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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.

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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Purification, crystallization and preliminary X-ray diffraction analysis of the kinase domain of human tousled-like kinase 2

The C-terminal kinase domain of TLK2 (a human tousled-like kinase) has been cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. Tousled-like kinases (TLKs) are an evolutionarily conserved family of serine/threonine protein kinases involved in chromatin dynamics, including DNA replication and repair, transcription and chromosome segregation. The two members of the family reported in humans, namely TLK1 and TLK2, localize to the cell nucleus and are capable of forming homo- or hetero-oligomers by themselves. To characterize the role of TLK2, its C-terminal kinase domain was cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. The latter produced the best diffracting crystal (3.4 Å resolution using synchrotron radiation), with unit-cell parameters a = b = c = 126.05 Å, α = β = γ = 90°. The asymmetric unit contained one protein molecule, with a Matthews coefficient of 4.59 Å{sup 3} Da{sup −1} and a solvent content of 73.23%.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans

YidC, a membrane-protein chaperone/insertase from B. halodurans, was expressed, purified and crystallized in the lipidic cubic phase. An X-ray diffraction data set was collected to 2.4 Å resolution. YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged to space group P2{sub 1}, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9 Å, β = 100.3°. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate

The periplasmic domain of the E. coli aspartate receptor Tar was cloned, expressed, purified and crystallized with and without bound ligand. The crystals obtained diffracted to resolutions of 1.58 and 1.95 Å, respectively. The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni{sup 2+}. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 were grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-Tar2 were grown and diffracted to resolutions of 1.95 and 1.58 Å, respectively. Crystals of apo-Tar1 and Asp-Tar1 adopted space group P4{sub 1}2{sub 1}2, while those of apo-Tar2 and Asp-Tar2 adopted space groups P2{sub 1}2{sub 1}2{sub 1} and C2, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-ray diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

l-Arabinonate dehydratase and d-xylonate dehydratase from the IlvD/EDD family were crystallized by the vapour-diffusion method. Diffraction data sets were collected to resolutions of 2.40 and 2.66 Å from crystals of l-arabinonate dehydratase and d-xylonate dehydratase, respectively. l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P2{sub 1}, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V{sub M} value of 3.2 Å{sup 3} Da{sup −1} and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V{sub M} value of 4.0 Å{sup 3} Da{sup −1} and a solvent content of 69%.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Application of differential resonant high-energy X-ray diffraction to three-dimensional structure studies of nanosized materials: A case study of Pt–Pd nanoalloy catalysts

Atoms in many of the increasingly complex nanosized materials of interest to science and technology do not necessarily occupy the vertices of Bravais lattices. The atomic scale structure of such materials is difficult to determine by traditional X-ray diffraction and so their functional properties remain difficult to optimize by rational design. Here, the three-dimensional structure of Pt x Pd 100– x nanoalloy particles is determined, where x = 0, 14, 36, 47, 64 and 100, by a non-traditional technique involving differential resonant high-energy X-ray diffraction experiments conducted at the K edge of Pt and Pd. The technique is coupled with three-dimensional modeling guided by the experimental total and element-specific atomic pair distribution functions. Furthermore, using DFT (density functional theory) calculation based on the positions of atoms in the obtained three-dimensional structure models, the catalytic performance of Pt–Pd particles is explained. Furthermore, differential resonant high-energy X-ray diffraction is shown to be an excellent tool for three-dimensional structure studies of nanosized materials. The experimental and modeling procedures are described in good detail, to facilitate their wider usage.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Modelling a Transition-Edge Sensor X-Ray Microcalorimeter Linear Array for Compton Profile Measurements and Energy Dispersive Diffraction

Transition-edge sensors (TES) are a type of superconducting detector that offers high energy resolution based on their sharp resistance-temperature feature in the superconducting-to-normal transition. TES X-ray microcalorimeters have typically been designed and used for spectroscopic applications. In this work, we present a design optimization for a TES X-ray microcalorimeter array for high-energy scattering and diffraction measurements. Specifically, Compton scattering provides information about the electron momentum distribution, while energy dispersive diffraction provides structural information about dense engineering materials. Compton scattering and energy dispersive diffraction experiments must be conducted in the very hard X-ray regime (~100 keV), demanding a high X-ray stopping power in the detector; therefore, an absorber with a large heat capacity is needed in conjunction with the TES. In addition, both applications would benefit from an array composed of parallel strips. We propose a design for a TES X-ray microcalorimeter optimized for such applications. In particular, we model the longitudinal position dependence due to the finite thermal diffusion time in the absorber.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Quantitative order-parameter measurement in lattice-mismatched AlInP using precession electron diffraction

Precession electron diffraction (PED) was used to measure the long-range order parameter in lattice-mismatched AlInP epitaxial films under investigation for solid-state-lighting applications. Both double- and single-variant films grown at 620, 650, and 680°C were analyzed in TEM cross-section. PED patterns were acquired in selected-area-diffraction mode through external microscope control using serial acquisition, which allows inline image processing. The integrated peak intensities from experimental patterns were fit using dynamical simulations of diffraction from the ordered domain structures. Included in the structure-factor calculations were mean atomic displacements of the anions (P) due to ordering, which were found by valence-force-field calculations to have a nearly linear dependence on order parameter. A maximum order parameter of S = 0.36 was measured for a double-variant specimen grown at 650°C.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

X-ray plane-wave diffraction effects in a crystal with third-order nonlinearity

The two-wave dynamical diffraction in the Laue geometry has been theoretically considered for a plane X-ray wave in a crystal with a third-order nonlinear response to the external field. An analytical solution to the problem stated is found for certain diffraction conditions. A nonlinear pendulum effect is analyzed. The nonlinear extinction length is found to depend on the incident-wave intensity. A pendulum effect of a new type is revealed: the intensities of the transmitted and diffracted waves periodically depend on the incidentwave intensity at a fixed crystal thickness. The rocking curves and Borrmann nonlinear effect are numerically calculated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°Ð¡, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Spectrometer of Synchrotron Radiation Based on Diffraction Focusing a Divergent Beam Formed by a Compound Refractive Lens

The results of the first experimental realization of a spectrometer based on the effect of diffraction focusing of X rays by a flat single crystal are discussed. A secondary X-ray source with a relatively high angular divergence and small sizes was formed at the focus of a compound refractive lens having 50 beryllium biconcave elements with a curvature radius of 50 μm. The silicon spectrometer crystal was cut in the form of a wedge of variable thickness, oriented perpendicular to the diffraction plane. The reflection 111 was used for energies of 8.3 and 12 keV. To simulate the experiment, a computer program was developed, which takes into account accurately and for the first time the focusing of radiation by the lens and its subsequent diffraction in the crystal. A calculated curve for a monochromatic beam has made it possible to determine the monochromator spectrum with high resolution from experimental data for a polychromatic beam. It is shown that monochromator resolution increases with an increase in the distance from the compound refractive lens to the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Dynamical Theory of X-Ray Diffraction in a Crystal with a Surface Grating of Another Material

A general theory is developed for dynamical X-ray diffraction in a crystal on the surface of which a lateral periodic structure of thin-film lines (strips) of another material is formed. On the basis of the model of edge forces, the fields of elastic lattice displacements in the substrate are calculated that arise as a result of formation of a lateral surface grating (SG). With the use of the formalism of diffraction of spatially restricted X-ray beams, solutions are obtained for the amplitudes of X-ray waves reflected from a crystal with an SG whose chemical composition differs from the composition of the substrate. A numerical simulation is carried out of X-ray diffraction in a silicon substrate with SGs of tungsten and SiO{sub 2} oxide. It is shown that the angular distributions of the scattering intensity by a silicon crystal with tungsten and oxide lines of identical size differ significantly, and the physical nature of such difference is established.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Low missing mass, single and double diffraction dissociation at the LHC

The cross sections for single and double diffraction dissociation at low missing masses are calculated for the LHC energies on the basis of the dual (Regge) model under the assumption of a dominant contribution of the exchange of the Pomeron Regge pole. The model reproduces the rich resonance structure in the region of low missing masses M{sub x}. Diffractively excited states lie on the nucleon trajectory M{sub x} supplemented with the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing-mass dependence of the differential and integrated single and double diffraction dissociation in the kinematical range of present and future LHC measurements are given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Defect identification in simulated Bragg coherent diffraction imaging by automated AI

X-ray Bragg coherent diffraction imaging is a powerful technique for operando and in situ materials characterization and provides a unique means of quantifying the influence of one-dimensional (1D) and two-dimensional (2D) material defects on material response. However, obtaining full images from raw x-ray diffraction data is nontrivial and computationally intensive, precluding real-time experimental feedback. Here, we present a machine learning approach to identify the presence of crystalline line defects (edge and screw) in samples from the raw, 2D, coherent diffraction data without the need for image reconstruction through iterative phase retrieval. Further, we compare different approaches to designing neural networks for this application and demonstrate the potential of automated ML (autoML) approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystallographic variant mapping using precession electron diffraction data

In this work, we developed three methods to map crystallographic variants of samples at the nanoscale by analyzing precession electron diffraction data using a high-temperature shape memory alloy and a VO2 thin film on sapphire as the model systems. The three methods are (I) a user-selecting-reference pattern approach, (II) an algorithm-selecting-reference-pattern approach, and (III) a k-means approach. In the first two approaches, Euclidean distance, Cosine, and Structural Similarity (SSIM) algorithms were assessed for the diffraction pattern similarity quantification. We demonstrated that the Euclidean distance and SSIM methods outperform the Cosine algorithm. We further revealed that the random noise in the diffraction data can dramatically affect similarity quantification. Denoising processes could improve the crystallographic mapping quality. With the three methods mentioned above, we were able to map the crystallographic variants in different materials systems, thus enabling fast variant number quantification and clear variant distribution visualization. The advantages and disadvantages of each approach are also discussed. We expect these methods to benefit researchers who work on martensitic materials, in which the variant information is critical to understand their properties and functionalities.

Crystallographic variant mapping↗
DOE OSTI2022

The crystal structure of Fe2S at 90 GPa based on single-crystal X-ray diffraction techniques

The Fe-S system was explored in a laser-heated diamond-anvil cell at 89(2) GPa and 2380(120) K to better understand the phase stability of Fe 2 S. Upon temperature quenching, crystallites of Fe 2 S were identified, and their structure was investigated using single-crystal X-ray diffraction techniques. At these conditions, Fe 2 S adopts the C23 structure (anti-PbCl 2 , Co 2 P) with space group Pnma (Z = 4). This structure consists of columns of corner-sharing, FeS 4 tetrahedra, and columns of edge-sharing FeS 5 square pyramids linked along edges in the b direction. Sulfur is in ninefold coordination with Fe. This work marks the first high-pressure structural solution and refinement of Fe 2 S synthesized in a multigrain Fe+FeS sample at 90 GPa and 2400 K and establishes the stability of C23 Fe 2 S at these conditions. A previous powder diffraction study reports an orthorhombic Fe 2 S phase with a C37, Co 2 Si-like unit cell above 190 GPa. A C23–C37 structural transition is inferred to explain the previously observed unit-cell parameters at higher pressures and temperatures. These results highlight the utility of applying single-crystal X-ray diffraction techniques to high P-T multigrain samples to explore the structural properties of iron-rich phases in Earth and planetary cores.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Ultrafast electron diffraction from aligned molecules

The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

74 ATOMIC AND MOLECULAR PHYSICS↗