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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

In Situ High-Temperature Structural Analysis of High-Entropy Rare-Earth Sesquioxides

High-entropy rare-earth (RE) sesquioxides (RE 2 O 3 ) containing five cations in equimolar amounts have been investigated for a variety of applications, but little is known about their polymorphic behavior and coefficient of thermal expansion. Here, in this work, we evaluate the effect of the average ionic radius (AIR) on the polymorphism of high-entropy RE 2 O 3 . Powder samples of compositions 1 (Lu,Y,Ho,Nd,La) 2 O 3 (AIR = 0.938 Å) and 2 (Gd,Eu,Sm,Nd,La) 2 O 3 (AIR = 0.982 Å) were synthesized via a wet chemical method, and bead samples were prepared for aerodynamic levitation by melting the powders in a copper hearth. Structural transitions were monitored upon cooling from the melt to 1000 °C via in situ X-ray diffraction on aerodynamically levitated samples. The phase evolution was liquid, hexagonal H-type, and monoclinic B-type for composition 1 and liquid, cubic X-type, H-type, and B-type for composition 2. Based on their AIR, the general polymorphic transformations of the high-entropy RE 2 O 3 follow the trend of single-RE RE 2 O 3 , but the transition temperatures differ from those of single-RE RE 2 O 3 . The coefficient of thermal expansion values of the B-type phase of compositions 1 and 2 are similar to those of Gd 2 O 3 and previously published high-entropy RE 2 O 3 .

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

Detailed magnetic and structural analysis mapping a robust magnetic C 4 dome in Sr 1 - x Na x Fe 2 As 2

The recently discovered C 4 tetragonal magnetic phase in hole-doped members of the iron-based superconductors provides new insights into the origin of unconventional superconductivity. Previously observed in Ba 1-x Na x Fe 2 As 2 (with A = K, Na), the C 4 magnetic phase exists within the well studied C 2 spin-density wave (SDW) dome, arising just before the complete suppression of antiferromagnetic (AFM) order but after the onset of superconductivity. Here in this paper, we present detailed x-ray and neutron diffraction studies of Sr 1-x Na x Fe 2 As 2 (0.10 ≤ x ≤ 0.60) to determine their structural evolution and the extent of the C 4 phase. Spanning Δx ~ 0.14 in composition, the C 4 phase is found to extend over a larger range of compositions, and to exhibit a significantly higher transition temperature, T r ~ 65K, than in either of the other systems in which it has been observed. The onset of this phase is seen near a composition (x~0:30) where the bonding angles of the Fe 2 As 2 layers approach the perfect 109.46° tetrahedral angle. We discuss the possible role of this return to a higher symmetry environment for the magnetic iron site in triggering the magnetic reorientation and the coupled re-entrance to the tetragonal structure. Finally, we present a new phase diagram, complete with the C 4 phase, and use its observation in a third hole-doped 122 system to suggest the universality of this phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206

The human mannose receptor expressed on macrophages and hepatic endothelial cells scavenges released lysosomal enzymes, glycopeptide fragments of collagen, and pathogenic microorganisms and thus reduces damage following tissue injury. The receptor binds mannose, fucose, or N-acetylglucosamine (GlcNAc) residues on these targets. C-type carbohydrate recognition domain 4 (CRD4) of the receptor contains the site for Ca 2+ -dependent interaction with sugars. To investigate the details of CRD4 binding, glycan array screening was used to identify oligosaccharide ligands. The strongest signals were for glycans that contain either Manα1-2Man constituents or fucosein various linkages. The mechanisms of binding to monosaccharides and oligosaccharide substructures present in many of these ligands were examined in multiple crystal structures of CRD4. Binding of mannose residues to CRD4 results primarily from interaction of the equatorial 3- and 4-OH groups with a conserved principal Ca 2+ common to almost all sugar-binding C-type CRDs. In the Manα1-2Man complex, supplementary interactions with the reducing mannose residue explain the enhanced affinity for this disaccharide. Bound GlcNAc also interacts with the principal Ca 2+ through equatorial 3- and 4-OH groups, whereas fucose residues can bind in several orientations, through either the 2- and 3-OH groups or the 3- and 4-OH groups. Secondary contacts with additional sugars in fucose-containing oligosaccharides, such as the Lewis-a trisaccharide, provide enhanced affinity for these glycans. These results explain many of the biologically important interactions of the mannose receptor with both mammalian glycoproteins and microbes such as yeast and suggest additional classes of ligands that have not been previously identified

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural analysis of substrate recognition by glucose isomerase in Mn2+ binding mode at M2 site in S. rubiginosus

Highlights: • A snapshot of metal binding at the SruGI M2 site in the presence of Mn{sup 2+}. • Metal binding at the M2 site elicits a configuration change at the M1 site. • Glucose molecule can only bind to the M1 site in presence of Mn{sup 2+} at the M2 site. • Two-step sequential process for SruGI substrate recognition, in Mn{sup 2+} at M2 site mode. Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn{sup 2+}, but not in the presence of Mg{sup 2+}. Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn{sup 2+} at the M2 site. Glucose and Mn{sup 2+} at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55–110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85–95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn{sup 2+} binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1990

A parallel-vector algorithm for rapid structural analysis on high-performance computers

A fast, accurate Choleski method for the solution of symmetric systems of linear equations is presented. This direct method is based on a variable-band storage scheme and takes advantage of column heights to reduce the number of operations in the Choleski factorization. The method employs parallel computation in the outermost DO-loop and vector computation via the loop unrolling technique in the innermost DO-loop. The method avoids computations with zeros outside the column heights, and as an option, zeros inside the band. The close relationship between Choleski and Gauss elimination methods is examined. The minor changes required to convert the Choleski code to a Gauss code to solve non-positive-definite symmetric systems of equations are identified. The results for two large scale structural analyses performed on supercomputers, demonstrate the accuracy and speed of the method.

Storaasli, Olaf O.↗
NASA NTRS1990

A parallel-vector algorithm for rapid structural analysis on high-performance computers

A fast, accurate Choleski method for the solution of symmetric systems of linear equations is presented. This direct method is based on a variable-band storage scheme and takes advantage of column heights to reduce the number of operations in the Choleski factorization. The method employs parallel computation in the outermost DO-loop and vector computation via the 'loop unrolling' technique in the innermost DO-loop. The method avoids computations with zeros outside the column heights, and as an option, zeros inside the band. The close relationship between Choleski and Gauss elimination methods is examined. The minor changes required to convert the Choleski code to a Gauss code to solve non-positive-definite symmetric systems of equations are identified. The results for two large-scale structural analyses performed on supercomputers, demonstrate the accuracy and speed of the method.

Storaasli, Olaf O.↗
DOE OSTI2012

Novel Synthesis and Structural Analysis of Ferrihydrite

Naturally occurring ferrihydrite is both impure and difficult to isolate, so the numerous applications and interesting properties of ferrihydrite have spurred the development of various synthetic techniques. Nearly all techniques are based on the hydrolysis of an iron salt and require careful control of temperature, pH, and concentration. In this Article, we report a new synthetic method which does not require such control and is perhaps the fastest and simplest route to synthesizing ferrhydrite. XRD, TEM, BET, and chemical purity characterizations show that the chemically pure, 2-line ferrihydrite product consists of crystallites 2-6 nm in diameter which aggregate to form mesoporous, high surface area agglomerates that are attractive candidates for the many adsorption applications of ferrihydrite. X-ray PDF data were also collected for the ferrihydrite product and refined against the hexagonal structural model recently proposed by Michel et al. These analyses suggest that ferrihydrite has a consistent, repeatable structure independent of variation in the synthetic method, water content of the sample, or particle size of the crystallites, and this structure can be adequately described by the proposed hexagonal model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Substitution behavior of x(Na{sub 0.5}K{sub 0.5})NbO{sub 3}-(1 − x)BaTiO{sub 3} ceramics for multilayer ceramic capacitors by a near edge x-ray absorption fine structure analysis

The doping effect of (Na{sub 0.5}K{sub 0.5})NbO{sub 3} (NKN) as alternatives for rare-earth elements on the electrical properties of BaTiO{sub 3} has been investigated, in terms of their substitution behavior. The dielectric constant of a specimen with x = 0.05 was about 79% higher than that of pure BaTiO{sub 3}, and the temperature coefficient of capacitance was satisfied by the X7R specification. The specimen with x = 0.05 showed the lowest tetragonality among the four compositions and had a fine grain size of <2 μm. Although the addition of NKN decreased the specimen's tetragonality, the electrical properties were enhanced by the formation of defect dipoles and conduction electrons, which resulted from an acceptor and donor substitution behavior. Through O K-edge near edge x-ray absorption fine structure spectroscopy, the practical substitution behavior was defined by the change in Ti 3d orbital states. The energy separation of the Ti 3d orbitals was more apparent with the specimen of x = 0.05, which is related to the donor level from the donor substitution of Nb{sup 5+} ion for Ti-sites. Therefore, the simultaneous substitution of Na{sup +}/K{sup +} and Nb{sup 5+} ions into BaTiO{sub 3} can improve dielectric properties, based on the charge-transfer process.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

A STRUCTURAL ANALYSIS OF STAR-FORMING REGION AFGL 490

We present Spitzer IRAC and MIPS observations of the star-forming region containing intermediate-mass young stellar object (YSO) AFGL 490. We supplement these data with near-IR Two Micron All Sky Survey photometry and with deep Simultaneous Quad Infrared Imaging Device observations off the central high-extinction region. We have more than doubled the known membership of this region to 57 Class I and 303 Class II YSOs via the combined 1-24 {mu}m photometric catalog derived from these data. We construct and analyze the minimum spanning tree of their projected positions, isolating one locally overdense cluster core containing 219 YSOs (60.8% of the region's members). We find this cluster core to be larger yet less dense than similarly analyzed clusters. Although the structure of this cluster core appears irregular, we demonstrate that the parsec-scale surface densities of both YSOs and gas are correlated with a power-law slope of 2.8, as found for other similarly analyzed nearby molecular clouds. We also explore the mass segregation implications of AFGL 490's offset from the center of its core, finding that it has no apparent preferential central position relative to the low-mass members.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Structural analysis and biochemical properties of laccase enzymes from two Pediococcus species

Prokaryotic laccases are emergent biocatalysts. However, they have not been broadly found and characterized in bacterial organisms, especially in lactic acid bacteria. Recently, a prokaryotic laccase from the lactic acid bacterium Pediococcus acidilactici 5930, which can degrade biogenic amines, was discovered. Thus, our study aimed to shed light on laccases from lactic acid bacteria focusing on two Pediococcus laccases, P. acidilactici 5930 and Pediococcus pentosaceus 4816, which have provided valuable information on their biochemical activities on redox mediators and biogenic amines. Both laccases are able to oxidize canonical substrates as ABTS, ferrocyanide and 2,6-DMP, and non-conventional substrates as biogenic amines. With ABTS as a substrate, they prefer an acidic environment and show sigmoidal kinetic activity, and are rather thermostable. Moreover, this study has provided the first structural view of two lactic acid bacteria laccases, revealing new structural features not seen before in other well-studied laccases, but which seem characteristic for this group of bacteria. We believe that understanding the role of laccases in lactic acid bacteria will have an impact on their biotechnological applications and provide a framework for the development of engineered lactic acid bacteria with enhanced properties.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Structural analysis, optical and dielectric function of [Ba{sub 0.9}Ca{sub 0.1}](Ti{sub 0.9}Zr{sub 0.1})O{sub 3} nanocrystals

This work presents the identification of inter-band transitions in the imaginary part of the dielectric function (ε{sub 2}) derived from the Kramers–Kronig analysis for [Ba{sub 0.9}Ca{sub 0.1}](Ti{sub 0.9}Zr{sub 0.1})O{sub 3} (BCZT) nanocrystals synthesized by the modified Pechini method. The analysis started with the chemical identification of the atoms that conform BCZT in the valence loss energy region of a high energy-resolution of electron energy loss spectroscopy. The indirect band energy (E{sub g}) was determined in the dielectric response function. This result is in agreement with the UV-Vis technique, and it obtained an optical band gap of 3.16 eV. The surface and volume plasmon peaks were observed at 13.1 eV and 26.2 eV, respectively. The X-ray diffraction pattern and the Rietveld refinement data of powders heat treated at 700 °C for 1 h suggest a tetragonal structure with a space group (P4 mm) with the average crystal size of 35 nm. The average particle size was determined by transmission electron microscopy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1976

Structural analysis of wind turbine rotors for NSF-NASA Mod-0 wind power system

Preliminary estimates are presented of vibratory loads and stresses in hingeless and teetering rotors for the proposed NSF-NASA Mod-0 wind power system. Preliminary blade design utilizes a tapered tubular aluminum spar which supports nonstructural aluminum ribs and skin and is joined to the rotor hub by a steel shank tube. Stresses in the shank of the blade are calculated for static, rated, and overload operating conditions. Blade vibrations were limited to the fundamental flapping modes, which were elastic cantilever bending for hingeless rotor blades and rigid-body rotation for teetering rotor blades. The MOSTAB-C computer code was used to calculate aerodynamic and mechanical loads. The teetering rotor has substantial advantages over the hingeless rotor with respect to shank stresses, fatigue life, and tower loading. The hingeless rotor analyzed does not appear to be structurally stable during overloads.

Spera, D. A.↗
DOE OSTI2021

Combined Structural Analysis of Core and Image Log of TGH 76-31 South East of Mt Baker, Washington State

Despite active volcanism, few geothermal energy resources have been developed in the Cascades Range. Temperature Gradient Hole 76-31 was drilled to ~440 m measured depth to probe for zones where fractures provide fluid conduits that transport deep volcanic heat to shallow depths that could support baseload, carbon neutral electrical generation. These zones were predicted by a Play Fairway assessment (PFA) of resource potential along a zone 11 km west-southwest of the summit of Mount Baker Volcano. Rock core, temperature logs, and an acoustic image log were obtained. By comparison to outcrops, the core has been initially interpreted as the Chilliwack group comprised of partially metamorphosed basaltic to andesitic volcanics. Core mapping reveals complex, steeply dipping networks of fractures and brecciation along slickensided strike slip faults; clay alteration is common in many of these structures. The majority of fractures are thoroughly healed by layers of chlorite and calcite; preservation of pyrite indicates anoxic conditions. The majority of fracture porosity resides in very dense fractures a few centimeters or less in length. The image log provides good insights into attitude of fractures that fully transect the core, but generally underestimates fracture density. The combination of complex, non-planar fracture zones containing many short fractures and healing promote misinterpretation of natural fracture attitude and density in the image log. The healing and anoxic minerals are consistent with the conductive temperature gradient measured in the well below a shallow isothermal zone, although, several fractures are open or only partially healed and resulted in fluid entries into the well. Here, the equilibrated measured temperature gradient of 64ºC/km and calculated heat flow of 145 mW/m2 is more than twice the regional average, indicating local influence of the Mt Baker magmatic system at the Little Park Creek TGH site.

Cascades↗
DOE OSTI2015

Recalcitrance and structural analysis by water-only flowthrough pretreatment of 13 C enriched corn stover stem

This article presents high temperature water-only continuous flowthrough pretreatment coupled with nuclear magnetic resonance (NMR) as a promising analytical tool to examine the plant cell wall, to understand its recalcitrance (i.e., cell wall resistance to deconstruction), and to probe the chemistry occurring during batch pretreatment of biomass. 13 C-enriched corn stover stems were pretreated at 170 °C for 60 minutes with a hot-water flow rate of 20 mL/min to control fractionation of the cell wall. This approach helped elucidate the nature of plant cell wall chemical recalcitrance and biomass pretreatment chemistry by tracking cell wall fragmentation as a function of time. Fractions of the reactor effluent were collected in a time-resolved fashion and characterized by various NMR techniques to determine the degree and sequence of fragments released, as well as, the chemical composition, molecular structure, and relative molecular weight of those released fragments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Crystallization and Preliminary Structural Analysis of the Giant Haemoglobin from Glossoscolex paulistus at 3.2 Angstrom

Glossoscolex paulistus is a free-living earthworm encountered in south-east Brazil. Its oxygen transport requirements are undertaken by a giant extracellular haemoglobin, or erythrocruorin (HbGp), which has an approximate molecular mass of 3.6 MDa and, by analogy with its homologue from Lumbricus terrestris (HbLt), is believed to be composed of a total of 180 polypeptide chains. In the present work the full 3.6 MDa particle in its cyanomet state was purified and crystallized using sodium citrate or PEG8000 as precipitant. The crystals contain one-quarter of the full particle in the asymmetric unit of the I222 cell and have parameters of a = 270.8 {angstrom}, b = 320.3 {angstrom} and c = 332.4 {angstrom}. Diffraction data were collected to 3.15 {angstrom} using synchrotron radiation on beamline X29A at the Brookhaven National Laboratory and represent the highest resolution data described to date for similar erythrocruorins. The structure was solved by molecular replacement using a search model corresponding to one-twelfth of its homologue from HbLt. This revealed that HbGp belongs to the type I class of erythrocruorins and provided an interpretable initial electron density map in which many features including the haem groups and disulfide bonds could be identified.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Structural analysis of the yeast exosome Rrp6p–Rrp47p complex by small-angle X-ray scattering

Highlights: • We show that S. cerevisiae Rrp6p and Rrp47p stabilise each other in vitro. • We determine molecular envelopes of the Rrp6p–Rrp47p complex by SAXS. • Rrp47p binds at the top of the Rrp6p exonuclease domain. • Rrp47p modulates the activity of Rrp6p on a variety of RNA substrates. • Rrp47p does not affect RNA affinity by Rrp6p. - Abstract: The RNase D-type 3′–5′ exonuclease Rrp6p from Saccharomyces cerevisiae is a nuclear-specific cofactor of the RNA exosome and associates in vivo with Rrp47p (Lrp1p). Here, we show using biochemistry and small-angle X-ray scattering (SAXS) that Rrp6p and Rrp47p associate into a stable, heterodimeric complex with an elongated shape consistent with binding of Rrp47p to the nuclease domain and opposite of the HRDC domain of Rrp6p. Rrp47p reduces the exonucleolytic activity of Rrp6p on both single-stranded and structured RNA substrates without significantly altering the affinity towards RNA or the ability of Rrp6p to degrade RNA secondary structure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗
DOE OSTI2018

Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure–Activity Studies, Biological and X-ray Structural Analysis

The design, synthesis, and biological evaluation of a new class of HIV-1 protease inhibitors containing stereochemically defined fused tricyclic polyethers as the P2 ligands and a variety of sulfonamide derivatives as the P2' ligands are described. A number of ring sizes and various substituent effects were investigated to enhance the ligand–backbone interactions in the protease active site. Inhibitors 5c and 5d containing this unprecedented fused 6–5–5 ring system as the P2 ligand, an aminobenzothiazole as the P2' ligand, and a difluorophenylmethyl as the P1 ligand exhibited exceptional enzyme inhibitory potency and maintained excellent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The umbrella-like P2 ligand for these inhibitors has been synthesized efficiently in an optically active form using a Pauson–Khand cyclization reaction as the key step. The racemic alcohols were resolved efficiently using a lipase catalyzed enzymatic resolution. As a result, two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗