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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Surface structures of L1 0 -MnGa (001) by scanning tunneling microscopy and first-principles theory

We report on the surface reconstructions of L10-ordered MnGa (001) thin films grown by molecular beam epitaxy on a 50 nm Mn 3 N 2 (001) layer freshly grown on a magnesium oxide (001) substrate. Scanning tunneling microscopy, Auger electron spectroscopy, and reflection high energy electron diffraction, are combined with first-principles density functional theory calculations to determine the reconstructions of the L1 0 -ordered MnGa (001) surface. We find two lowest energy reconstructions of the MnGa(001) face: a 1×1 Ga-terminated structure and a 1×2 structure with a Mn replacing a Ga in the 1×1 Ga-terminated surface. The 1×2 reconstruction forms a row structure along [100]. The manganese:gallium stoichiometry within the surface based on the oretical modeling is in good agreement with experiment. Magnetic moment calculations for the two lowest energy structures reveal important surface and bulk effects leading to oscillatory total magnetization for ultra-thin MnGa(001) films.

density functional theory↗
DOE OSTI2024

Accommodating a hexagonal ζ- phase Mn 2 N film on a cubic MgO (001) substrate

The thin films of c -plane dominated hexagonal ζ- phase Mn 2 N were successfully grown on a cubic MgO (001) substrate directly using plasma-assisted molecular beam epitaxy. The surface was comprehensively studied through experimental and theoretical approaches. Reflection high energy electron diffraction revealed two pseudo-cubic domains along [100] MgO and [110] MgO , and one hexagonal domain, which is 30° apart from the [100] MgO direction. Scanning tunneling microscopy was used to image and resolve the high-quality surface, revealing a distorted hexagonal surface structure. Furthermore, atomic resolution of the hexagonal domain with a 2 × 2 reconstructed surface is presented. For c-plane surface, theoretical investigations were carried out using first principles studies to determine the surface formation energy for various reconstructed surfaces. The theoretical study shows that the nitrogen terminated 2 × 2 structure with a manganese adatom on the surface as the most stable reconstruction that reproduces the experimental results. A corresponding simulated scanning tunneling microscopy model is also presented, providing strong support for the experimentally observed in-plane lattice structures. Furthermore, the manganese: nitrogen stoichiometry within the bulk and surface is in good agreement with the expected ratio of 2:1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Analysis of various types of single-polypeptide-chain (sc) heterodimeric A{sub 2A}R/D{sub 2}R complexes and their allosteric receptor–receptor interactions

Highlights: • Various scA{sub 2A}R/D{sub 2}R constructs, with spacers between the two receptors, were created. • Using whole cell binding assay, constructs were examined for their binding activity. • Although the apparent ratio of A{sub 2A}R to D{sub 2}R binding sites should be 1, neither was 1. • Counter agonist-independent binding cooperativity occurred in context of scA{sub 2A}R/D{sub 2}R. - Abstract: Adenosine A{sub 2A} receptor (A{sub 2A}R) heteromerizes with dopamine D{sub 2} receptor (D{sub 2}R). However, these class A G protein-coupled receptor (GPCR) dimers are not fully formed, but depend on the equilibrium between monomer and dimer. In order to stimulate the heteromerization, we have previously shown a successful design for a fusion receptor, single-polypeptide-chain (sc) heterodimeric A{sub 2A}R/D{sub 2}R complex. Here, using whole cell binding assay, six more different scA{sub 2A}R/D{sub 2}R constructs were examined. Not only in scA{sub 2A}R/D{sub 2}R ‘liberated’ with longer spacers between the two receptors, which confer the same configuration as the prototype, the A{sub 2A}R-odr4TM-D{sub 2L}R, but differ in size (Forms 1–3), but also in scA{sub 2A}R/D{sub 2L}R (Form 6) fused with a transmembrane (TM) of another type II TM protein, instead of odr4TM, neither of their fixed stoichiometry (the apparent ratios of A{sub 2A}R to D{sub 2}R binding sites) was 1, suggesting their compact folding. This suggests that type II TM, either odr4 or another, facilitates the equilibrial process of the dimer formation between A{sub 2A}R and D{sub 2L}R, resulting in the higher-order oligomer formation from monomer of scA{sub 2A}R/D{sub 2L}R itself. Also, in the reverse type scA{sub 2A}R/D{sub 2L}R, i.e., the D{sub 2L}R-odr4TM-A{sub 2A}R, counter agonist-independent binding cooperativity (cooperative folding) was found to occur (Forms 4 and 5). In this way, the scA{sub 2A}R/D{sub 2L}R system has unveiled the cellular phenomenon as a snapshot of the molecular behavior in A{sub 2A}R/D{sub 2L}R dimer. Thus, these results indicate that the various designed types of functional A{sub 2A}R/D{sub 2}R exist even in living cells and that this fusion expression system would be useful to analyze as a model of the interaction between class A GPCRs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Biophysical characterization of Ca{sup 2+}-binding of S100A5 and Ca{sup 2+}-induced interaction with RAGE

S100A5 is a calcium-binding protein of S100 family, which represents a major ligand to the receptor for advanced glycation end product (RAGE), a pattern recognition receptor engaged in diverse pathological processes. Here we have characterized calcium binding of S100A5 and the complex formation between S100A5 and RAGE using calorimetry and NMR spectroscopy. S100A5 binds to calcium ions in a sequential manner with the equilibrium dissociation constants (K{sub D}) of 1.3 μM and 3.5 μM, which corresponds to the calcium-binding at the C-terminal and N-terminal EF-hands. Upon calcium binding, S100A5 interacts with the V domain of RAGE (RAGE-v) to form a heterotrimer (K{sub D} ∼5.9 μM) that is distinct among the S100 family proteins. Chemical shift perturbation data from NMR titration experiments indicates that S100A5 employs the periphery of the dimer interface to interact with RAGE-v. Distinct binding mode and stoichiometry of RAGE against different S100 family proteins could be important to modulate diverse RAGE signaling. - Highlights: • Thermodynamic of sequential Ca{sup 2+}-binding to S100A5 is determined quantitatively. • S100A5 binds to RAGE-v to form a distinct dynamic heterotrimer with K{sub D} ∼5.9 μM. • RAGE-v binds to the rim of the S100A5 dimer interface via hydrophobic interaction. • Different binding modes of S100 proteins to RAGE may modulate RAGE signaling.

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

Phosphorylation of synaptic GTPase-activating protein (synGAP) by polo-like kinase (Plk2) alters the ratio of its GAP activity toward HRas, Rap1 and Rap2 GTPases

Highlights: • Phosphorylation by Plk2 regulates Ras and Rap specificity of synGAP's GAP activity. • Phosphorylation by both Plk2 and CDK5 additively increases RasGAP activity by 230%. • Together, CaMKII, Plk2, and CDK5 act like a rheostat to finely tune GAP specificity. SynGAP is a Ras and Rap GTPase-activating protein (GAP) found in high concentration in the postsynaptic density (PSD) fraction from mammalian forebrain where it binds to PDZ domains of PSD-95. Phosphorylation of pure recombinant synGAP by Ca{sup 2+}/calmodulin-dependent protein kinase II (CaMKII) shifts the balance of synGAP's GAP activity toward inactivation of Rap1; whereas phosphorylation by cyclin-dependent kinase 5 (CDK5) has the opposite effect, shifting the balance toward inactivation of HRas. These shifts in balance contribute to regulation of the numbers of surface AMPA receptors, which rise during synaptic potentiation (CaMKII) and fall during synaptic scaling (CDK5). Polo-like kinase 2 (Plk2/SNK), like CDK5, contributes to synaptic scaling. These two kinases act in concert to reduce the number of surface AMPA receptors following elevated neuronal activity by tagging spine-associated RapGAP protein (SPAR) for degradation, thus raising the level of activated Rap. Here we show that Plk2 also phosphorylates and regulates synGAP. Phosphorylation of synGAP by Plk2 stimulates its GAP activity toward HRas by 65%, and toward Rap1 by 16%. Simultaneous phosphorylation of synGAP by Plk2 and CDK5 at distinct sites produces an additive increase in GAP activity toward HRas (∼230%) and a smaller, non-additive increase in activity toward Rap1 (∼15%). Dual phosphorylation also produces an increase in GAP activity toward Rap2 (∼40–50%), an effect not produced by either kinase alone. As we previously observed for CDK5, addition of Ca{sup 2+}/CaM causes a substrate-directed doubling of the rate and stoichiometry of phosphorylation of synGAP by Plk2, targeting residues also phosphorylated by CaMKII. In summary, phosphorylation by Plk2, like CDK5, shifts the ratio of GAP activity of synGAP to produce a greater decrease in active Ras than in active Rap, which would produce a shift toward a decrease in the number of surface AMPA receptors in neuronal dendrites.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Bioenergetic consequences of compromised mitochondrial DNA repair in the mouse heart

Highlights: • Loss of mitochondrial DNA repair compromises bioenergetic efficiency. • Impairments in bioenergetic efficiency result from ETS stoichiometry shifts. • Bioenergetic flux in Polg{sup m/m} mitochondria favors accelerated electron leak. The progeroid phenotype of mitochondrial DNA (mtDNA) mutator mice has been nebulously attributed to general mitochondrial ‘dysfunction’, though few studies have rigorously defined the bioenergetic consequences of accumulating mtDNA mutations. Comprehensive mitochondrial diagnostics was employed to interrogate the bioenergetic properties of isolated cardiac mitochondria from mtDNA mutator mice and wild type littermates. Assessment of respiratory flux in conjunction with parallel measurements of mitochondrial free energy all point to the cause of respiratory flux limitations observed in mtDNA mutator mouse mitochondria being due to impairments within the energy transduction step catalyzed by the electron transport system in which NADH/NAD{sup +} free energy is transduced to the proton motive force (ΔP). The primary bioenergetic consequence of this limitation appears to be hyper-reduction of NAD(P)H/NAD(P){sup +} redox poise across multiple substrate conditions, particularly evident at moderate to high respiration rates. This hyper-reduced phenotype appears to result from specific reductions in both complex I and complex IV expression, presumably due to compromised mtDNA integrity. Translation of these findings to the working heart would suggest that the primary biological consequence of accumulated mtDNA damage is accelerated electron leak driven by an increase in electron redox pressure for a given rate of oxygen consumption.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase

Precursor molecules for biomass incorporation must be imported into cells and made available to the molecular machines that build the cell. Sulfur-containing macromolecules require that sulfur be in its S2- oxidation state before assimilation into amino acids, cofactors, and vitamins that are essential to organisms throughout the biosphere. In α-proteobacteria, NADPH-dependent assimilatory sulfite reductase (SiR) performs the final six-electron reduction of sulfur. SiR is a dodecameric oxidoreductase composed of an octameric flavoprotein reductase (SiRFP) and four hemoprotein metalloenzyme oxidases (SiRHPs). SiR performs the electron transfer reduction reaction to produce sulfide from sulfite through coordinated domain movements and subunit interactions without release of partially reduced intermediates. Efforts to understand the electron transfer mechanism responsible for SiR’s efficiency are confounded by structural heterogeneity arising from intrinsically disordered regions throughout its complex, including the flexible linker joining SiRFP’s flavin-binding domains. As a result, high-resolution structures of SiR dodecamer and its subcomplexes are unknown, leaving a gap in the fundamental understanding of how SiR performs this uniquely large-volume electron transfer reaction. In this work, we use deuterium labeling, in vitro reconstitution, analytical ultracentrifugation (AUC), small-angle neutron scattering (SANS), and neutron contrast variation (NCV) to observe the relative subunit positions within SiR’s higher-order assembly. AUC and SANS reveal SiR to be a flexible dodecamer and confirm the mismatched SiRFP and SiRHP subunit stoichiometry. NCV shows that the complex is asymmetric, with SiRHP on the periphery of the complex and the centers of mass between SiRFP and SiRHP components over 100 Å apart. SiRFP undergoes compaction upon assembly into SiR’s dodecamer and SiRHP adopts multiple positions in the complex. The resulting map of SiR’s higher-order structure supports a cis/trans mechanism for electron transfer between domains of reductase subunits as well as between tightly bound or transiently interacting reductase and oxidase subunits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tunable amorphous carbon films formed on ultralow wear, Pt–Au alloys

The mechanocatalytic formation of carbonaceous films at the interface between sliding metallic contacts is simultaneously advantageous for reducing friction and adhesion in several tribological applications and detrimental for electrical contacts as they can induce device failure by increasing the contact resistance. Yet, remarkably little is still known about the chemistry, structural and mechanical properties, and tunability of these interfacial layers. In this study, we performed contact pressure-dependent tribological experiments in dry nitrogen containing trace organics on four, nanocrystalline Pt–Au alloys ([Au] from 0 at.% to 10 at.%) – a promising class of alloys for ultralow wear and electrical contact applications. The ex-situ, multi-technique characterization results did not only provide insights into the chemical nature and mechanical behavior of the mechanocatalytic, carbon-rich films formed on Pt–Au surfaces, but also revealed the interplay between catalytic and mechanochemical tribofilm formation controlled by the composition-dependent electronic structure of the Pt–Au substrate and the applied contact pressure. The results of this work provide guidelines for tailoring nanocrystalline alloys to control their mechanocatalytic activity on the basis of variations of the alloy mechanical properties and element's electronic structure with the alloy stoichiometry.

AFM↗
DOE OSTI2020

O 2 dosage as a descriptor of TWC performance under lean/rich dithering in stoichiometric natural gas engines

The effects of oscillations in gas composition, known as lean/rich dithering, on the performance of a commercial Pd-based three-way catalyst (TWC) for stoichiometric natural gas (NG) engines were evaluated using synthetic exhaust flow reactor experiments. Under simulated NG exhaust conditions, NO conversion was intimately correlated to CH 4 conversion at slightly fuel-rich operating conditions. CH 4 conversion significantly varied with lambda (or O 2 concentration) and depended on the direction of the lambda change. The dynamic CH 4 conversion is likely related to the change of catalyst oxidation state and structures of Pd active sites. The CH 4 -NO cross-over point was found at a rich-biased lambda rather than stoichiometry. Compared to static operation, catalyst performance was much higher under a realistic dithering condition. The impacts of dithering parameters including amplitude and frequency on CH 4 and NO conversions were explored. O 2 dosage is proposed as an effective descriptor of the TWC dithering performance. In the O 2 -dosage space, the performance of distinct dithering parameters collapse, helping to elucidate the fundamental influence of dithering parameters on TWC performance. With the help of O2 dosage, an optimal operating window leading to high CH 4 and NO conversions was identified. A higher dithering amplitude is required to keep the catalyst in a reduced state for higher CH 4 and NO conversions, while an appropriate O 2 dosage that does not exceed the breakthrough OSC is necessary to avoid excess O 2 that results in NO slip. The dithering amplitude and O 2 -dosage-metric maps provide a new method for studying dynamic TWC performance and identifying optimum operation strategies.

03 NATURAL GAS↗
DOE OSTI2019

Optimizing complexity in the kinetic modelling of integrated flue gas purification for pressurized oxy-combustion

A 5-step mechanism and a corresponding kinetic model are presented for integrated flue gas purification, where SOx and NOx are removed during pressurized oxy-coal combustion. Three coupled subsystems (‘blocks”) of gas–liquid transformations are considered: 1) oxidation of NO to NO 2 and dissolution of NO 2 in water; 2) dissolution of SO 2 in the water; and 3) interactions between S- and N- containing substances in the liquid phase. The model has been formulated in terms of only species that can be experimentally measured (model of optimal complexity). Subsystem I is limiting regarding NO removal. Subsystem II is very fast in comparison with the other subsystems and can be treated separately. Analytical expressions for all independent subsystems have been found and compared with computational results for the whole system. The temporal domain of validity of all these subsystems is presented. Finally, the validity of the NO 2 quasi-steady-state assumption is verified, and it is reported that variables such as NO, NO 2 and HNO 3 can be considered decoupled from the whole system since they appear in only Subsystem I, while HSO 3 - and HNO 2 are coupled. The presented kinetic model was verified experimentally by determining the 1:1 ratio of HNO 2 and HNO 3 , in gas–liquid NO-O 2 interaction. Additionally, new experimental facts on kinetic orders and stoichiometry between HNO 2 and HSO 3 - have been used to optimize the model. It is concluded that all NO x - SO x interactions can be essentially grasped by a sequence of only 4 irreversible reactions considering, in addition, the 5th reaction, i.e. the fast ‘SO 2 -water’ equilibrium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form

The Ebola virus matrix protein VP40 forms distinct structures linked to distinct functions in the virus life cycle. Dimeric VP40 is a structural protein associated with virus assembly, while octameric, ring-shaped VP40 is associated with transcriptional control. In this study, we show that suitable nucleic acid is sufficient to trigger a dynamic transformation of VP40 dimer into the octameric ring. Deep sequencing reveals a binding preference of the VP40 ring for the 3' untranslated region of cellular mRNA and a guanine- and adenine-rich binding motif. Complementary analyses of the nucleic-acid-induced VP40 ring by native mass spectrometry, electron microscopy, and X-ray crystal structures at 1.8 and 1.4 Å resolution reveal the stoichiometry of RNA binding, as well as an interface involving a key guanine nucleotide. The host factor-induced structural transformation of protein structure in response to specific RNA triggers in the Ebola virus life cycle presents unique opportunities for therapeutic inhibition.

3′ UTR↗
DOE OSTI2021

Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates

Variable stoichiometry and silicate polymorphism in calcium-silicate-hydrates (C-S-H) has impeded the revelation of point defects distribution in the silicate tetrahedral network of C-S-H, which resembles tobermorite crystal structure with some bridging tetrahedra (BT) and paired tetrahedra (PT) vacancies in dreierketten chains. Here we use a computational approach to characterize silicate polymorphism by introducing the vacancy ratio of BT to PT (α) and establishing a three-term empirical mean chain length (MCL) formula for different calcium-to‑silicon ratios (Ca/Si) ranging from 1.2 to 2.3. The formula identifies BT and PT controls at low and high α respectively and allows an inverse mapping of polymorphic range based on NMR experiments. The proposed computational framework quantitatively describes silicate polymorphs and links NMR-measured MCL to C-S-H atomistic configurations at the molecular level.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Balance of oxygen throughout the conversion of a high-level waste melter feed to glass

Gases evolve from nuclear waste melter feed during conversion to glass in response to heating. This article is focused on oxygen mass balance based on the stoichiometry of feed melting reactions and evolved-gas analysis data. Whereas O 2 -producing and -consuming batch-melting reactions are complete in the reacting and primary-foam layers of the cold cap, O 2 from redox reactions continues to evolve as long as melt temperature increases, and thus generates secondary foam. Also, we discuss the relationship between the oxygen mass balance and the temperature-dependent iron redox ratio and the O 2 partial pressure, as they evolve during the feed-to-glass conversion.

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

In-situ observation of oxygen mobility and abnormal lattice expansion in ceria during flash sintering

Flash sintering has been shown to be an effective method of sintering for many types of ceramics. However, the characteristics of flash sintering for each type of ceramic varies. When ionically conducting ceramics are sintered under a DC electric field, a strong dependence of densification with respect to position is observed. Microstructural analysis of the effect of electric field on oxygen ion conductors shows non-stoichiometry (oxygen deficiency) at the cathode which continues to build up over time under flash. In oxygen ion conductors, dominant charge carriers during flash are oxygen ions and the final density of the specimen is related to the availability of oxygen. This effect is no longer evident when using an AC power supply. In conclusion, use of AC instead of DC electric field is preferable for flash sintering of ionically conducting ceramics.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Development, characterization, and modeling of a high-performance Ru/B2CA catalyst for ammonia synthesis

This paper documents the development and performance of a nano-phase Ru catalyst on a (BaO) x (CaO) y (Al 2 O 3 ) support. Extensive screening of the support’s ternary composition shows the best stoichiometry is (BaO) 2 (CaO)(Al 2 O 3 ), denoted B2CA. The paper first describes catalyst preparation and characterization. The paper reports a detailed 12-step reaction mechanism that represents ammonia synthesis over wide ranges of temperature, pressure, space velocity, and feed composition. Additionally, the mechanism is developed and validated using results of packed-bed experiments. The elementary reaction pathways consider surface adsorbates, including catalyst-poisoning behaviors. The rate expressions include important coverage-dependent activation barriers. Machine learning models assist interpretation of the catalyst-support interactions. The detailed chemistry is much more predictive than is possible with global representations (N 2 + 3H 2 ⇌ 2NH 3 ). The validated models can be applied to assist optimizing reactor design and operating conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗