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At least 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil

The structure of bacterial uridine phosphorylase (UPh) belonging to the NP-I family in complex with 6-methyluracil was determined for the first time at 1.17 Å resolution. The structural features of bacterial UPh from the bacterium Vibrio cholerae (VchUPh) responsible for selectivity toward 6-methyluracil acting as a pseudosubstrate were revealed. The repulsion between the hydrophilic hydroxyl group of the active-site residue Thr93 of VchUPh and the hydrophobic methyl group of 6-methyluracil prevents the oxygen atom O4' of the ribose moiety and the phosphate oxygen atom O3P of ribose 1-phosphate from forming hydrogen bonds with OG1-Thr93, which are essential for the enzymatic reaction. This, apparently, makes VchUPh inactive in the enzymatic synthesis of 6-methyluridine from 6-methyluracil. Hence, Thr93 is the residue, the modification of which will allow VchUPh to catalyze the biotechnologically important synthesis of 6-methyluridine from 6-methyluracil. Taking into account high structural homology of the functionally significant regions of bacterial UPhs, this conclusion is also true for other bacterial UPhs. It was demonstrated that bacterial thymidine phosphorylases of the NP-II family cannot bind 6-methyluracil in a proper conformation required for the catalysis because of a close contact between the 6-methyl group and Phe210.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structural changes and self-activated photoluminescence in reductively annealed Sr{sub 3}AlO{sub 4}F

White light emission of self-activated photoluminescence (PL) in Sr{sub 3}AlO{sub 4}F under 254 nm light is only observed after annealing in a reducing atmosphere of 5%H{sub 2}/95%Ar. High-resolution neutron powder diffraction reveals that the FSr{sub 6} octahedrons and AlO{sub 4} tetrahedrons in this anti-perovskite structure are closer packed in reduced than in air-annealed samples which show no PL. Careful analysis of temperature-dependent neutron powder diffraction data establishes smaller isotropic displacement parameters for Sr(1) and O in Sr{sub 3}AlO{sub 4}F annealed in a reducing atmosphere indicating that the denser packing of the polyhedral sub-units leads to a slightly deeper potential for the Sr(1) and O atoms. Both the air- and reductively-annealed samples have identical thermal expansion within the temperature range between 3 and 350 K. The Debye temperatures were calculated using the atomic displacement parameters and show no significant differences between the air and reductively annealed samples making the Debye temperature a bad proxy for self-activated PL. - Graphical abstract: Annealing Sr{sub 3}AlO{sub 4}F under reducing conditions results in an intense self-activated photoluminescence which is correlated with a denser packing of FSr{sub 6} and AlO{sub 4} polyhedra. - Highlights: • Sr{sub 3}AlO{sub 4}F made in air does not show self-activated photoluminescence. • Only when annealing Sr{sub 3}AlO{sub 4}F in a reducing gas is photoluminescence observed. • FSr{sub 6} and AlO{sub 4} polyhedra in reduced Sr{sub 3}AlO{sub 4}F structure are packed more efficient. • Smaller displacement parameters are found for under-bonded Sr(1) and O sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

HIGH RESOLUTION He i 10830 Å NARROW-BAND IMAGING OF AN M-CLASS FLARE. I. ANALYSIS OF SUNSPOT DYNAMICS DURING FLARING

In this paper, we report our first-step results of high resolution He i 10830 Å narrow-band imaging (bandpass: 0.5 Å) of an M1.8 class two-ribbon flare on 2012 July 5. The flare was observed with the 1.6 m aperture New Solar Telescope at Big Bear Solar Observatory. For this unique data set, sunspot dynamics during flaring were analyzed for the first time. By directly imaging the upper chromosphere, running penumbral waves are clearly seen as an outward extension of umbral flashes; both take the form of absorption in the 10830 Å narrow-band images. From a space–time image made of a slit cutting across a flare ribbon and the sunspot, we find that the dark lanes for umbral flashes and penumbral waves are obviously broadened after the flare. The most prominent feature is the sudden appearance of an oscillating absorption strip inside the ribbon when it sweeps into the sunspot’s penumbral and umbral regions. During each oscillation, outwardly propagating umbral flashes and subsequent penumbral waves rush out into the inwardly sweeping ribbon, followed by a return of the absorption strip with similar speed. We tentatively explain the phenomena as the result of a sudden increase in the density of ortho-helium atoms in the area of the sunspot being excited by the flare’s extreme ultraviolet illumination. This explanation is based on the observation that 10830 Å absorption around the sunspot area gets enhanced during the flare. Nevertheless, questions are still open and we need further well-devised observations to investigate the behavior of sunspot dynamics during flares.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Comparison of Atomic and Electronic Structures of Silica and Sodium Silicate Glasses

Glass scintillators may hold great promise for low-cost, large-volume, shapeable radiation detectors. However, the light yield and energy resolution of glass scintillators to-date have been more than an order of magnitude worse than for crystalline scintillators and far from the theoretical limits. Glass scintillators are fabricated by dissolving rare-earth dopants into a glass matrix. Their operation relies on gamma ray absorption in the glass generating electrons and holes that must migrate to a rare-earth activator atom to emit light. The transport of carriers in the glass limits the performance, particularly in glasses where the solubility limit of activator is low, since carriers may recombine non-radiatively before reaching an activator atom. In this work, we aim to use atomistic simulations to discover the nature of electron transport in specific glass materials and how it may be enhanced by tuning the composition or forming process. The analysis proceeds in two steps: generation of a computational model of a given glass’s atomic structure, then extraction of the electronic structure to correlate electronic structure with carrier transport. Here we report results for two glasses: silica (SiO 2 ) and sodium silicate (Na 2 O:SiO 2 ). Multiple compositions of the latter are studied, namely Na 2 O:SiO 2 ratios of of 1:2, 1:3, and 3:7, with most results focused on the 3:7 composition. The overall goal is to establish a computational framework that can mimic a range of experimental glass structures by tuning computational parameters in the construction of the glass model, and enable studies of the correlation between atomic structure and electronic transport properties of the glass materials. These correlations would direct synthesis parameters for a given glass to optimize its transport properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Crystal structures and formation mechanisms of boron-rich tungsten borides

Boron-rich tungsten borides tend to adopt mechanically unfavorable layered structures but experimentally exhibit excellent mechanical properties rivalling traditional superhard solids. Unravelling the contraindicated structure-property relationship, however, has been impeded by their structural ambiguities because of the difficulty in probing boron and atomic deficiency of these borides. Here, we study crystal structures of boron-rich tungsten borides WB 3+x and WB 2+x by neutron diffraction based on high-quality samples prepared by a high-pressure method, leading to definitive structural resolutions for both borides with unique compositions of WB 5.14 and WB 2.34 . Combined with theoretical calculations, their structural stability is revealed to be closely related to atomic deficiency, which is governed by the valence-band filling with an optimal valence-electron concentration of ~10 per cell. The presence of interstitial boron trimers at the vacant W : 2b sites in WB 5.14 alters the crystal symmetry, making the Wyckoff 2d site more favorably occupied by W, rather than the 2c site, as previously misassigned. Here, the staggered planar boron layers and wrinkled boron bonding in WB 2.34 are identified to be crucial for stabilizing its structure. These findings unveil the longstanding structural mysteries of boron-rich tungsten borides and offer powerful insights for rational design of borides by defect chemistry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Sub-Ångstrom electric field measurements on a universal detector in a scanning transmission electron microscope

Scanning transmission electron microscopy (STEM) excels in accessing atomic-scale structure and chemistry. Enhancing our ability to directly image the functionalities of local features in materials has become one of the most important topics in the future development of STEM. Recently, differential phase contrast (DPC) imaging has been utilized to map the internal electric and magnetic fields in materials from nanoscale features such as p–n junctions, skyrmions, and even from individual atoms. Here, we use an ultra-low noise SCMOS detector in as the diffraction plane camera to collect four-dimensional (4D) datasets. The high angular resolution, efficient high-SNR acquisition, and modifiability of the camera allow it to function as a universal detector, where STEM imaging configurations, such as DPC, bright field, annular bright field, and annular dark field can all be reconstructed from a single 4D dataset. By examining a distorted perovskite, DyScO3, which possesses projected lattice spacings as small as 0.83 Å, we demonstrate DPC spatial resolution almost reaching the information limit of a 100 keV electron beam. In addition, the perovskite has ordered O-coordinations with alternating octahedral tilts, which can be quantitatively measured with single degree accuracy by taking advantage of DPC’s sensitivity to light atoms. The results, acquired on a standard Ronchigram camera as opposed to a specialized DPC detector, open up new opportunities to understand and design functional materials and devices that involve lattice and charge coupling at nano- and atomic-scales.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Atomistic Defect Makes a Phase Plate for the Generation and High-Angular Splitting of Electron Vortex Beams

Topological defects in solid-state materials by breaking the translational symmetry offer emerging properties that are not present in their parental phases. For example, edge dislocations—the 2π phase-winding topological defects—in antiferromagnetic NiO crystals can exhibit ferromagnetic behaviors. We study how these defects could give rise to topological orders when they interact with a high-energy electron beam. To probe this interaction, we formed a coherent electron nanobeam in a scanning transmission electron microscope and recorded the far-field transmitted patterns as the beam steps through the edge dislocation core in [001] NiO. Surprisingly, we found the amplitude patterns of the <020> Bragg disks evolve in a similar manner to the evolution of an annular solar eclipse. Using the ptychographic technique, we recovered the missing phase information in the diffraction plane and revealed the topological phase vortices in the diffracted beams. Through atomic topological defects, the wave function of electrons can be converted from plane wave to electron vortex. Technologically, this approach provides a feasible route for the fabrication of phase plates that can generate electron vortex beams with an angular separation that is three orders of magnitude larger than what traditional nanofabrication technology can offer. This advance will enable the collection of magnetic circular dichroism spectra with high spatial resolution and high efficiency, boosting the understanding of the relationship between symmetry breaking and magnetic property of individual topological defect at the atomic scale.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Control of Epitaxial BaFe 2 As 2 Atomic Configurations with Substrate Surface Terminations

Atomic layer controlled growth of epitaxial thin films of unconventional superconductors opens the opportunity to discover novel high temperature superconductors. For instance, the interfacial atomic configurations may play an important role in superconducting behavior of monolayer FeSe on SrTiO 3 and other Fe-based superconducting thin films. Here, we demonstrate a selective control of the atomic configurations in Co-doped BaFe 2 As 2 epitaxial thin films and its strong influence on superconducting transition temperatures by manipulating surface termination of (001) SrTiO 3 substrates. In a combination of first-principles calculations and high-resolution scanning transmission electron microscopy imaging, we show that Co-doped BaFe 2 As 2 on TiO 2 -terminated SrTiO 3 is a tetragonal structure with an atomically sharp interface and with an initial Ba layer. In contrast, Co-doped BaFe 2 As 2 on SrO-terminated SrTiO 3 has a monoclinic distortion and a BaFeO 3-x initial layer. Furthermore, the superconducting transition temperature of Co-doped BaFe 2 As 2 ultrathin films on TiO 2 -terminated SrTiO 3 is significantly higher than that on SrO-terminated SrTiO 3 , which we attribute to shaper interfaces with no lattice distortions. As a result, this study allows the design of the interfacial atomic configurations and the effects of the interface on superconductivity in Fe-based superconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Low-energy calibration of SuperCDMS HVeV cryogenic silicon calorimeters using Compton steps

Cryogenic calorimeters for low-mass dark matter searches have achieved sub-eV energy resolutions, driving advances in both low-energy calibration techniques and our understanding of detector physics. The energy deposition spectrum of gamma rays scattering off target materials exhibits step-like features, known as Compton steps, near the binding energies of atomic electrons. Here, we demonstrate a successful use of Compton steps for sub-keV calibration of cryogenic silicon calorimeters, utilizing four SuperCDMS High-Voltage eV-resolution detectors operated with 0 V bias across the crystal. This new calibration at 0 V is compared with the established high-voltage calibration using optical photons. The comparison indicates that the detector response at 0 V is about 30% weaker than expected, highlighting challenges in detector response modeling for low-mass dark matter searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Direct Observation of Infrared Plasmonic Fano Antiresonances by a Nanoscale Electron Probe

In this report, we exploit recent breakthroughs in monochromated aberration-corrected scanning transmission electron microscopy (STEM) to resolve infrared plasmonic Fano antiresonances in individual nanofabricated disk-rod dimers. Using a combination of electron energy-loss spectroscopy and theoretical modeling, we investigate and characterize a subspace of the weak coupling regime between quasi-discrete and quasi-continuum localized surface plasmon resonances where infrared plasmonic Fano antiresonances appear. Our research illustrates the capability of STEM instrumentation to experimentally observe nanoscale plasmonic responses that were previously the domain only of higher-resolution infrared spectroscopies.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Elastic-properties measurement at high temperatures through contact resonance atomic force microscopy

Miniaturization of products and need for further improvement of machines performance introduce new serious challenges in materials characterization. In particular non-destructive mechanical testing in the sub-micrometer scale is needed to better understand and improve micro-manufacturing operations. To this regard, some open issues are of particular interest: low depth of penetration, high lateral resolution and measurements at elevated temperatures. An interesting solution is given by acoustic microscopy techniques, which can be successfully implemented for advanced research in surface elasticity, allowing fast direct and non-destructive measurement of Young’s modulus and related surface parameters. In this work an instrument set up for Contact Resonance Atomic Force Microscopy is proposed, where the sample with is coupled to a heating stage and a piezoelectric transducer directly vibrate the cantilever during scanning, in order to allow exploitation of high resolution measurements at relatively high temperatures. Such instrument set up was undergone a set of calibration experiments in order to allow not only qualitative but also quantitative characterization of surfaces. The work was completed with a feasibility study with mechanical and topography measurements at temperatures as high as 150°C, with lateral resolution lower than 100 nm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Site-Selective Atomic Layer Deposition at Thermally Generated Surface Oxygen Vacancies on Rutile TiO 2

Unique atomic arrangements (i.e., defects) on material surfaces may exhibit distinctive reactivity that affords opportunities for selective surface chemistry exclusively at those sites. While theoretically appealing, site-selective atomic layer deposition (ALD) processes remain largely unrealized experimentally. Here we provide evidence for site-selective ALD that exclusively targets oxygen vacancies thermally generated at the surface of TiO 2 single crystals. High-resolution in situ ellipsometry reveals the nucleation behavior of dimethylaluminum isopropoxide (DMAI) and water at process conditions precisely tuned for selective hydroxylation of surface defects. An island growth model for nucleation and atomic force microscopy (AFM) imaging are consistent with a site-selective growth mechanism that depends on the surface oxygen vacancy density. This approach to direct ALD reactions at defective surface sites may provide future opportunities for targeted remediation of electronically imperfect interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Kelvin Probe Force Microscopy for High-Resolution Imaging of Hydrogen in Steel and Aluminum Alloys

SRNL is working with Sandia NL, Pacific Northwest NL and Oak Ridge NL in the H-Mat consortium with the objective of developing materials with a higher resistance to hydrogen attack. Understanding the mechanism of hydrogen interactions in metal alloys is continually a topic of interest for applications which involve the long-term storage of hydrogen. Atomic hydrogen segregates to regions of extended defects, such as grain and phase boundaries, and can cause stress and premature cracking through a process known as hydrogen embrittlement. Advanced microstructural imaging techniques, with minimal sample preparation needs, that are capable of resolving hydrogen segregation at the nanometer scale is needed. Current imaging technologies to aid in understanding the effects of hydrogen in metals involve primarily fractography after mechanical testing. Hydrogen segregated at the surface and particularly at surface defect sites changes the local work function of the material. This can be measured by Kelvin Probe Force Microscopy, KPFM, a variant of atomic force microscopy (AFM). KPFM produces surface potential images and is capable of measuring the local change in work function of surfaces with very high spatial resolution. The spatial resolution of KPFM is optimally ~5 nm, yielding very high hydrogen concentration/microstructure coloration capabilities. By locating the presence of hydrogen and its relationship with extended defects, it may be possible to develop microstructures less susceptible to hydrogen embrittlement. The objective of this effort is to assess the utility of KPFM to determine the H 2 concentration profiles surrounding complex microstructural features in high strength steel and aluminum alloys subjected to high pressure hydrogen exposure.

08 HYDROGEN↗
DOE OSTI2017

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and the acetate ion is different from that reported by Yoshimoto et al.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Au 329– x Ag x (SR) 84 Nanomolecules: Plasmonic Alloy Faradaurate-329

Though significant progress has been made to improve the monodispersity of larger (>10 nm) alloy metal nanoparticles, there still exists a significant variation in nanoparticle composition, ranging from ±1000s of atoms. Here in this paper, for the first time, we report the synthesis of atomically precise (±0 metal atom variation) Au 329–x Ag x (SCH 2 CH 2 Ph) 84 alloy nanomolecules. The composition was determined using high resolution electrospray ionization mass sp ectrometry. In contrast to larger (>10 nm) Au–Ag nanoparticles, the surface plasmon resonance (SPR) peak does not show a major shift, but a minor ~10 nm red-shift, upon increasing silver content. The intensity of the SPR peak also varies in an intriguing manner, where a dampening is observed with medium silver incorporation, and a significant sharpening is observed upon higher Ag content. The report outlines (a) an unprecedented advance in nanoparticle mass spectrometry of high mass at atomic precision; and (b) the unexpected optical behavior of Au–Ag alloys in the region where nascent SPR emerges; specifically, in this work, the SPR-like peak does not show a major ~100 nm blue-shift with Ag alloying of Au 329 nanomolecules, as shown to be common in larger nanoparticles.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Nonuniform Ionic and Electronic Transport of Ceramic and Polymer/Ceramic Hybrid Electrolyte by Nanometer-Scale Operando Imaging for Solid-State Battery

Replacing the liquid electrolyte in lithium batteries with solid-state ion conductor is promising for next-generation energy storage that is safe and has high energy density. In this work, nanometer-resolution ionic and electronic transport imaging of Li 3 PS 4 (LPS), a solid-state electrolyte (SSE), is reported. This nm resolution is achieved by using a logarithm-scale current amplifier that enhances the current sensitivity to the fA range. Large fluctuations of ion current—one to two orders of magnitude on the LPS and on the LPS region of a polymer/LPS bulk hybrid SSE—that must be mitigated to eliminate Li dendrite formation and growth, are found. This ion current fluctuation is understood in terms of highly anisotropic transport kinetic barriers along the different crystalline axes due to different grain orientations in the polycrystalline and glass ceramic materials. The results on the bulk hybrid SSE show a sharp transition of ionic and electronic transport at the LPS/polymer boundary and decreases in average ionic current with decreasing polyimine particle size and with extensive cycling. The results elucidate the mechanism of polyimine extension into interparticles to prevent Li dendrite growth. This work opens up novel characterization of charge transport, which relates to Li plating and stripping for solid-state-batteries.

Li3PS4↗