-cubic ground state. Rather surprisingly, all of these structures exhibit polar ground states (except NaNb 8 O 12 ). We propose a new structural parameter, the cluster tolerance factor (CTF), to determine whether a particular chemistry will result in a polar ground state nanodot, analogous to the Goldschmidt factor for bulk ferroelectrics. In addition, we find that all A–O terminated (except Ca 8 TiO 6 ) and all polar B–O 2 terminated nanodots are magnetic, where none show magnetism in the bulk. As with bulk systems, multiferroicity in the B–O 2 terminated dots originates from separation between spin density in peripheral B atoms and polarity primarily caused by the off-center central A atom. Our findings stress that surface termination plays a crucial role in determining whether ferroelectricity is completely suppressed in perovskite-based materials at their limit of miniaturization.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33–9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032–0.131 (g/g) and lipid contents were 13.5–53.7% (g/g). Four strains had significantly higher lipid yields and contents. Finally, one of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Tiny Bubbles: Combined HR(S)TEM and 4D-STEM Analysis of Sub-Nanometer He Bubbles in Au

Irradiation produces a distribution of defect sizes in materials, with the smallest defects often below one nanometer in size and approaching the scale of a single unit cell in metals. While high-resolution scanning transmission electron microscopy (STEM)-based imaging can directly image structures at this level, techniques such as four-dimensional STEM (4D-STEM) enable characterization of materials across large fields of view, capturing a more representative volume that can be valuable for quantifying defects, their distributions, and the associated strain fields. Here we present a combined HRSTEM and 4D-STEM approach to study the model system of He bubble implantation in an Au thin film. The present work is of general interest for the study of materials in extreme environments, as it demonstrates an effective way to characterize even the tiniest sub-nanometer sized He bubbles in addition to larger irradiation defects.

atomic-resolution STEM↗
DOE OSTI2025

Cleavable quaternary oxychlorides with high magnetic ordering temperatures

Quaternary oxychlorides derived from Ruddlesden–Popper 3d transition metal oxides offer a route to cleavable crystals with bulk antiferromagnetic ordering temperatures reaching at least 550 K. Here, we study the magnetic, optical, and mechanical behavior of Sr 2 FeO 3 Cl, Ca 2 FeO 3 Cl, Ca 3 Fe 2 O 5 Cl 2 , and Sr 3 Fe 2 O 5 Cl 2 . Through optical absorption measurements, we show that these antiferromagnetic semiconductors have optical band gaps of ≈2.1(1) eV. The magnetic ordering symmetries and temperatures were probed by neutron powder diffraction and Mössbauer spectroscopy on polycrystalline samples, demonstrating Néel temperatures (T N ) near room temperature in the single layer Sr 2 FeO 3 Cl (T N ≈ 311 K) and Ca 2 FeO 3 Cl (T N ≈ 360 K), and the double-layer compound Sr 3 Fe 2 O 5 Cl 2 has T N ≈ 545 K. The high-spin moments of Fe 3+ lie within the basal plane and the magnetic structures are compensated within each magnetic layer and characterized by magnetic propagation vectors k = ($\frac{1}{2}$ $\frac{1}{2}$ 0). Magnetization results demonstrate the quasi-2D nature of the magnetism, with a broad maximum in the susceptibility near 2T N for Sr 2 FeO 3 Cl. Scotch tape tests and mechanical exfoliation onto SiO 2 confirm the micaceous nature of these crystals with cleavage down to a single unit cell (two magnetic layers) achieved for Sr 3 Fe 2 O 5 Cl 2 . In conclusion, this paper highlights strong antiferromagnetic interactions, semiconducting band gaps, and cleavability of quaternary Fe-based oxychlorides and motivates future work on crystals and exfoliated flakes of these and related oxyhalide systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Charge Trap Layer Supercharging for Improved Bit Reliability in 3-D NAND Flash Under Proton Irradiation

Single-event upset (SEU) cross sections are reduced in 176-layer charge trap (CT) 3-D nand devices under proton irradiation when multiple write operations are applied sequentially without the typical erase-before-write. Here, this effect is observed for multiple data patterns and in both single-level cell (SLC) and triple-level cell (TLC) operating modes. SEU cross section calculation methodologies are discussed for highly scaled 3-D devices both with and without the application of rewrites, and potential implications for long-term endurance effects are proposed.

Breeding, Matthew Luel [Sandia National Laboratori↗
DOE OSTI2023

Targeted synthesis of predicted metastable compounds using modulated elemental reactants

Three metastable compounds predicted to be kinetically stable using an “island” approach were successfully synthesized from designed modulated elemental reactants. Fe0.8V0.2Se2 was synthesized by depositing ultrathin elemental layers in a V|Fe|Se sequence to control the local composition. An alloyed rock salt structured Pb3Mn2Se5 constituent layer, which does not exist as a bulk compound, was synthesized in the heterostructure (Pb3Mn2Se5)0.6VSe2 by depositing a precursor with a V|Se|Pb|Se|Mn|Se|Pb|Se|Mn|Se|Pb|Se sequence of elemental layers that mimicked the compositional profile of the targeted heterostructure. The heterostructure (PbSe)1+δ(FeSe2)2 was prepared by depositing a precursor with a repeating layering sequence of Fe|Pb|Fe|Se, where each sequence contains the number of atoms required to form a single unit cell. In all three systems, the local compositions in the layer sequence kinetically favored the nucleation and growth of the targeted products during the deposition. The diffusion lengths to form the targeted compounds were short, and the diffusion was limited by postdeposition low temperature annealing to favor the growth of the targeted compounds and avoid the decomposition into a mixture of thermodynamically stable compounds.

Lemon, Mellie (ORCID:0000000328705881)↗
DOE OSTI2025

Superconductivity in an ultrathin multilayer nickelate

We report the appearance of superconductivity in single-unit-cell Nd 6 Ni 5 O 12 , exhibiting a transition temperature similar to that of thicker films. In situ synchrotron x-ray scattering performed during growth of the parent phase, Nd 6 Ni 5 O 16 , shows that the necessary layer-by-layer deposition sequence does not follow the sequence of the formula unit but an alternate order due to the relative stability of the perovskite unit cell. We exploit this insight to grow ultrathin Nd 6 Ni 5 O 16 heterostructures and conduct in situ studies of topotactic reduction, finding that formation of the square-planar phase occurs rapidly and is highly sensitive to reduction temperature, with small deviations from the optimum condition leading to inhomogeneity and the loss of superconductivity. The fluorite layer within the unit cell facilitates reduction by initially stabilizing the square-planar phase in the upper half of the unit cell. Our findings provide insight into growth of the Ruddlesden-Popper nickelates, highlighting the need for in situ studies of the metastable phases key to superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Capturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placenta

Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step itself might require induction. To capture this early gene regulation event, here, we integrated fine-scale cryosectioning with whole-transcriptome sequencing to dissect gene expression at the single-hyphal-cell scale (tens of micrometers). This improved the spatial resolution 50-fold, relative to previous work, and we were able to capture the activity of the first 100 μm of hyphal front growth by Rhodonia placenta in aspen wood. This early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation [LOX]) that were previously and incorrectly assumed to be constitutively expressed. These delayed DEGs, which include those with and without predicted functions, also create a focused subset of target genes for functional genomics. However, this delayed pattern was not universal, with a few genes being upregulated immediately at the hyphal front. Most notably, this included a gene commonly implicated in hydroquinone and iron redox cycling: benzoquinone reductase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mass Spectrometry–Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine

Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Computational Analysis of Anode and Cathode Structuring Effects on Charge and Discharge in Graphite|LiNi 0.6 Mn 0.2 Co 0.2 O 2 Batteries

Structured electrodes (SEs) improve the rate capability of Lithium-ion batteries by engineering micrometer-scale electrolyte regions into the electrode, promoting rapid ionic transport. Prior research has focused on structuring one electrode (anode or cathode) with an analysis on either the charge or discharge performance. We present a holistic study using three-dimensional models to investigate the isolated effects of structuring either electrode and the combined effects of structuring both electrodes on the charge and discharge capacity of single-layer cells at 4 C and 6 C. Volumetric and gravimetric discharge energy density (Wh/L stack and Wh/kg stack ) and charge capacity (Ah/kg stack and Ah/L stack ) are evaluated for multi-layer pouch cell stacks. Pairing SE anodes with SE cathodes demonstrated improvements up to 15% in discharge Wh/kg stack and up to 33% in charge Ah/kg stack over a conventional cell; Energy required to charge per Ah/kg stack was improved by 13%–14%. SE cathodes paired with a conventional anode exhibited improvements of 0.3%–22% across all performance metrics evaluated. Conversely, pairing a SE anode with a conventional cathode demonstrated improved charge capacity up to 13% but showed a 2%–23% lower discharge energy density. The importance of aligning SEs in a cell from a performance and manufacturing perspective is also analyzed.

25 ENERGY STORAGE↗
DOE OSTI2023

Epistasis and evolution: recent advances and an outlook for prediction

As organisms evolve, the effects of mutations change as a result of epistatic interactions with other mutations accumulated along the line of descent. This can lead to shifts in adaptability or robustness that ultimately shape subsequent evolution. Here, we review recent advances in measuring, modeling, and predicting epistasis along evolutionary trajectories, both in microbial cells and single proteins. We focus on simple patterns of global epistasis that emerge in this data, in which the effects of mutations can be predicted by a small number of variables. The emergence of these patterns offers promise for efforts to model epistasis and predict evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Background - Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva. Results - We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously. Conclusions - Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.

59 BASIC BIOLOGICAL SCIENCES↗