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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Harvesting 88 Zr from heavy-ion beam irradiated tungsten at the National Superconducting Cyclotron Laboratory

Tungsten is a commonly used material at many heavy-ion beam facilities, and it often becomes activated due to interactions with a beam. Many of the activation products are useful in basic and applied sciences if they can be recovered efficiently. In order to develop the radiochemistry for harvesting group (IV) elements from irradiated tungsten, a heavy-ion beam containing 88 Zr was embedded into a stack of tungsten foils at the National Superconducting Cyclotron Laboratory and a separation methodology was devised to recover the 88 Zr. The foils were dissolved in 30% hydrogen peroxide, and the 88 Zr was chemically purified from the tungsten matrix and from other co-implanted radionuclides (such as 85 Sr and 88 Y) using strong cation-exchange (AG MP-50) chromatographic resin in sulfuric acid media. The procedure provided 88 Zr in approximately 60 mL 0.5 M sulfuric acid with no detectable radio-impurities. The overall recovery yield for 88 Zr was (92.3 ± 1.2)%. In conclusion, this proof-of-concept experiment has facilitated the development of methodologies to harvest from tungsten and tungsten-alloy parts that are regularly irradiated at heavy-ion beam facilities.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

The Gearbox of the Bacterial Flagellar Motor Switch

Switching of flagellar motor rotation sense dictates bacterial chemotaxis. Multi-subunit FliM-FliG rotor rings couple signal protein binding in FliM with reversal of a distant FliG C-terminal (FliGC) helix involved in stator contacts. Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures. Principal component analysis extracted collective motions. Interfacial loop immobilization by complex formation coupled elastic fluctuations of the FliM middle (FliMM) and FliG middle (FliGM) domains. Coevolved mutations captured interfacial dynamics as well as contacts. FliGM rotation was amplified via two central hinges to the FliGC helix. Intrinsic flexibility, reported by the FliGMC ensembles, reconciled conformers with opposite FliGC helix orientations. FliG domain stacking deformed the inter-domain linker and reduced flexibility; but conformational changes were not triggered by engineered linker deletions that cause a rotation-locked phenotype. These facts suggest that binary rotation states arise from conformational selection by stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Caught before Released: Structural Mapping of the Reaction Trajectory for the Sofosbuvir Activating Enzyme, Human Histidine Triad Nucleotide Binding Protein 1 (hHint1)

Human histidine triad nucleotide binding protein 1 (hHint1) is classified as an efficient nucleoside phosphoramidase and acyl-adenosine monophosphate hydrolase. Human Hint1 has been shown to be essential for the metabolic activation of nucleotide antiviral pronucleotides (i.e., proTides), such as the FDA approved hepatitis C drug, sofosbuvir. The active site of hHint1 comprises an ensemble of strictly conserved histidines, including nucleophilic His112. To structurally investigate the mechanism of hHint1 catalysis, herein we have designed and prepared nucleoside thiophosphoramidate substrates that are able to capture the transiently formed nucleotidylated-His112 intermediate (E*) using time-dependent crystallography. Utilizing a catalytically inactive hHint1 His112Asn enzyme variant and wild-type enzyme, the enzyme–substrate (ES 1 ) and product (EP 2 ) complexes were also cocrystallized, respectively, thus providing a structural map of the reaction trajectory. On the basis of these observations and the mechanistic necessity of proton transfers, proton inventory studies were carried out. Although we cannot completely exclude the possibility of more than one proton in flight, the results of these studies were consistent with the transfer of a single proton during the formation of the intermediate. Interestingly, structural analysis revealed that the critical proton transfers required for intermediate formation and hydrolysis may be mediated by a conserved active site water channel. Taken together, our results provide mechanistic insights underpinning histidine nucleophilic catalysis in general and hHint1 catalysis, in particular, thus aiding the design of future proTides and the elucidation of the natural function of the Hint family of enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Water-Mediated Carbon–Oxygen Hydrogen Bonding Facilitates S -Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase

The C-terminal domain of cobalamin-dependent methionine synthase (MetH) has an essential role in catalyzing the reactivation of the enzyme following the oxidation of its cobalamin cofactor. This reactivation occurs through reductive methylation of the cobalamin using S-adenosylmethionine (AdoMet) as the methyl donor. Here, we examine the molecular recognition of AdoMet by the MetH reactivation domain utilizing structural, biochemical, and computational approaches. Crystal structures of the Escherichia coli MetH reactivation domain in complex with AdoMet, the methyl transfer product S-adenosylhomocysteine (AdoHcy), and the AdoMet analogue inhibitor sinefungin illustrate that the ligands exhibit an analogous conformation within the solvent-exposed substrate binding cleft of the enzyme. AdoMet binding is stabilized by an intramolecular sulfur–oxygen chalcogen bond between the sulfonium and carboxylate groups of the substrate and by water-mediated carbon–oxygen hydrogen bonding between the sulfonium cation and the side chains of Glu1097 and Glu1128 that bracket the substrate binding cleft. AdoMet and sinefungin exhibited similar binding affinities for the MetH reactivation domain, whereas AdoHcy displayed an affinity for the enzyme that was an order of magnitude lower. Mutations of Glu1097 and Glu1128 diminished the AdoMet/AdoHcy binding selectivity ratio to approximately 2-fold, underscoring the role of these residues in enabling the enzyme to discriminate between the substrate and product. Together, these findings indicate that Glu1097 and Glu1128 in MetH promote high-affinity recognition of AdoMet and that sinefungin and potentially other AdoMet-based methyltransferase inhibitors can abrogate MetH reactivation, which would result in off-target effects associated with alterations in methionine homeostasis and one-carbon metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Wavelength-shifting properties of luminescence nanoparticles for high energy particle detection and specific physics process observation

Here, ultraviolet (UV) photon detection is becoming increasingly important in the quest to understand the fundamental building blocks of our universe. Basic properties of neutrinos and Dark Matter are currently being explored through interactions with noble elements. In response to interactions with fundamental particles, these elements emit scintillation photons in the UV range. However, most available detectors have poor response in the UV so it is typically necessary to shift UV to a wavelength, matching the sensitivity of the viable detectors. We report on development of UV-enhanced photosensors using wavelength-shifting properties of nanoparticles. Several nanoparticle coatings were tested for absorption of UV light with subsequent emission in the visible wavelength for high energy particle detection. ZnS:Mn, Eu, ZnS: Mn, CuCy (Copper Cysteamine) and CdTe nanoparticles all exhibited enhanced detection for wavelengths in the range 200-320 nm in several different tests, while ZnS:Ag and CdS nanoparticle showed little or no enhancement in that range. In addition, various LaF3:Ce nanoparticle concentrations in approximately constant thickness of 2,5-diphenyloxazole (PPO)/polystyrene bases were also tested to optimize the nanoparticle concentration for the best outcome. Our studies indicated that ZnS:Mn, Eu, ZnS: Mn, Cu-Cy, CdTe and LaF 3 :Ce nanoparticles show potential for light detection from fundamental particle interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Divergent kinase regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole

Apicomplexan parasites replicate within a protective organelle, called the parasitophorous vacuole (PV). The Toxoplasma gondii PV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients. Despite being critical to parasite virulence, there is scant mechanistic understanding of the network’s functions. Here, we identify the parasite-secreted kinase WNG1 (With-No-Gly-loop) as a critical regulator of tubular membrane biogenesis. WNG1 family members adopt an atypical protein kinase fold lacking the glycine rich ATPbinding loop that is required for catalysis in canonical kinases. Unexpectedly, we find that WNG1 is an active protein kinase that localizes to the PV lumen and phosphorylates PV-resident proteins, several ofwhich are essential for the formation of a functional intravacuolar network. Moreover, we show thatWNG1-dependent phosphorylation of these proteins is required for their membrane association, and thus their ability to tubulate membranes. Consequently, WNG1 knockout parasites have an aberrant PV membrane ultrastructure. Collectively, our results describe a unique family of Toxoplasma kinases and implicate phosphorylation of secreted proteins as a mechanism of regulating PV development during parasite infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Characterization of Radiation Effects and Ion Tracks with Spallation Neutron Probes

Swift heavy ions are typically defined as high-mass charged particles of kinetic energy above ~1 MeV per nucleon (MeV/u). In this regime, the energy deposition of the ions is dominated by electronic stopping, and each individual ion may induce a linear trail of damage with a width of a few nanometers and a length of several tens of micrometers or more. During the last decade, ion tracks and other radiation effects induced by swift heavy ions have been studied in a wide range of materials for basic research, as well as for a wide variety of applications. The interactions of swift heavy ions with matter are significantly different from those induced by lower energy ions (keV-MeV), where atoms are directly displaced from their lattice sites via elastic collisions. In contrast, swift ions (MeV-GeV) transfer their kinetic energy to the electrons of the target, inducing ionization and initiating a cascade of secondary electrons that quickly spreads radially. The extremely high energy densities (up to tens of eV/atom) along the ion path lead to a confined plasma-like state that is dissipated through electron–phonon coupling to the lattice. Further, subsequent rapid transitions through equilibrium and non-equilibrium states trigger complex structural modifications within a highly localized nanoscale damage zone, forming ion tracks in materials ion tracks.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi

1. The putative benefits to seeds in myrmecochory (ant- mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant-handling. 2. We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species. 3. Ant-handling altered measures of both alpha and beta diversity of fungal communities. Ant-handled seeds harboured different overall fungal communities and plant pathogen communities than non-ant-handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant-handled and control seeds, while beta diversity measures for ant- handled seeds and seeds with manually removed elaiosomes were less dissimilar. 4. Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction in the seed coat pathogenic community, which may be driven by elaiosome removal or as a by-product of ant cleaning behaviours and chemical secretions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure of Fission Yeast Transcription Factor Pho7 Bound to pho1 Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis

Pho7 is the Schizosaccharomyces pombe fission yeast Zn 2 Cys 6 transcriptional factor that drives a response to phosphate starvation in which phosphate acquisition genes are upregulated. Here we report a crystal structure at 1.6-Å resolution of the Pho7 DNA-binding domain (DBD) bound at its target site 2 in the pho1 promoter (5'-TCGGAAATTAAAAA). Comparison to the previously reported structure of Pho7 DBD in complex with its binding site in the tgp1 promoter (5'-TCGGACATTCAAAT) reveals shared determinants of target site specificity as well as variations in the protein-DNA interface that accommodate different promoter DNA sequences. Mutagenesis of Pho7 amino acids at the DNA interface identified nucleobase contacts at the periphery of the footprint that are essential for the induction of pho1 expression in response to phosphate starvation and for Pho7 binding to site 1 in the pho1 promoter.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

What a Difference a Dalton Makes: Bacterial Virulence Factors Modulate Eukaryotic Host Cell Signaling Systems via Deamidation

Pathogenic bacteria commonly deploy enzymes to promote virulence. These enzymes can modulate the functions of host cell targets. While the actions of some enzymes can be very obvious (e.g., digesting plant cell walls), others have more subtle activities. Depending on the lifestyle of the bacteria, these subtle modifications can be crucially important for pathogenesis. In particular, if bacteria rely on a living host, subtle mechanisms to alter host cellular function are likely to dominate. Several bacterial virulence factors have evolved to use enzymatic deamidation as a subtle posttranslational mechanism to modify the functions of host protein targets. Deamidation is the irreversible conversion of the amino acids glutamine and asparagine to glutamic acid and aspartic acid, respectively. Interestingly, all currently characterized bacterial deamidases affect the function of the target protein by modifying a single glutamine residue in the sequence. Deamidation of target host proteins can disrupt host signaling and downstream processes by either activating or inactivating the target. Despite the subtlety of this modification, it has been shown to cause dramatic, context-dependent effects on host cells. Several crystal structures of bacterial deamidases have been solved. All are members of the papain-like superfamily and display a cysteine-based catalytic triad. However, these proteins form distinct structural subfamilies and feature combinations of modular domains of various functions. Based on the diverse pathogens that use deamidation as a mechanism to promote virulence and the recent identification of multiple deamidases, it is clear that this enzymatic activity is emerging as an important and widespread feature in bacterial pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Neutrino Masses from the Point of View of Economy and Simplicity

In the framework of such basic principles as local gauge invariance, unification of the weak and electromagnetic interactions and spontaneous symmetry breaking in the Standard Model the most economical and simplest possibilities are realized. We discuss the problem of neutrino masses from the point of view of economy and simplicity. It is unlikely that neutrino masses are of the same SM origin as masses of leptons and quarks. The Weinberg effective Lagrangian is the simplest and the most economical, beyond the Standard Model mechanism of the generation of small Majorana neutrino masses. The resolution of the sterile neutrino anomaly and observation of the neutrinoless double β-decay would be crucial tests of this mechanism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2012

AvrRpm1 Missense Mutations Weakly Activate RPS2-Mediated Immune Response in Arabidopsis thaliana

Plants recognize microbes via specific pattern recognition receptors that are activated by microbe-associated molecular patterns (MAMPs), resulting in MAMP-triggered immunity (MTI). Successful pathogens bypass MTI in genetically diverse hosts via deployment of effectors (virulence factors) that inhibit MTI responses, leading to pathogen proliferation. Plant pathogenic bacteria like Pseudomonas syringae utilize a type III secretion system to deliver effectors into cells. These effectors can contribute to pathogen virulence or elicit disease resistance, depending upon the host plant genotype. In disease resistant genotypes, intracellular immune receptors, typically belonging to the nucleotide binding leucine-rich repeat family of proteins, perceive bacterial effector(s) and initiate downstream defense responses (effector triggered immunity) that include the hypersensitive response, and transcriptional re-programming leading to various cellular outputs that collectively halt pathogen growth. Nucleotide binding leucine-rich repeat sensors can be indirectly activated via perturbation of a host protein acting as an effector target. AvrRpm1 is a P. syringae type III effector. Upon secretion into the host cell, AvrRpm1 is acylated by host enzymes and directed to the plasma membrane, where it contributes to virulence. This is correlated with phosphorylation of Arabidopsis RIN4 in vivo. RIN4 is a negative regulator of MAMP-triggered immunity, and its modification in the presence of four diverse type III effectors, including AvrRpm1, likely enhances this RIN4 regulatory function. The RPM1 nucleotide binding leucine-rich repeat sensor perceives RIN4 perturbation in disease resistant plants, leading to a successful immune response. Here, demonstrate that AvrRpm1 has a fold homologous to the catalytic domain of poly(ADP-ribosyl)polymerase. Site-directed mutagenesis of each residue in the putative catalytic triad, His63-Tyr122-Asp185 of AvrRpm1 results in loss of both AvrRpm1-dependent virulence and AvrRpm1-mediated activation of RPM1, but, surprisingly, causes a gain of function: the ability to activate the RPS2 nucleotide binding leucine-rich repeat sensor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Final Technical Report: Targeting DOE-Relevant Ions with Supramolecular Strategies, DE-SC0010555

The effectiveness of three popular supramolecular strategies to selectively target negatively charged ions (anions) was evaluated. Ions of interest included oxo anions, particularly sulfate, that hamper nuclear waste remediation. Three objectives were pursued using a simple building block strategies and by strategically placing anion-binding sites at appropriate positions on organic host molecules. The goal of the first objective was to assess the influence of secondary, tertiary and quaternized amines on binding tetrahedral anions using mixed amide/amine macrocyclic and urea/amine hosts containing aromatic or heteroaromatic spacers. Objective 2 focused on the design of ion pair hosts, using mixed macrocyclic anion hosts joined through polyether linkages. Objective 3 was to explore the synthesis of new metal-linked extended macrocyclic frameworks to leverage anion binding. Key findings were that smaller 24-membered macrocycles provided the most complementary binding for sulfate ion and mixed urea/amine chelates showed enhanced binding over amide corollaries in addition to being highly selective for SO 4 2- in the presence of small quantities of water. In addition to obtaining prototype metal-linked macrocyclic anion hosts, a new dipincer ligand was designed that can be used to link macrocyclic or other supramolecular hosts in extended frameworks. When the tetraamide-based pincers are bound to two metal ions, an interesting phenomenon occurs. Upon deprotonation of the amides, two new protons appear between adjacent carbonyl pairs on the ligand, which may modify the chemistry, and metal-metal interactions in the complexes. Gel formation occurred for some of these extended hosts, and the physical properties are currently under investigation. The new tetracarboxamide-based pincers can also provide basic frameworks for double macrocycles capable of binding ion pairs as well as for binding metal ions and exploring intermetallic interactions through the pyrazine π system. Additionally appendages capable of influencing solvation effects can be introduced, and a number of other potential applications can be realized in areas such as soft materials chemistry, catalysis, sensing, and proton switches, the latter for binding and release of targeted guests. These findings provide a better foundation for understanding the selective binding of anions by targeted placement of hydrogen binding sites, and the strengths and weaknesses of various functional groups, that will allow for more the design of more effective anion sequestering agents. Our design strategy also used simple, cost-effective building blocks for host synthesis to allow for scale-up should real-world applications be forthcoming.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Broadband Outdoor Radiometer Calibration (BORCAL) Process for the Atmospheric Radiation Measurement (ARM) Program: Second Edition

The Atmospheric Radiation Measurement program (ARM) maintains a fleet of monitoring stations to aid in the improved scientific understanding of the basic physics related to radiative feedback processes in the atmosphere, particularly the interactions among clouds and aerosols. ARM obtains continuous measurements and conducts field campaigns to provide data products that aid in the improvement and further development of climate models. All of the measurement campaigns include a suite of solar measurements. The Solar Radiation Research Laboratory at the National Renewable Energy Laboratory supports ARM's full suite of stations in a number of ways, including troubleshooting issues that arise as part of the data-quality reviews; managing engineering changes to the standard setup; and providing calibration services and assistance to the full fleet of solar-related instruments, including pyranometers, pyrgeometers, pyrheliometers, as well as the temperature/relative humidity probes, multimeters, and data acquisition systems that are used in the calibrations performed at the Southern Great Plains Radiometer Calibration Facility. This paper discusses all aspects related to the support provided to the calibration of the instruments in the solar monitoring fleet.

14 SOLAR ENERGY↗
DOE OSTI2021

Structural analyses of macromolecules by solution scattering (CRADA Final Report)

New innovative Small Angle X-ray Scattering (SAXS) methods to visualized macromolecules in solution at low resolution has led the SIBYLS group at Lawrence Berkeley Lab in being a world leader in biological SAXS. This research is particularly important now as LBNL establishes high-priority research topics including molecular to mesoscale analysis. This new expanding area of research relies on and ties in with our efforts towards developing a solution structure modeling tool for RNA structure prediction. Due to the pandemic our efforts focused on the SARS-CoV-2 proteins and RNA interactions. Specifically, we characterized SARS-CoC-2 proteins interaction with RNA (Wilanowski et al. 2021 -Hammel group) and Nucleoprotein interaction with RNA (Schneidman group).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Identification of plant host and microbe model system for study of rhizophagy cycle

Rhizophagy (“root eating”) is a process by which plants actively uptake soil microbes into their roots and use oxidative degradation to extract micronutrients from the cells. This phenomenon has been proposed to be a general mechanism for plants to acquire nutrients from the environment via bacteria and fungi. Determining the conditions under which rhizophagy occurs and its prevalence in different plant species will improve our understanding of nutrient dynamics and plant-microbe metabolic interactions at the molecular level. This project aims to (1) optimize methods for plant and microbial growth, imaging, and analysis for the study of rhizophagy and (2) identify a bioenergy-relevant model system for future rhizophagy studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Elucidating Photoinduced Processes of Photosystem I Via Multidimensional Electronic and Vibrational Spectroscopies

This project was motivated by an overarching goal to elucidate the mechanism of energy and electron transfer that governs the efficient charge separation in photosystem I (PSI) complexes. PSI is a natural light harvesting complex that drives oxygenic photosynthesis in plants, algae, and cyanobacteria. It uses ~300 tightly packed chlorophylls (Chls) to absorb photons, transfer the excitation energy to the reaction center (RC), and generate a charge separated state with near unity quantum efficiency (QE). A better understanding of the mechanism of energy transfer and charge separation in PSI is required for understanding the high QE of natural light harvesting complexes, and it could lead to the further development of artificial photosynthetic systems for solar energy conversion and modification of light harvesting complexes to improve crop yields. We applied two-dimensional optical spectroscopies to different cyanobacterial photosystem I complexes, including PSI complexes that contain Chl f molecules, to map energy transfer pathways and gain insight into the efficient light harvesting of PSI. We used two-dimensional electronic spectroscopies (2DES) to map energy transfer in Chl a and Chl f containing PSI complexes. To investigate the Chl f PSI complexes, we modified our spectrometer to probe the lower energy states associated with Chl f molecules. We interpreted the 2DES spectra through global analysis procedures to generate maps of energy transfer. We also constructed a two-dimensional electronic vibrational (2DEV) spectrometer that will be used to investigate charge transfer transitions and dynamics within PSI complexes. Measurements were performed on model systems to establish general data analysis procedures for interpreting 2D spectra and gain insight into protein cofactor interactions.

14 SOLAR ENERGY↗
DOE OSTI2020

A Guide to Conquer the Biological Network Era Using Graph Theory

Networks are one of the most common ways to represent biological systems as complex sets of binary interactions or relations between different bioentities. In this article, we discuss the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs. In addition, we describe several network properties and we highlight some of the widely used network topological features. We briefly mention the network patterns, motifs and models, and we further comment on the types of biological and biomedical networks along with their corresponding computer- and human-readable file formats. Finally, we discuss a variety of algorithms and metrics for network analyses regarding graph drawing, clustering, visualization, link prediction, perturbation, and network alignment as well as the current state-of-the-art tools. We expect this review to reach a very broad spectrum of readers varying from experts to beginners while encouraging them to enhance the field further.

59 BASIC BIOLOGICAL SCIENCES↗