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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

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

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

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

Systematic improvements in transmon qubit coherence enabled by niobium surface encapsulation

Abstract We present a transmon qubit fabrication technique that yields systematic improvements in T 1 relaxation times. We encapsulate the surface of niobium and prevent the formation of its lossy surface oxide. By maintaining the same superconducting metal and only varying the surface, this comparative investigation examining different capping materials, such as tantalum, aluminum, titanium nitride, and gold, as well as substrates across different qubit foundries demonstrates the detrimental impact that niobium oxides have on coherence times of superconducting qubits, compared to native oxides of tantalum, aluminum or titanium nitride. Our surface-encapsulated niobium qubit devices exhibit T 1 relaxation times 2–5 times longer than baseline qubit devices with native niobium oxides. When capping niobium with tantalum, we obtain median qubit lifetimes above 300 μs, with maximum values up to 600 μs. Our comparative structural and chemical analysis provides insight into why amorphous niobium oxides may induce higher losses compared to other amorphous oxides.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Impact of metal diffusion, lattice distortions, native defects, and ambient on dielectric breakdown in Ni–Ga 2 O 3 Schottky diodes

Ga 2 O 3 unipolar devices are of high interest due to their ~8 MV/cm predicted breakdown fields, which have not yet been achieved due to premature device failure. Pre- and post-failure defect analysis of Ni–Ga 2 O 3 Schottky diodes in ultrahigh vacuum (UHV) and air were performed using depth-resolved cathodoluminescence, high angle annular dark field scanning transmission electron microscopy, and energy dispersive x-ray analysis to understand the physical mechanisms that precede premature breakdown. The breakdown voltage in UHV was dramatically reduced by nearly 40% compared with the breakdown in air. This reduction in the breakdown voltage correlated with post-breakdown differences in Ni distribution, indicating that the coordination and bonding of Ni contribute strongly to electrical behavior in Ni–Ga 2 O 3 Schottky diodes. Breakdown studies in UHV revealed that Ni diffuses away more from the metal–semiconductor interface than with air breakdown, where Ni localizes more near the interface, indicative of the preferential formation of a Ni oxide under O-poor conditions. These measurements also identified the formation of divacancy-interstitial complexes and their characteristic luminescence signature ~150 nm from the interface, the densities of which correlated with breakdown fields. These findings show that electric-field-induced degradation occurs via the rearrangement of native point defects, which act as an additional precursor to device failure. Macroscopically, they show the impact of both vacuum conditions and metal reactivity on Ga 2 O 3 device fabrication.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Covalent Functionalization of Nickel Phosphide Nanocrystals with Aryl-Diazonium Salts

Covalent functionalization of Ni 2 P nanocrystals was demonstrated using aryl-diazonium salts. Spontaneous adsorption of aryl functional groups was observed, with surface coverages ranging from 20 to 96% depending on the native reactivity of the salt as determined by the aryl substitution pattern. Increased coverage was possible for low reactivity species using a sacrificial reductant. Functionalization was confirmed using thermogravimetric analysis, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The structure and energetics of this nanocrystal electrocatalyst system, as a function of ligand coverage, were explored with density functional theory calculations. The Hammett parameter of the surface functional group was found to linearly correlate with the change in Ni and P core-electron binding energies and the nanocrystal's experimentally and computationally determined work function. The electrocatalytic activity and stability of the functionalized nanocrystals for hydrogen evolution were also improved when compared to the unfunctionalized material, but a simple trend based on electrostatics was not evident. Density functional theory was used to understand this discrepancy, revealing that H adsorption energies on the covalently functionalized Ni 2 P also do not follow the electrostatic trend and are predictive descriptors of the experimental results.

14 SOLAR ENERGY↗
DOE OSTI2022

Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology

Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

MicroResonators for Compacts Optical Sensors (μRCOS)

As the demand for continuous, in-situ surveillance of health of systems and environments rapidly increases, miniaturized sensors with fast responses are sought. Optical dielectric resonators supporting Whispering Gallery Modes (WGMs) have exceptional properties, like very high-power density, very narrow spectral linewidth, and extremely small mode volume. As the footprint of these sensors is drastically reduced, measurements of microvolumes samples with dramatic reduction in analysis time are possible, enabling large numbers of parallel analyses using microarrays. The high sensitivity and speed of WGM resonators combined with the ability to detect molecules in their native state have great future potential for basic and applied research such as reliable single molecule, trace-gas detection, environmental monitoring, chemical threat sensing, and biodefense Such appealing peculiarities motivated us developing WMG resonators (WGMRs) for Cavity Enhanced Absorption Spectroscopy (CEAS) for chem-bio detection. Specifically, we designed and batch-fabricated microspheres and fiber tapers for resonances excitation. We successfully detected gases (N 2 and CO 2 ) in customized environmental chambers, and bio-organisms (Inf. A and E. Coli) with integrated microfluidic systems. Background calibration and environmental isolation were always accounted for in proving the performances.

36 MATERIALS SCIENCE↗
DOE OSTI2021

MicroResonators for Compacts Optical Sensors (μRCOS)

As the demand for continuous, in-situ surveillance of health of systems and environments rapidly increases, miniaturized sensors with fast responses are sought. Optical dielectric resonators supporting Whispering Gallery Modes (WGMs) have exceptional properties, like very high-power density, very narrow spectral linewidth, and extremely small mode volume. As the footprint of these sensors is drastically reduced, measurements of microvolumes samples with dramatic reduction in analysis time are possible, enabling large numbers of parallel analyses using microarrays. The high sensitivity and speed of WGM resonators combined with the ability to detect molecules in their native state have great future potential for basic and applied research such as reliable single molecule, trace-gas detection, environmental monitoring, chemical threat sensing, and biodefense Such appealing peculiarities motivated us developing WMG resonators (WGMRs) for Cavity Enhanced Absorption Spectroscopy (CEAS) for chem-bio detection. Specifically, we designed and batch-fabricated microspheres and fiber tapers for resonances excitation. We successfully detected gases (N 2 and CO 2 ) in customized environmental chambers, and bio-organisms (Inf. A and E. Coli) with integrated microfluidic systems. Background calibration and environmental isolation were always accounted for in proving the performances.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Technical Assistance Opportunities for Tribes

The National Renewable Energy Laboratory (NREL) offers many forms of technical assistance for Tribes to support local clean energy priorities and challenges. With broad support from the U.S. Department of Energy (DOE) and local partners, NREL provides technical expertise to enable data-driven, informed clean energy decision making. Technical assistance may address energy strategy, project financing, policy design and development, data analysis, economic development, infrastructure planning, energy justice, climate change, resilience, or other energy priorities. NREL has a long history of partnering with Tribes and Tribal organizations, including in Alaska Native Villages where the extreme Arctic climate poses unique energy challenges. NREL works directly with Tribes to find solutions that address their self-defined energy priorities, challenges, and goals.

Alaska native village↗
DOE OSTI2026

Metalloproteins in an Era of Modern Crystallography and Why the Beamline Matters

The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.

Maggiolo, Ailiena O. [SLAC National Accelerator La↗
DOE OSTI2021

Quantifying the influence of natural climate variability on in situ measurements of seasonal total and extreme daily precipitation

Abstract While various studies explore the relationship between individual sources of climate variability and extreme precipitation, there is a need for improved understanding of how these physical phenomena simultaneously influence precipitation in the observational record across the contiguous United States. In this work, we introduce a single framework for characterizing the historical signal (anthropogenic forcing) and noise (natural variability) in seasonal mean and extreme precipitation. An important aspect of our analysis is that we simultaneously isolate the individual effects of seven modes of variability while explicitly controlling for joint inter-mode relationships. Our method utilizes a spatial statistical component that uses in situ measurements to resolve relationships to their native scales; furthermore, we use a data-driven procedure to robustly determine statistical significance. In Part I of this work we focus on natural climate variability: detection is mostly limited to DJF and SON for the modes of variability considered, with the El Niño/Southern Oscillation, the Pacific–North American pattern, and the North Atlantic Oscillation exhibiting the largest influence. Across all climate indices considered, the signals are larger and can be detected more clearly for seasonal total versus extreme precipitation. We are able to detect at least some significant relationships in all seasons in spite of extremely large (> 95%) background variability in both mean and extreme precipitation. Furthermore, we specifically quantify how the spatial aspect of our analysis reduces uncertainty and increases detection of statistical significance while also discovering results that quantify the complex interconnected relationships between climate drivers and seasonal precipitation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerol

Abstract Background Sugar alcohols are widely used as low-calorie sweeteners in the food and pharmaceutical industries. They can also be transformed into platform chemicals. Yarrowia lipolytica , an oleaginous yeast, is a promising host for producing many sugar alcohols. In this work, we tested whether heterologous expression of a recently identified sugar alcohol phosphatase (PYP) from Saccharomyces cerevisiae would increase sugar alcohol production in Y. lipolytica . Results Y. lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica . We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). This strain was able to produce 27.5 ± 0.7 g/L erythritol from glycerol during batch growth and 58.8 ± 1.68 g/L erythritol during fed-batch growth in shake-flasks experiments. In addition, the glycerol utilization was increased by 2.5-fold. We were also able to demonstrate that this strain efficiently produces erythritol from crude glycerol, a major byproduct of the biodiesel production. Conclusions We demonstrated the application of a promising enzyme for increasing erythritol production in Y. lipolytica . We were further able to boost production by combining the expression of this enzyme with other approaches known to increase erythritol production in Y. lipolytica . This suggest that this new enzyme provides an orthogonal route for boosting production and can be stacked with existing designs known to increase sugar alcohol production in yeast such as Y. lipolytica . Collectively, this work establishes a new route for increasing sugar alcohol production and further develops Y. lipolytica as a promising host for erythritol production from cheap substrates such as glycerol.

09 BIOMASS FUELS↗
DOE OSTI2021

Metabolic Engineering of the Oleaginous Yeast Yarrowia lipolytica PO1f for Production of Erythritol from Glycerol

Yarrowia lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica . We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). These data show the growth and titers produced.

Conversion↗
DOE OSTI2026

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing↗
DOE OSTI2021

Cost Analysis Framework for Comparing AC and DC Design Alternatives for Building Electrical Distribution Systems

In recent years, in response to the changing nature of building load, direct current (DC) distribution systems for buildings have been proposed as alternatives to traditional alternating current (AC) systems. DC distribution offers a closer match to the types of loads and generation sources found in modern buildings, the majority of which use DC electricity internally either natively or as a power conditioning stage. The proposed benefits of DC distribution compared to AC distribution within buildings include higher efficiency, lower installation cost, lower operating cost, higher reliability, improved communication and control, and simplicity. Most recent DC distribution research has focused on quantifying the efficiency advantage of DC distribution over AC distribution. However, energy savings alone do not guarantee cost savings; a more complete cost accounting is required to establish financial benefit. This report provides a framework for cost analysis and comparison of building electrical distribution systems, including common variants for both AC and DC distribution systems. The framework includes all major cost categories, including up-front costs (capital, installation labor, soft costs) and long-term costs (energy, operations and maintenance).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers↗
DOE OSTI2023

EvoProtGrad (Directed Evolution for Proteins with Gradients) [SWR-23-48]

A Python package for directed evolution on a protein sequence with gradient-based discrete Markov chain monte carlo (MCMC). Users are able to compose custom models that map sequence to function with pretrained models, including protein language models (PLMs), to guide and constrain search. Our package natively integrates with the HuggingFace platform and supports PLMs from transformers. Our MCMC sampler identifies promising amino acids to mutate via model gradients taken with respect to the input (i.e., sensitivity analysis). We allow users to compose their own custom target function for MCMC by leveraging the Product of Experts MCMC paradigm. Each model is an "expert" that contributes its own knowledge about the protein's fitness landscape to the overall target function. The sampler is designed to be more efficient and effective than brute force and random search while maintaining most of the generality and flexibility. Additional information can be found in the related publication: https://iopscience.iop.org/article/10.1088/2632-2153/accacd

Emami, Patrick↗