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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Materials Data on V(HO)2 by Materials Project

V(OH)2 crystallizes in the orthorhombic Pnnm space group. The structure is three-dimensional. V2+ is bonded to six equivalent O2- atoms to form a mixture of corner and edge-sharing VO6 octahedra. The corner-sharing octahedral tilt angles are 51°. There are four shorter (2.22 Å) and two longer (2.23 Å) V–O bond lengths. H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.98 Å. O2- is bonded in a distorted single-bond geometry to three equivalent V2+ and one H1+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Insights into the Mechanism of Neptunium Oxidation to the Heptavalent State

Abstract Neptunium can exist in multiple oxidation states, including the rare and poorly understood heptavalent form. In this work, we monitored the formation of heptavalent neptunium [Np(VII)O 4 (OH) 2 ] 3− during ozonolysis of aqueous M OH ( M =Li, Na, K) solutions using a combined experimental and theoretical approach. All experimental reactions were closely monitored via absorption and vibrational spectroscopy to follow both the oxidation state and the speciation of neptunium guided by the calculated vibrational frequencies for various neptunium species. The mechanism of the reaction partly involves oxidative dissolution of transient Np(VI) oxide/hydroxide solid phases, the identity of which are dependent on the co‐precipitating counter‐cation Li + /Na + /K + . Additional calculations suggest that the most favorable energetic pathway occurs through the reaction of a [Np(V)O 2 (OH) 4 ] 3− with the hydroxide radical to form [Np(VI)O 2 (OH) 4 ] 2− , followed by an additional oxidation with HO⋅ to create [Np(VII)O 4 (OH) 2 ] 3− .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Materials Data on K2RbHoV2O8 by Materials Project

RbK2HoV2O8 crystallizes in the trigonal P-3m1 space group. The structure is three-dimensional. Rb1+ is bonded to twelve O2- atoms to form RbO12 cuboctahedra that share edges with six equivalent RbO12 cuboctahedra, edges with six equivalent VO4 tetrahedra, and faces with two equivalent HoO6 octahedra. There are six shorter (3.15 Å) and six longer (3.48 Å) Rb–O bond lengths. K1+ is bonded in a 1-coordinate geometry to ten O2- atoms. There are a spread of K–O bond distances ranging from 2.60–3.35 Å. Ho3+ is bonded to six equivalent O2- atoms to form HoO6 octahedra that share corners with six equivalent VO4 tetrahedra and faces with two equivalent RbO12 cuboctahedra. All Ho–O bond lengths are 2.25 Å. V5+ is bonded to four O2- atoms to form VO4 tetrahedra that share corners with three equivalent HoO6 octahedra and edges with three equivalent RbO12 cuboctahedra. The corner-sharing octahedral tilt angles are 16°. There is one shorter (1.69 Å) and three longer (1.77 Å) V–O bond length. There are two inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted linear geometry to three equivalent Rb1+, one K1+, and one V5+ atom. In the second O2- site, O2- is bonded in a 2-coordinate geometry to one Rb1+, three equivalent K1+, one Ho3+, and one V5+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Conversion of Formic Acid on Single- and Nano-Crystalline Anatase TiO 2 (101)

Understanding thermochemical transformations of formic acid (FA) on metal oxide surfaces is important for many catalytical reactions. Here we study thermally induced reactions of FA on a single-crystalline and nanocrystalline anatase TiO 2 (101). We employ a combination of scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), infrared reflection absorption spectroscopy (IRAS), diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and density functional theory (DFT) to follow the FA surface intermediates and reaction products above room temperature. We find that the primary reaction products desorbing at about 300, 480, and 515 K are molecular water, carbon monoxide, and formaldehyde, respectively. Bidentate (BD) formate and bridging hydroxyl (HO b ) are identified as central intermediates in the FA transformations. Bridging oxygen vacancies (V O ) are also likely participants despite their low stability at the surface. In conclusion, the parallel studies on single crystals and faceted TiO 2 (101) nanoparticles reveal the spectroscopic commonalities of surface species and of the thermal conversion of molecular and deprotonated forms of FA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗
NASA NTRS1993

The ionizing radiation of Seyfert 2 galactic nuclei

We report the discovery of a nonrandom trend in the dispersion of emission-line intensity ratios for Seyfert 2 galaxies. The sense of this pattern suggests the influence of a single physical parameter, the hardness of the ionizing continuum, which controls the heating energy per ionizing photon. We compare the observed line ratios with new photoionization calculations and find that the observed distributions can be reproduced if the ionizing continuum is parametrized by a power law. Our results also suggest an inverse correlation between luminosity and continuum hardness for Seyfert 2 nuclei; if true, this trend extends a similar pattern known in quasars and Seyfert 1 galaxies to active galactic nuclei of lower luminosity. Samples of Seyfert 2 nuclei with improved selection uniformity are desirable for elaboration of these findings.

Ho, Luis C.↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
DOE OSTI2022

Stability and Activity of Cobalt Antimonate for Oxygen Reduction in Strong Acid

Guided by computational Pourbaix screening and high-throughput experiments aimed at the development of precious-metal-free fuel cells, we investigate rutile CoSb 2 O 6 as an electrocatalyst for oxygen reduction in 1 M sulfuric acid. Following 4 h of catalyst conditioning at 0.7 V vs RHE, operation at this potential for 20 h yielded an average current density of –0.17 mA cm –2 with corrosion at a rate of 0.04 nm hour –1 that is stoichiometric with catalyst composition. Surface Pourbaix analysis of the (111) surface identified partial H coverage under operating conditions. The Sb active site has an HO* binding free energy of 0.49 eV, which is near the peak of the kinetic 4e – ORR volcano for transition-metal oxides in acidic conditions. Furthermore, the experimental demonstration of operational stability and computational identification of a reaction pathway with favorable energetics place rutile CoSb 2 O 6 among the most promising precious-metal-free electrocatalysts for oxygen reduction in acidic media.

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

Effects of drive pulse shape on graded metal pushered single shell capsule implosions on the National Ignition Facility

Graded metal pushered single shells (PSS) are a viable alternative to low-Z capsules (Z is the atomic number) for indirect drive inertial confinement fusion implosions due to enhanced core tamping and radiation trapping, but they can be compromised by the pusher mixing with the fuel. We compare 2-shock and 3-shock laser pulses for Be/Cr PSS capsules filled with deuterium–tritium gas fuel at 6 mg/cc density. 1D radiation-hydrodynamic simulations predict higher core compression and, hence, ∼2× higher fusion yield for the 3-shock drive than for 2-shock. Nevertheless, we observe similar core ion temperatures and fusion yields for both drives. The implosion burn duration is 25% shorter and the core volume is ∼2.5× smaller for the 3-shock drive than for 2-shock, consistent with a higher compression. 1D LASNEX mix simulations using a buoyancy-drag model matching the measured yields also agree with the observed core sizes and burn durations and suggest ∼40% and ∼70% yield degradations for 2-shock and 3-shock drives due to hydrodynamic instabilities and atomic mix at the pusher–fuel interface. At the same time, 2D HYDRA simulations show that mid-mode (2–250) instability degradations are negligible for the 2-shock implosion (9%) and significant (45%) for 3-shock. Subtracting these from the 1D mix simulations, we infer similar degradations from high-mode instabilities and atomic mix for both drives. Due to its robustness to mid-mode instabilities, future pusher–gas mix studies will use the 2-shock drive.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2022

Trace Element Partitioning Between Olivine and Melt in Lunar Basalts

Mineral/melt partition coefficients have been widely used to provide insights into magmatic processes. Olivine is one of the most abundant and important minerals in the lunar mantle and mare basalts. Yet, no systematic olivine/melt partitioning data are available for lunar conditions. We report trace element partition data between host mineral olivine and its melt inclusions in lunar basalts. Equilibrium is evaluated using the Fe-Mg exchange coefficient, leading to the choice of melt inclusion-host olivine pairs in lunar basalts 12040, 12009, 15016, 15647, and 74235. Partition coefficients of 21 elements (Li, Mg, Al, Ca, Ti, V, Cr, Mn, Fe, Co, Y, Zr, Nb, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu) were measured. Except for Li, V, and Cr, these elements show no significant difference in olivine-melt partitioning compared to the data for terrestrial samples. The partition coefficient of Li between olivine and melt in some lunar basalts with low Mg# (Mg# < 0.75 in olivine, or < ~0.5 in melt) is higher than published data for terrestrial * Corresponding author. Email address: youxue@umich.edu 2 samples, which is attributed to the dependence of DLi on Mg# and the lack of literature DLi data with low Mg#. The partition coefficient of V in lunar basalts is measured to be 0.17 to 0.74, significantly higher than that in terrestrial basalts (0.003 to 0.21), which can be explained by the lower oxygen fugacity in lunar basalts. The significantly higher DV can explain why V is less enriched in evolved lunar basalts than terrestrial basalts. The partition coefficient of Cr between olivine and basalt melt in the Moon is 0.11 to 0.62, which is lower than those in terrestrial settings by a factor of approximately 2. This is surprising because previous authors showed that Cr partition coefficient is independent of fO2. A quasi-thermodynamically based model is developed to correlate Cr partition coefficient to olivine and melt composition and fO2. The lower Cr partition coefficient between olivine and basalt in the Moon can lead to more Cr enrichment in the lunar magma ocean, as well as more Cr enrichment in mantle-derived basalts in the Moon. Hence, even though Cr is typically a compatible element in terrestrial basalts, it is moderately incompatible in primitive lunar basalts, with a similar degree of incompatibility as V based on partition coefficients in this work, as also evidenced by the relatively constant V/Cr ratio of 0.039 ± 0.011 in lunar basalts. The confirmation of constant V/Cr ratio is important for constraining concentrations of Cr (slightly volatile and siderophile) and V (slightly siderophile) in the bulk silicate Moon.

partition coefficients↗
DOE OSTI2021

Role of Pr-Vacancies and O-Interstitials on the Activity and Stability of (Pr 1−x Ln x ) 2 NiO 4 (Ln = La, Nd, Pm, Sm, Gd, Tb, Dy, and Ho) towards Oxygen Reduction Reactions: A DFT Study

Praseodymium nickelate, Pr 2 NiO 4 (PNO), is a promising electrode to promote oxygen reduction reaction (ORR) in a solid oxide fuel cell, but it exhibits phase transformation during electrochemical operation. The origin of the simultaneous phase transformation and high electrochemical performance remains obscure. We carried out a systematic density functional theory study to elucidate the mechanism for this conjugated phenomenon. Charge, electronic structure, and normal-mode analysis suggest the presence of peroxide. Our study shows that the formation of peroxide (O 2 2– ) is attributed to both oxygen interstitials and Pr vacancies. The peroxide species limits the oxygen ion migration due to the additional energy required to break its O–O bond, which leads to a decrease in ORR activity. Subsequently, we investigate the diffusion paths of Pr-ions while comparing them with those of other Ln 3+ ions (La, Nd, Pm, Sm, Gd, Tb, Dy, and Ho) in PNO. The formation energies for various Ln 3+ cation occupancies are calculated, as well as segregation energies in CeO 2 (111) surfaces. Lastly, criteria for effective Ln 3+ dopants are developed. La, Nd, and Pm are proposed as potential substituents in PNO to obtain a stable structure.

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

Synthesis and characterization of the rare-earth chloride complexes with N,N,N',N' -tetramethylmalonamide

Exploration of the solid-state chemistry of the f-elements and their coordination chemistry can assist in understanding the speciation of these elements in solution, which, in turn, can aid in the interpretation of their chemical behavior in complex liquid-liquid separations. Within these separation processes, malonamides are common organic extractants that are used for complexing both lanthanides and actinides, thus it is relevant to understand the malonamide ligand complexation under various conditions. In this work, we investigate solid-state complexes of the rare-earth chlorides with N,N,N',N' -tetramethylmalonamide (TMMA) across the entire lanthanide series. Here, we isolated two structural families of compounds Ln(TMMA) 2 Cl 3 Ln = La–Dy and [Ln(TMMA) 2 (H 2 O) 4 ]Cl 3 • x H 2 O x = 0,4 Ln = Ho–Lu, showing differences in chloride coordination from the inner-sphere complex for early lanthanides to outer-sphere for the late lanthanides. Both structural series were additionally analyzed by both IR and Raman spectroscopy confirming similarities in malonamide ligand coordination modes, while showing differences in vibrational features associated with chloride and aqua ligand coordination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

Torrelles, Jose M.↗
DOE OSTI2023

Reversible Electrochemical Lithium Cycling in a Vanadium(IV)- and Niobium(V)-Based Wadsley–Roth Phase

Fast charging remains one of the greatest safety challenges in Li-ion batteries due to Li-dendrite growth occurring on graphite anodes if they are lithiated too quickly. The search for high-rate anodes has highlighted materials in the Wadsley–Roth (WR) shear phase family. The relative abundance of V compared with traditional WR compositions of Nb and W makes V-based phases attractive. However, the high voltage and poor reversibility typically associated with V redox have made V-rich WR phases less studied than Nb- and W-rich phases. Here, we show that a new V-rich Wadsley–Roth phase, V 7 Nb 6 O 29 , achieves excellent rate capability and 80% capacity retention after 228 cycles with a relatively low average voltage of 1.76 V vs Li/Li + compared with other V-rich WR phases. Single-crystal X-ray diffraction reveals a P4/m space group with repeating 2 × 2 × ∞ and 3 × 3 × ∞ blocks of V 4+ and Nb 5+ octahedra. Finally, combined neutron pair distribution function analysis, X-ray absorption spectroscopy, and density functional theory calculations show that V redox is the primary source of capacity and that cycling stability is provided by the stable octahedral coordination adopted by V 4+ in the material.

25 ENERGY STORAGE↗
DOE OSTI2022

Experimental and modeling studies of the plasma chemistry in a humid Ar radiofrequency atmospheric pressure plasma jet

Abstract While humid atmospheric pressure plasmas are extensively modeled, reaction set validation for these conditions remains limited. We present a detailed comparison of a modelling and experimental study with a goal to elucidate the plasma chemistry in a humid Ar radiofrequency-driven atmospheric pressure plasma jet. A large group of species including radicals (H, OH, O, HO 2 ) and long-lived species (H 2 , O 2 and H 2 O 2 ) in the jet effluent was experimentally quantified by molecular beam mass spectroscopy (MBMS). MBMS measurements of H 2 O 2 , OH and H were validated by direct comparison with a liquid phase colorimetric measurement, laser-induced fluorescence (LIF) and two-photon absorption LIF respectively. While an excellent agreement was found for OH and H 2 O 2 by both techniques, a significant difference was found for H and shown to be due to boundary layer effects at the MBMS sampling substrate. The measured O, OH, HO 2 and H 2 are in good agreement with the plug model while H and O 2 were underestimated and H 2 O 2 was overestimated by the model. The accuracy of both the used reaction set and the diagnostics, as well as the observed discrepancies between the modeling and experimental results, are critically assessed. The results presented in this work enable us to identify further data needs for describing H 2 O vapor chemistry in low-temperature plasmas.

Physics↗
DOE OSTI2021

Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

A NICER view of PSR J0030+0541: Millisecond Pulsar Parameter Estimation

We report on Bayesian parameter estimation of the mass and equatorial radius of the millisecond pulsar PSRJ0030+0451, conditional on pulse-profile modeling of Neutron Star Interior Composition Explorer X-ray spectral timing event data. We perform relativistic ray-tracing of thermal emission from hot regions of the pulsar’s surface. We assume two distinct hot regions based on two clear pulsed components in the phase-folded pulse-profile data; we explore a number of forms (morphologies and topologies) for each hot region, inferring their parameters in addition to the stellar mass and radius. For the family of models considered, the evidence (prior predictive probability of the data) strongly favors a model that permits both hot regions to be located in the same rotational hemisphere. Models wherein both hot regions are assumed to be simply connected circular single-temperature spots, in particular those where the spots are assumed to be reflection-symmetric with respect to the stellar origin, are strongly disfavored. For the inferred configuration, one hot region subtends an angular extent of only a few degrees (in spherical coordinates with origin at the stellar center) and we are insensitive to other structural details; the second hot region is far more azimuthally extended in the form of a narrow arc, thus requiring a larger number of parameters to describe. The inferred mass M and equatorial radius Req are, respectively, -1.34+ M 0.16 0.15 and-12.71+ km 1.19 1.14 , while the compactness = -GM R c 0.156+ eq 2 0.010 0.008 is more tightly constrained; the credible interval bounds reported here are approximately the 16% and 84% quantiles in marginal posterior mass.

T E Riley↗