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At least 109 records · Page 6

A Compact X-Ray System for Macromolecular Crystallography

We describe the design and performance of a high flux x-ray system for macromolecular crystallography that combines a microfocus x-ray generator (40 gm FWHM spot size at a power level of 46.5Watts) and a 5.5 mm focal distance polycapillary optic. The Cu K(sub alpha) X-ray flux produced by this optimized system is 7.0 times above the X-ray flux previously reported. The X-ray flux from the microfocus system is also 3.2 times higher than that produced by the rotating anode generator equipped with a long focal distance graded multilayer monochromator (Green optic; CMF24-48-Cu6) and 30% less than that produced by the rotating anode generator with the newest design of graded multilayer monochromator (Blue optic; CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 Watts, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42,540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym) 5.0% for the data extending to 1.7A, and 4.8% for the complete set of data to 1.85A. The amplitudes of the reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

Gubarev, Mikhail↗

A Compact X-Ray System for Macromolecular Crystallography

We describe the design and performance of a high flux x-ray system for a macromolecular crystallography that combines a microfocus x-ray generator (40 micrometer full width at half maximum spot size at a power level of 46.5 W) and a collimating polycapillary optic. The Cu Ka lpha x-ray flux produced by this optimized system through a 500,um diam orifice is 7.0 times greater than the x-ray flux previously reported by Gubarev et al. [M. Gubarev et al., J. Appl. Crystallogr. 33, 882 (2000)]. The x-ray flux from the microfocus system is also 2.6 times higher than that produced by a rotating anode generator equipped with a graded multilayer monochromator (green optic, Osmic Inc. CMF24-48-Cu6) and 40% less than that produced by a rotating anode generator with the newest design of graded multilayer monochromator (blue optic, Osmic, Inc. CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 W, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42 540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym)=5.0% for data extending to 1.70 A, and 4.8% for the complete set of data to 1.85 A. The amplitudes of the observed reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

Gubarev, Mikhail↗

Colour thresholding and objective quantification in bioimaging

Computer imaging is rapidly becoming an indispensable tool for the quantification of variables in research and medicine. Whilst its use in medicine has largely been limited to qualitative observations, imaging in applied basic sciences, medical research and biotechnology demands objective quantification of the variables in question. In black and white densitometry (0-256 levels of intensity) the separation of subtle differences between closely related hues from stains is sometimes very difficult. True-colour and real-time video microscopy analysis offer choices not previously available with monochrome systems. In this paper we demonstrate the usefulness of colour thresholding, which has so far proven indispensable for proper objective quantification of the products of histochemical reactions and/or subtle differences in tissue and cells. In addition, we provide interested, but untrained readers with basic information that may assist decisions regarding the most suitable set-up for a project under consideration. Data from projects in progress at Tulane are shown to illustrate the advantage of colour thresholding over monochrome densitometry and for objective quantification of subtle colour differences between experimental and control samples.

NASA Discipline Neuroscience↗

The Spatial Standard Observer

The spatial standard observer is a computational model that provides a measure of the visibility of a target in a uniform background image or of the visual discriminability of two images. Standard observers have long been used in science and industry to quantify the discriminability of colors. Color standard observers address the spectral characteristics of visual stimuli, while the spatial standard observer (SSO), as its name indicates, addresses spatial characteristics. The SSO is based on a model of human vision. The SSO was developed in a process that included evaluation of a number of earlier mathematical models that address optical, physiological, and psychophysical aspects of spatial characteristics of human visual perception. Elements of the prior models are incorporated into the SSO, which is formulated as a compromise between accuracy and simplicity. The SSO operates on a digitized monochrome still image or on a pair of such images. The SSO consists of three submodels that operate sequentially on the input image(s): 1. A contrast model, which converts an input monochrome image to a luminance contrast image, wherein luminance values are expressed as excursions from, and normalized to, a mean; 2. A contrast-sensitivity-filter model that includes an oblique-effect filter (which accounts for the decline in contrast sensitivity at oblique viewing angles); and 3. A spatial summation model, in which responses are spatially pooled by raising each pixel to the power beta, adding the results, and raising the sum to the 1/b power. In this model, b=2.9 was found to be a suitable value. The net effect of the SSO is to compute a numerical measure of the perceptual strength of the single image, or of the visible difference (denoted the perceptual distance) between two images. The unit of a measure used in the SSO is the just noticeable difference (JND), which is a standard measure of perceptual discriminability. A target that is just visible has a measure of 1 JND.

Watson, Andrew B.↗

Simple, Compact, High-Resolution Monochromatic X-Ray Source for Characterization of X-Ray Calorimeter Arrays

X-ray calorimeters routinely achieve very high spectral resolution, typically a few eV full width at half maximum (FWHM). Measurements of calorimeter line shapes are usually dominated by the natural linewidth of most laboratory calibration sources. This compounds the data acquisition time necessary to statistically sample the instrumental line broadening and can add systematic uncertainty if the intrinsic line shape of the source is not well known. To address these issues, we have built a simple, compact monochromatic x-ray source using channel cut crystals. A commercial x-ray tube illuminates a pair of channel cut crystals that are aligned in a dispersive configuration to select the Kα1 line of the x-ray tube anode material. The entire device, including the x-ray tube, can be easily hand-carried by one person and may be positioned manually or using a mechanical translation stage. The output monochromatic beam provides a collimated image of the anode spot with magnification of unity in the dispersion direction (typically 100 μm–200 μm for the x-ray tubes used here) and is unfocused in the cross-dispersion direction so that the source image in the detector plane appears as a line. We measured output count rates as high as 10 count/s/pixel for the Hitomi soft x-ray spectrometer, which had 819 μm square pixels. We implemented different monochromator designs for energies of 5.4 keV (one design) and 8.0 keV (two designs), which have effective theoretical FWHM energy resolution of 0.125 eV, 0.197 eV, and 0.086 eV, respectively; these are well-suited for optimal calibration measurements of state-of-the art x-ray calorimeters. We measured an upper limit for the energy resolution of our Cr Kα1 monochromator of 0.7 eV FWHM at 5.4 keV, consistent with the theoretical prediction of 0.125 eV.

M A Leutenegger↗

Nonequivalent Atomic Vibrations at Interfaces in a Polar Superlattice

In heterostructures made from polar materials, e.g., AlN–GaN–AlN, the nonequivalence of the two interfaces is long recognized as a critical aspect of their electronic properties; in that, they host different 2D carrier gases. Interfaces play an important role in the vibrational properties of materials, where interface states enhance thermal conductivity and can generate unique infrared-optical activity. The nonequivalence of the corresponding interface atomic vibrations, however, is not investigated so far due to a lack of experimental techniques with both high spatial and high spectral resolution. Herein, the nonequivalence of AlN–(Al 0.65 Ga 0.35 )N and (Al 0.65 Ga 0.35 )N–AlN interface vibrations is experimentally demonstrated using monochromated electron energy-loss spectroscopy in the scanning transmission electron microscope (STEM-EELS) and density-functional-theory (DFT) calculations are employed to gain insights in the physical origins of observations. It is demonstrated that STEM-EELS possesses sensitivity to the displacement vector of the vibrational modes as well as the frequency, which is as critical to understanding vibrations as polarization in optical spectroscopies. The combination enables direct mapping of the nonequivalent interface phonons between materials with different phonon polarizations. Furthermore, the results demonstrate the capacity to carefully assess the vibrational properties of complex heterostructures where interface states dominate the functional properties.

36 MATERIALS SCIENCE↗

Nanoscale Mapping and Defect-Assisted Manipulation of Surface Plasmon Resonances in 2D Bi 2 Te 3 /Sb 2 Te 3 In-Plane Heterostructures

Here, the Bi 2 Te 3 /Sb 2 Te 3 in-plane heterostructure is reported as a low-dimensional tunable chalcogenide well suited as plasmonic building block for the visible-UV spectral range. Electron-driven plasmon excitations of low-dimensional Bi 2 Te 3 /Sb 2 Te 3 are investigated by monochromated electron energy loss spectroscopy spectrum imaging. To resolve the nanoscale spatial distribution of various local plasmonic resonances, singular value decomposition is used to disentangle the spectral data and identify the individual spectral contributions of various corner, edge, and face modes. Furthermore, defect-plasmon interactions are investigated both for nanoscale intrinsic and thermally induced extrinsic polygonal defects (in situ sublimation). Signature of defect-induced red shift ranging from a several hundreds of millielectronvolts to a few electronvolts, broadening of various plasmon response, together with selective enhancement and significant variations in their intensity are detected. This study highlights the presence of a heterointerface and identifies defects as physical tuning pathways to modulate the plasmonic response over a broad spectral range. Finally, the experimental observations are compared qualitatively and validated with numerical simulations using the electron-driven discrete dipole approximation. Low-dimensional Bi 2 Te 3 /Sb 2 Te 3 as a less explored plasmonic system holds great promises as emerging platform for integrated plasmonics. Furthermore, introducing controlled structural defects can open the door for nanoengineering of plasmonic properties in such systems.

36 MATERIALS SCIENCE↗

Revealing Nanoscale Confinement Effects on Hyperbolic Phonon Polaritons with an Electron Beam

Hyperbolic phonon polaritons (HPhPs) in hexagonal boron nitride (hBN) enable the direct manipulation of mid-infrared light at nanometer scales, many orders of magnitude below the free-space light wavelength. High-resolution monochromated electron energy-loss spectroscopy (EELS) facilitates measurement of excitations with energies extending into the mid-infrared while maintaining nanoscale spatial resolution, making it ideal for detecting HPhPs. The electron beam is a precise source and probe of HPhPs, which allows the observation of nanoscale confinement in HPhP structures and directly extract hBN polariton dispersions for both modes in the bulk of the flake and modes along the edge. The measurements reveal technologically important nontrivial phenomena, such as localized polaritons induced by environmental heterogeneity, enhanced and suppressed excitation due to 2D interference, and strong modification of high-momenta excitations such as edge-confined polaritons by nanoscale heterogeneity on edge boundaries. Finally, the work opens exciting prospects for the design of real-world optical mid-infrared devices based on hyperbolic polaritons.

2D materials↗

A multi-wavelength streaked optical pyrometer for dynamic shock compression measurements above 2500 K

This work presents a concept and implementation of a calibrated streaked spectral pyrometer (SSP) temperature diagnostic used in dynamically driven shock experiments on a two-stage gas gun. This system relies upon measuring the total system response using a tunable monochromator, a NIST-traceable calibrated power meter, and a SSP. The diagnostic performance is validated against previously measured temperatures of shock driven z-cut quartz at 99 GPa and 93 GPa. The results are found to agree with the literature to within 5% and are discussed in this manuscript. The experimental setup utilizes measurements from multiple SSP systems per sample, providing several independent measurements and substantially increasing confidence in the extrapolated shock driven sample temperature.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Measurements of ion velocity distributions in a large scale laser-produced plasma

Laser-produced plasma velocity distributions are an important, but difficult quantity to measure. In this work, we present a noninvasive technique for measuring individual charge state velocity distributions of laser-produced plasmas using a high temporal and spectral resolution monochromator. The novel application of this technique is its ability to detect particles up to seven meters from their inception (significantly larger than most laboratory plasma astrophysics experiments, which take place at or below the millimeter scale). The design and assembly of this diagnostic is discussed in terms of maximizing the signal to noise ratio, maximizing the spatial and temporal resolution, and other potential use cases. The analysis and results of this diagnostic are demonstrated by directly measuring the time-of-flight velocity of all ion charge states in a laser produced carbon plasma.

47 OTHER INSTRUMENTATION↗

High-resolution inelastic x-ray scattering at the high energy density scientific instrument at the European X-Ray Free-Electron Laser

We introduce a setup to measure high-resolution inelastic x-ray scattering at the High Energy Density scientific instrument at the European X-Ray Free-Electron Laser (XFEL). The setup uses the Si (533) reflection in a channel-cut monochromator and three spherical diced analyzer crystals in near-backscattering geometry to reach a high spectral resolution. An energy resolution of 44 meV is demonstrated for the experimental setup, close to the theoretically achievable minimum resolution. The analyzer crystals and detector are mounted on a curved-rail system, allowing quick and reliable changes in scattering angle without breaking vacuum. The entire setup is designed for operation at 10 Hz, the same repetition rate as the high-power lasers available at the instrument and the fundamental repetition rate of the European XFEL. Among other measurements, it is envisioned that this setup will allow studies of the dynamics of highly transient laser generated states of matter.

47 OTHER INSTRUMENTATION↗

High-resolution Compton spectroscopy using x-ray microcalorimeters

X-ray Compton spectroscopy is one of the few direct probes of the electron momentum distribution of bulk materials in ambient and operando environments. Herein, we report high-resolution inelastic x-ray scattering experiments with high momentum and energy transfer performed at a storage-ring-based high-energy x-ray light source facility using an x-ray transition-edge sensor (TES) microcalorimeter detector. The performance was compared with a silicon drift detector (SDD), an energy-resolving semiconductor detector, and Compton profiles were measured for lithium and cobalt oxide powders relevant to lithium-ion battery research. Spectroscopic analysis of the measured Compton profiles demonstrates the high-sensitivity to the low- Z elements and oxidation states. The line shape analysis of the measured Compton profiles in comparison with computed Hartree–Fock profiles is usually limited by the resolution of the semiconductor detector. We have characterized an x-ray TES microcalorimeter detector for high-resolution Compton scattering experiments using a bending magnet source at the Advanced Photon Source with a double crystal monochromator, providing monochromatic photon energies near 27.5 keV. The momentum resolution below 0.16 atomic units (a.u.) was measured, yielding an improvement of more than a factor of 7 over a state-of-the-art SDD for the same scattering geometry. Furthermore, the lineshapes of narrow valence and broad core electron profiles of sealed lithium metal were clearly resolved using an x-ray TES compared to smeared and broadened lineshapes observed when using the SDD. High-resolution Compton scattering using the energy-resolving area detector shown here presents new opportunities for spatial imaging of electron momentum distributions for a wide class of materials with applications ranging from electrochemistry to condensed matter physics.

47 OTHER INSTRUMENTATION↗

Dynamic pulse-to-pulse thermal load effects in pulse-train-mode self-seeded X-ray free-electron laser

Thermal load has been a haunting factor that undermines the brightness and coherence of the self-seeded X-ray free-electron laser. Additionally, different from uniformly pulsed mode, in pulse train mode a thermal quasi-steady state of the crystal monochromator may not be reached. This leads to a dynamic thermal distortion of the spectral transmission curves and seed quality degradation. In this paper, the pulse-to-pulse thermal load effects on the spectral transmission curves and seed quality are shown, and some instructive information for the tuning process is provided.

47 OTHER INSTRUMENTATION↗