Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structured”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

The structures of penicillin-binding protein 4 (PBP4) and PBP5 from Enterococci provide structural insights into β-lactam resistance

The final steps of cell-wall biosynthesis in bacteria are carried out by penicillin-binding proteins (PBPs), whose transpeptidase domains form the cross-links in peptidoglycan chains that define the bacterial cell wall. These enzymes are the targets of β-lactam antibiotics, as their inhibition reduces the structural integrity of the cell wall. Bacterial resistance to antibiotics is a rapidly growing concern; however, the structural underpinnings of PBP-derived antibiotic resistance are poorly understood. PBP4 and PBP5 are low-affinity, class B transpeptidases that confer antibiotic resistance to Enterococcus faecalis and Enterococcus faecium, respectively. We report the crystal structures of PBP4 (1.8 Å) and PBP5 (2.7 Å) in their apo and acyl-enzyme complexes with the β-lactams benzylpenicillin, imipenem, and ceftaroline. We found that, although these three β-lactams adopt geometries similar to those observed in other class B PBP structures, there are small, but significant, differences that likely decrease antibiotic efficacy. Further, we also discovered that the N-terminal domain extensions in this class of PBPs undergo large rigid-body rotations without impacting the structure of the catalytic transpeptidase domain. Together, our findings are defining the subtle functional and structural differences in the Enterococcus PBPs that allow them to support transpeptidase activity while also conferring bacterial resistance to antibiotics that function as substrate mimics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Canonical symplectic structure and structure-preserving geometric algorithms for Schrödinger–Maxwell systems

An infinite dimensional canonical symplectic structure and structure-preserving geometric algorithms are developed for the photon–matter interactions described by the Schrödinger–Maxwell equations. The algorithms preserve the symplectic structure of the system and the unitary nature of the wavefunctions, and bound the energy error of the simulation for all time-steps. This new numerical capability enables us to carry out first-principle based simulation study of important photon–matter interactions, such as the high harmonic generation and stabilization of ionization, with long-term accuracy and fidelity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Structure and thermodynamics of uranium-containing iron garnets

Use of crystalline garnet as a waste form phase appears to be advantageous for accommodating actinides from nuclear waste. Previous studies show that large amounts of uranium (U) and its analogues such as cerium (Ce) and thorium (Th) can be incorporated into the garnet structure. In this study, we synthesized U loaded garnet phases, Ca 3 U x Zr 2–x Fe 3 O 12 (x = 0.5–0.7), along with the endmember phase, Ca 3 (Zr 2 )SiFe 3+ 2 O 12 , for comparison. The oxidation states of U were determined by X-ray photoelectron and absorption spectroscopies, revealing the presence of mixed pentavalent and hexavalent uranium in the phases with x = 0.6 and 0.7. The oxidation states and coordination environments of Fe were measured using transmission 57 Fe-Mössbauer spectroscopy, which shows that all iron is tetrahedrally coordinated Fe 3+ . U substitution had a significant effect on local environments, the extent of U substitution within this range had a minimal effect on the structure, and unlike in the x = 0 sample, Fe exists in two different environments in the substituted garnets. The enthalpies of formation of garnet phases from constituent oxides and elements were first time determined by high temperature oxide melt solution calorimetry. The results indicate that these substituted garnets are thermodynamically stable under reducing conditions. Furthermore, our structural and thermodynamic analysis further provides explanation for the formation of natural uranium garnet, elbrusite-(Zr), and supports the potential use of Ca 3 U x Zr 2–x Fe 3 O 12 as viable waste form phases for U and other actinides.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures

Whereas the structures of small to medium-sized well folded RNA molecules often can be determined by either X-ray crystallography or NMR spectroscopy, obtaining structural information for large RNAs using experimental, computational, or combined approaches remains a major interest and challenge. RNA is very sensitive to small-angle X-ray scattering (SAXS) due to high electron density along phosphate-sugar backbones, whose scattering contribution dominates SAXS intensity. For this reason, SAXS is particularly useful in obtaining global RNA structural information that outlines backbone topologies and, therefore, molecular envelopes. Such information is extremely valuable in bridging the gap between the secondary structures and three-dimensional topological structures of RNAmolecules, particularly those that have proven difficult to study using other structuredetermination methods. Here we review published results of RNA topological structures derived from SAXS data or in combination with other experimental data, as well as details on RNA sample preparation for SAXS experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structural and chemical ordering of Heusler C o x M n y G e z epitaxial films on Ge (111): Quantitative study using traditional and anomalous x-ray diffraction techniques

Epitaxial films of C o x M n y G e z grown on Ge (111) substrates by molecular-beam-epitaxy techniques have been investigated as a continuous function of composition using combinatorial synchrotron x-ray diffraction (XRD) and x-ray fluorescence (XRF) spectroscopy techniques. A high-resolution ternary epitaxial phase diagram is obtained, revealing a small number of structural phases stabilized over large compositional regions. Ordering of the constituent elements in the compositional region near the full Heusler alloy C o 2 MnGe has been examined in detail using both traditional XRD and a new multiple-edge anomalous diffraction (MEAD) technique. Multiple-edge anomalous diffraction involves analyzing the energy dependence of multiple reflections across each constituent absorption edge in order to detect and quantify the elemental distribution of occupation in specific lattice sites. Results of this paper show that structural and chemical ordering are very sensitive to the Co : Mn atomic ratio, such that the ordering is the highest at an atomic ratio of 2 but significantly reduced even a few percent off this ratio. The in-plane lattice is nearly coherent with that of the Ge substrate, while the approximately 2% lattice mismatch is accommodated by the out-of-plane tetragonal strain. The quantitative MEAD analysis further reveals no detectable amount (<0.5%) of Co-Mn site swapping, but instead high levels (26%) of Mn-Ge site swapping. Increasing Ge concentration above the Heusler stoichiometry ( C o 0.5 M n 0.25 G e 0.25 ) is shown to correlate with increased lattice vacancies, antisites, and stacking faults, but reduced lattice relaxation. The highest degree of chemical ordering is observed off the Heusler stoichiometry with a Ge enrichment of 5 at.%.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Structural characterization of Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3} as a function of temperature using neutron powder diffraction and extended X-ray absorption fine structure techniques

The structure of Bi{sub 2}Te{sub 3} (Seebeck coefficient Standard Reference Material (SRM™ 3451)) and the related phase Sb{sub 2}Te{sub 3} have been characterized as a function of temperature using the neutron powder diffraction (NPD) and the extended X-ray absorption fine structure (EXAFS) techniques. The neutron structural studies were carried out from 20 K to 300 K for Bi{sub 2}Te{sub 3} and from 10 K to 298 K for Sb{sub 2}Te{sub 3}. The EXAFS technique for studying the local structure of the two compounds was conducted from 19 K to 298 K. Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3} are isostructural, with a space group of R3{sup ¯}m. The structure consists of repeated quintuple layers of atoms, Te2-M-Te1-M-Te2 (where M = Bi or Sb) stacking along the c-axis of the unit cell. EXAFS was used to examine the bond distances and static and thermal disorders for the first three shells of Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3} as a function of temperature. The temperature dependencies of thermal disorders were analyzed using the Debye and Einstein models for lattice vibrations. The Debye and Einstein temperatures for the first two shells of Bi{sub 2}Te{sub 3} are similar to those of Sb{sub 2}Te{sub 3} within the uncertainty in the data. However, the Debye and Einstein temperatures for the third shell of Bi-Bi are significantly lower than those of the third shell of Sb-Sb. The Einstein temperature for the third shell is consistent with a soft phonon mode in both Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3}. The lower Einstein temperature of Bi-Bi relative to Sb-Sb is consistent with the lower value of thermal conductivity of Bi{sub 2}Te{sub 3} relative to Sb{sub 2}Te{sub 3}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Contact ion-pair structure in concentrated cesium chloride aqueous solutions: An extended X-ray absorption fine structure study

The hydration and ion pair structure of Cl- ion in aqueous cesium chloride solutions at 0.5, 6 and 11 mol/kg (H2O) has been studied using Extended X-ray Absorption Fine Structure (EXAFS) at the Cl K-edge. The co-refinement of multiple EXAFS datasets shows the hydration structure of the free Cl- ion is consistent with previously reported studies. In concentrated solution the Cl- ion is strongly associated with the cation forming contact ion pairs with 1.6 and 2.8 Cs ions in 6 and 11 mol/kg aqueous CsCl, respectively. The fact that the degree of ion pairing of Cs-Cl is higher than that of both aqueous RbCl and RbBr at the same concentration is an interesting result as it deviates from the Collins’s law of matching water affinities. The reported Cs-Cl ion-pair structure provides a basis for the development and testing of improved interaction potentials leading to more realistic structures from molecular dynamics (MD) simulations. ACKNOWLEDGEMENT VTP was supported by the Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 103.99-2013.19. Work by JLF was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The PNC/XSD facilities at the Advanced Photon Source, and research at these facilities, are supported by DOE/BES, the Canadian Light Source and its funding partners, the University of Washington, and the Advanced Photon Source. Use of the Advanced Photon Source, an Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory, was supported by the DOE under Contract No. DE-AC02-06CH11357.

Pham, Van-Thai↗
DOE OSTI2015

A new multi-scale structure finding algorithm to identify cosmological structure

We introduce a new structure finding algorithm that self-consistently parses large scale cosmological structure into clusters, filaments and voids. This structure finding algorithm probes the structure at multiple scales and classifies the appropriate regions with the most probable structure type and size. We show that it can identify the baryon fraction of intercluster medium and cosmological voids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Structure and thermodynamic stability of UTa 3 O 10 , a U( v )-bearing compound

Heating a mixture of uranyl(VI) nitrate and tantalum(V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3 O 10 . The honey colored to yellow brown crystals of UTa 3 O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6 ] 7- octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6 ] 7- octahedra are formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2 ] + , with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3 O 10 from Ta 2 O 5 , β-U 3 O 7 , and U 3 O 8 has been determined to be 13.1 ± 18.1 kJ mol -1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. The close to zero enthalpy of formation of UTa 3 O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3 O 10 compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗