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At least 91 records · Page 5

Spatial Phase Imaging

Frequently, scientists grow crystals by dissolving a protein in a specific liquid solution, and then allowing that solution to evaporate. The methods used next have been, variously, invasive (adding a dye that is absorbed by the protein), destructive (crushing protein/salt-crystal mixtures and observing differences between the crushing of salt and protein), or costly and time-consuming (X-ray crystallography). In contrast to these methods, a new technology for monitoring protein growth, developed in part through NASA Small Business Innovation Research (SBIR) funding from Marshall Space Flight Center, is noninvasive, nondestructive, rapid, and more cost effective than X-ray analysis. The partner for this SBIR, Photon-X, Inc., of Huntsville, Alabama, developed spatial phase imaging technology that can monitor crystal growth in real time and in an automated mode. Spatial phase imaging scans for flaws quickly and produces a 3-D structured image of a crystal, showing volumetric growth analysis for future automated growth.

Source record↗

Phase sensitive x-ray diffraction imaging of defects in biological macromolecular crystals

Conventional x-ray diffraction topography is currently used to map defects in the bulk of protein crystals, but the lack of sufficient contrast is frequently a limiting factor. We experimentally demonstrate that this barrier can be circumvented using a method that combines phase sensitive and diffraction imaging principles. Details of defects revealed in tetragonal lysozyme and cubic ferritin crystals are presented and discussed. The approach enabling the detection of the phase changes of diffracted x rays should prove to be useful in the study of defect structures in a broad range of biological macromolecular crystals.

Muramidase/chemistry↗

Analytical Tools for Cloudscope Ice Measurement

The cloudscope is a ground or aircraft instrument for viewing ice crystals impacted on a sapphire window. It is essentially a simple optical microscope with an attached compact CCD video camera whose output is recorded on a Hi-8 mm video cassette recorder equipped with digital time and date recording capability. In aircraft operation the window is at a stagnation point of the flow so adiabatic compression heats the window to sublimate the ice crystals so that later impacting crystals can be imaged as well. A film heater is used for ground based operation to provide sublimation, and it can also be used to provide extra heat for aircraft operation. The compact video camera can be focused manually by the operator, and a beam splitter - miniature bulb combination provide illumination for night operation. Several shutter speeds are available to accommodate daytime illumination conditions by direct sunlight. The video images can be directly used to qualitatively assess the crystal content of cirrus clouds and contrails. Quantitative size spectra are obtained with the tools described in this report. Selected portions of the video images are digitized using a PCI bus frame grabber to form a short movie segment or stack using NIH (National Institute of Health) Image software with custom macros developed at DRI. The stack can be Fourier transform filtered with custom, easy to design filters to reduce most objectionable video artifacts. Particle quantification of each slice of the stack is performed using digital image analysis. Data recorded for each particle include particle number and centroid, frame number in the stack, particle area, perimeter, equivalent ellipse maximum and minimum radii, ellipse angle, and pixel number. Each valid particle in the stack is stamped with a unique number. This output can be used to obtain a semiquantitative appreciation of the crystal content. The particle information becomes the raw input for a subsequent program (FORTRAN) that synthesizes each slice and separates the new from the sublimating particles. The new particle information is used to generate quantitative particle concentration, area, and mass size spectra along with total concentration, solar extinction coefficient, and ice water content. This program directly creates output in html format for viewing with a web browser.

Arnott, W. Patrick↗

X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation

Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage–cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.

59 BASIC BIOLOGICAL SCIENCES↗

Optical stereo video signal processor

An otpical video signal processor is described which produces a two-dimensional cross-correlation in real time of images received by a stereo camera system. The optical image of each camera is projected on respective liquid crystal light valves. The images on the liquid crystal valves modulate light produced by an extended light source. This modulated light output becomes the two-dimensional cross-correlation when focused onto a video detector and is a function of the range of a target with respect to the stereo camera. Alternate embodiments utilize the two-dimensional cross-correlation to determine target movement and target identification.

Craig, G. D.↗

A new real-time non-coherent to coherent light image converter - The hybrid field effect liquid crystal light valve

A new, high-performance device has been developed for application to real-time coherent optical data processing. The new device embodies a CdS photoconductor, a CdTe light-absorbing layer, a dielectric mirror, and a liquid crystal layer sandwiched between indium-tin-oxide transparent electrodes deposited on optical quality glass flats. The noncoherent image is directed onto the photoconductor; this reduces the impedance of the photoconductor, thereby switching the ac voltage that is impressed across the electrodes onto the liquid crystal to activate the device. The liquid crystal is operated in a hybrid field effect mode. It utilizes the twisted nematic effect to create a dark off-state and the optical birefringence effect to create the bright on-state. The liquid crystal modulates the polarization of the coherent read-out light so an analyzer must be used to create an intensity modulated output beam.

Grinberg, J.↗

Structural relations between collagen and mineral in bone as determined by high voltage electron microscopic tomography

Aspects of the ultrastructural interaction between collagen and mineral crystals in embryonic chick bone have been examined by the novel technique of high voltage electron microscopic tomography to obtain three-dimensional information concerning extracellular calcification in this tissue. Newly mineralizing osteoid along periosteal surfaces of mid-diaphyseal regions from normal chick tibiae was embedded, cut into 0.25 microns thick sections, and documented at 1.0 MV in the Albany AEI-EM7 high voltage electron microscope. The areas of the tissue studied contained electron dense mineral crystals associated with collagen fibrils, some marked by crystals disposed along their cylindrically shaped lengths. Tomographic reconstructions of one site with two mineralizing fibrils were computed from a 5 degrees tilt series of micrographs over a +/- 60 degrees range. Reconstructions showed that the mineral crystals were platelets of irregular shape. Their sizes were variable, measured here up to 80 x 30 x 8 nm in length, width, and thickness, respectively. The longest crystal dimension, corresponding to the c-axis crystallographically, was generally parallel to the collagen fibril long axis. Individual crystals were oriented parallel to one another in each fibril examined. They were also parallel in the neighboring but apparently spatially separate fibrils. Crystals were periodically (approximately 67 nm repeat distance) arranged along the fibrils and their location appeared to correspond to collagen hole and overlap zones defined by geometrical imaging techniques. The crystals appeared to be continuously distributed along a fibril, their size and number increasing in a tapered fashion from a relatively narrow tip containing smaller and infrequent crystals to wider regions having more densely packed and larger crystals. Defined for the first time by direct visual 3D imaging, these data describe the size, shape, location, orientation, and development of early crystals in normal bone collagen. The results suggest that platelet-shaped crystals are arranged in channels or grooves which are formed by collagen hole zones in register and that crystal sizes may exceed the dimensions of hole zones. Such data agree with those from mineral-matrix interaction in normally calcifying avian tendon obtained by similar high voltage tomographic means, but in addition they indicate a possible gradual and continuous deposition of crystals in collagen of bone unlike tendon and imply that individual collagen fibrils in local regions of osteoid are organized such that they all may be aligned in a coherent manner.

NASA Discipline Number 40-40↗

Optical storage device

A new holographic image storage device which uses four-wave mixing in two photorefractive crystals is described. Photorefractive crystals promise information storage densities on the order of 10(exp 9) to 10(exp 12) bits per cubic centimeter at real-time rates. Several studies in recent years have investigated the use of photorefractive crystals for storing holographic image information. However, all of the previous studies have focused on techniques for storing information in a single crystal. The disadvantage of using a single crystal is that the read process is destructive. Researchers have developed techniques for fixing the information in a crystal so that it may be read many times. However, when fixed, the information cannot be readily erased and overwritten with new information. It two photorefractive crystals are used, holographic image information may be stored dynamically. That is, the stored image information may be read out more than once, and it may be easily erased and overwritten with new image information.

Welch, Sharon S.↗

Imaging of gamma-Irradiated Regions of a Crystal

A holographic technique has been devised for generating a visible display of the effect of exposure of a photorefractive crystal to gamma rays. The technique exploits the space charge that results from trapping of electrons in defects induced by gamma rays. The technique involves a three-stage process. In the first stage, one writes a holographic pattern in the crystal by use of the apparatus shown in Figure 1. A laser beam of 532-nm wavelength is collimated and split into signal and reference beams by use of a polarizing beam splitter. On its way to the crystal, the reference beam goes through a two-dimensional optical scanner that contains two pairs of lenses (L1y, L2y and L1x,L2x) and mirrors M1 and M2, which can be rotated by use of micrometer drives to make fine adjustments. The signal beam is sent through a spatial light modulator that imposes the holographic pattern, then through two imaging lenses L(sub img) on its way to the crystal. An aperture is placed at the common focus of lenses Limg to suppress high-order diffraction from the spatial light modulator. The hologram is formed by interference between the signal and reference beams. A camera lens focuses an image of the interior of the crystal onto a charge-coupled device (CCD). If the crystal is illuminated by only the reference beam once the hologram has been formed, then an image of the hologram is formed on the CCD: this phenomenon is exploited to make visible the pattern of gamma irradiation of the crystal, as described next. In the second stage of the process, the crystal is removed from the holographic apparatus and irradiated with rays at a dose of about 100 krad. In the third stage of the process, the crystal is remounted in the holographic apparatus in the same position as in the first stage and illuminated with only the reference beam to obtain the image of the hologram as modified by the effect of the rays. The orientations of M1 and M2 can be adjusted slightly, if necessary, to maximize the intensity of the image. Figure 2 shows such an image that was formed in a crystal of Fe:LiNbO3.

Dragoi, Danut↗

High strain-rate strength response of single crystal tantalum through in-situ hole closure imaging experiments

The properties of crystalline materials often depend on directionality and operating conditions. Specifically, the strength of materials can depend anisotropically on crystal direction and the loading condition. To probe these effects, a preliminary series of high strain-rate (> 105/s) strength plate-impact hole closure experiments were performed on high purity single crystal Tantalum cubes. The orientation of the single crystals with respect to impact/loading were varied to provide data to inform crystal plasticity modeling efforts. The experiments consist of in-situ high-resolution X-ray radiographic imaging of the hole collapse under dynamic compression conditions to infer the material strength via its resistance to closure at increasing levels of plastic strain. The experiments are compared against hydrocode simulation predictions. Here, a comparison with simple elastic perfectly plastic strength model predictions is presented to elucidate the response of the different crystal orientations at high strain-rate and large plastic strains.

36 MATERIALS SCIENCE↗

Identification and control of a multizone crystal growth furnace

This paper presents an intelligent adaptive control system for the control of a solid-liquid interface of a crystal while it is growing via directional solidification inside a multizone transparent furnace. The task of the process controller is to establish a user-specified axial temperature profile and to maintain a desirable interface shape. Both single-input-single-output and multi-input-multi-output adaptive pole placement algorithms have been used to control the temperature. Also described is an intelligent measurement system to assess the shape of the crystal while it is growing. A color video imaging system observes the crystal in real time and determines the position and the shape of the interface. This information is used to evaluate the crystal growth rate, and to analyze the effects of translational velocity and temperature profiles on the shape of the interface. Creation of this knowledge base is the first step to incorporate image processing into furnace control.

Batur, C.↗

Double-Diffusive Convection During Growth of Halides and Selenides

Heavy metal halides and selenides have unique properties which make them excellent materials for chemical, biological and radiological sensors. Recently it has been shown that selenohalides are even better materials than halides or selenides for gamma-ray detection. These materials also meet the strong needs of a wide band imaging technology to cover ultra-violet (UV), midwave infrared wavelength (MWIR) to very long wavelength infrared (VLWIR) region for hyperspectral imager components such as etalon filters and acousto-optic tunable filters (AO). In fact AOTF based imagers based on these materials have some superiority than imagers based on liquid crystals, FTIR, Fabry-Perot, grating, etalon, electro-optic modulation, piezoelectric and several other concepts. For example, broadband spectral and imagers have problems of processing large amount of information during real-time observation. Acousto-Optic Tunable Filter (AOTF) imagers are being developed to fill the need of reducing processing time of data, low cost operation and key to achieving the goal of covering long-wave infrared (LWIR). At the present time spectral imaging systems are based on the use of diffraction gratings are typically used in a pushbroom or whiskbroom mode. They are mostly used in systems and acquire large amounts of hyperspectral data that is processed off-line later. In contrast, acousto-optic tunable filter spectral imagers require very little image processing, providing new strategies for object recognition and tracking. They are ideally suited for tactical situations requiring immediate real-time image processing. But the performance of these imagers depends on the quality and homogeneity of acousto-optic materials. In addition for many systems requirements are so demanding that crystals up to sizes of 10 cm length are desired. We have studied several selenides and halide crystals for laser and AO imagers for MWIR and LWIR wavelength regions. We have grown and fabricated crystals of several materials such as mercurous chloride, mercurous bromide, mercurous iodide, lead chloride lead bromide, lead iodide, thallium arsenic selenide, gallium selenide, zince sulfide zinc selenide and several crystals into devices. We have used both Bridgman and physical vapor transport (PVT) crystal growth methods. In the past have examined PVT growth numerically for conditions where the boundary of the enclosure is subjected to a nonlinear thermal profile. Since past few months we have been working on binary and ternary materials such as selenoiodides, doped zinc sulfides and mercurous chloro bromide and mercurous bromoiodides. In the doped and ternary materials thermal and solutal convection play extremely important role during the growth. Very commonly striations and banding is observed. Our experiments have indicated that even in highly purified source materials, homogeneity in 1-g environment is very difficult. Some of our previous numerical studies have indicated that gravity level less than 10-4 (-g) helps in controlling the thermosolutal convection. We will discuss the ground based growth results of HgClxBr(1-x) and ZnSe growth results for the mm thick to large cm size crystals. These results will be compared with our microgravity experiments performed with this class of materials. For both HgCl-HgBr and ZnS-ZnSe the lattice parameters of the mixtures obey Vagard's law in the studied composition range. The study demonstrates that properties are very anisotropic with crystal orientation, and performance achievement requires extremely careful fabrication to utilize highest figure of merit. In addition, some parameters such as crystal growth fabrication, processing time, resolution, field of view and efficiency will be described based on novel solid solution materials. It was predicted that very similar to the pure compounds solid solutions also have very large anisotropy, and very precise oriented and homogeneous bulk and thin film crystals is required to achieve maximum performance of laser or imagers. Some of the parameters controlling the homogeneity such as thermos-solutal convection driven forces can be controlled in microgravity environments to utilize the benefits of these unique materials.

Singh, N. B.↗

A New Digital Holographic Instrument for Measuring Microphysical Properties of Contrails in the SASS (Subsonic Assessment) Program

SPEC incorporated designed, built and operated a new instrument, called a pi-Nephelometer, on the NASA DC-8 for the SUCCESS field project. The pi-Nephelometer casts an image of a particle on a 400,000 pixel solid-state camera by freezing the motion of the particle using a 25 ns pulsed, high-power (60 W) laser diode. Unique optical imaging and particle detection systems precisely detect particles and define the depth-of-field so that at least one particle in the image is almost always in focus. A powerful image processing engine processes frames from the solid-state camera, identifies and records regions of interest (i.e. particle images) in real time. Images of ice crystals are displayed and recorded with 5 micron pixel resolution. In addition, a scattered light system simultaneously measures the scattering phase function of the imaged particle. The system consists of twenty-eight 1-mm optical fibers connected to microlenses bonded on the surface of avalanche photo diodes (APDs). Data collected with the pi-Nephelometer during the SUCCESS field project was reported in a special issue of Geophysical Research Letters. The pi-Nephelometer provided the basis for development of a commercial imaging probe, called the cloud particle imager (CPI), which has been installed on several research aircraft and used in More than a dozen field programs.

Lawson, R. Paul↗

Analyses of Cometary Silicate Crystals: DDA Spectral Modeling of Forsterite

Comets are the Solar System's deep freezers of gases, ices, and particulates that were present in the outer protoplanetary disk. Where comet nuclei accreted was so cold that CO ice (approximately 50K) and other supervolatile ices like ethane (C2H2) were preserved. However, comets also accreted high temperature minerals: silicate crystals that either condensed (greater than or equal to 1400 K) or that were annealed from amorphous (glassy) silicates (greater than 850-1000 K). By their rarity in the interstellar medium, cometary crystalline silicates are thought to be grains that formed in the inner disk and were then radially transported out to the cold and ice-rich regimes near Neptune. The questions that comets can potentially address are: How fast, how far, and over what duration were crystals that formed in the inner disk transported out to the comet-forming region(s)? In comets, the mass fractions of silicates that are crystalline, f_cryst, translate to benchmarks for protoplanetary disk radial transport models. The infamous comet Hale-Bopp has crystalline fractions of over 55%. The values for cometary crystalline mass fractions, however, are derived assuming that the mineralogy assessed for the submicron to micron-sized portion of the size distribution represents the compositional makeup of all larger grains in the coma. Models for fitting cometary SEDs make this assumption because models can only fit the observed features with submicron to micron-sized discrete crystals. On the other hand, larger (0.1-100 micrometer radii) porous grains composed of amorphous silicates and amorphous carbon can be easily computed with mixed medium theory wherein vacuum mixed into a spherical particle mimics a porous aggregate. If crystalline silicates are mixed in, the models completely fail to match the observations. Moreover, models for a size distribution of discrete crystalline forsterite grains commonly employs the CDE computational method for ellipsoidal platelets (c:a:b=8.14x8.14xl in shape with geometrical factors of x:y:z=1:1:10, Fabian et al. 2001; Harker et al. 2007). Alternatively, models for forsterite employ statistical methods like the Distribution of Hollow Spheres (Min et al. 2008; Oliveira et al. 2011) or Gaussian Random Spheres (GRS) or RGF (Gielen et al. 200S). Pancakes, hollow spheres, or GRS shapes similar to wheat sheaf crystal habit (e.g., Volten et al. 2001; Veihelmann et al. 2006), however, do not have the sharp edges, flat faces, and vertices seen in images of cometary crystals in interplanetary dust particles (IDPs) or in Stardust samples. Cometary forsterite crystals often have equant or tabular crystal habit (J. Bradley). To simulate cometary crystals, we have computed absorption efficiencies of forsterite using the Discrete Dipole Approximation (DDA) DDSCAT code on NAS supercomputers. We compute thermal models that employ a size distribution of discrete irregularly shaped forsterite crystals (nonspherical shapes with faces and vertices) to explore how crystal shape affects the shape and wavelength positions of the forsterite spectral features and to explore whether cometary crystal shapes support either condensation or annealing scenarios (Lindsay et al. 2012a, b). We find forsterite crystal shapes that best-fit comet Hale-Bopp are tetrahedron, bricks or brick platelets, essentially equant or tabular (Lindsay et al. 2012a,b), commensurate with high temperature condensation experiments (Kobatake et al. 2008). We also have computed porous aggregates with crystal monomers and find that the crystal resonances are amplified. i.e., the crystalline fraction is lower in the aggregate than is derived by fitting a linear mix of spectral features from discrete subcomponents, and the crystal resonances 'appear' to be from larger crystals (Wooden et al. 2012). These results may indicate that the crystalline mass fraction in comets with comae dominated by aggregates may be lower than deduced by popular methods that only emoy ensembles of discrete crystals.

Wooden, Diane↗

Measurement of Microscopic Growth Rates in Float-Zone Silicon Crystals

Time dependent convective flows during crystal growth of doped semiconductors lead to fluctuations of the composition, so called dopant striations. In general, it is difficult to decide which is the main mechanism for the generation of these striations, it might be either the fluctuation of the concentration field in the melt and the extent of the solute boundary layer ahead of the solid-liquid interface or a variation of the growth velocity. Direct access to the concentration field is rather complicated to achieve, especially considering the high process temperature and the chemical activity of liquid silicon. The contribution of growth rate fluctuations to the formation of compositional fluctuations can be determined by measuring microscopic growth rates. The classical method of current pulses requires electrical feed-throughs and good electrical contacts, both are critical issues for the growth of high purity silicon crystals. Using a radiation based heating system, the heating power can be modulated very fast and effectively. We added to the normal heater power a sinusoidal off-set in the frequency range of 1 to 10 Hz, generating a narrow spaced weak rippling in the grown crystals which are superposed to the dopant striations caused by natural and by thermocapillary convection. The pulling speed was varied between 1 and 4mm/min. The microscope images of etched crystals slices have been analyzed by peak-search algorithms (measuring the spacing between each artificially induced marker) and by FFT. Performing growth experiments under a time-dependent flow regime, fluctuations of the microscopic growth velocity of Delta(v)/v(sub average) up to 50% have been measured. Damping the time-dependent convection by the use of an axial, static magnetic field of 500mT, the microscopic growth rate became constant within the resolution limit of this method. The results will be discussed using analytical methods for the calculation of microscopic growth velocity and by comparing them with measurements of temperature fluctuations in the melt during growth experiments itself.

Dold, P.↗

Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages ( Dozor and DIALS ), demonstrating that this is an appropriate framework to support future extensions and improvements.

36 MATERIALS SCIENCE↗

Computer synthesis of high resolution electron micrographs

Specimen damage, spherical aberration, low contrast and noisy sensors combine to prevent direct atomic viewing in a conventional electron microscope. The paper describes two methods for obtaining ultra-high resolution in biological specimens under the electron microscope. The first method assumes the physical limits of the electron objective lens and uses a series of dark field images of biological crystals to obtain direct information on the phases of the Fourier diffraction maxima; this information is used in an appropriate computer to synthesize a large aperture lens for a 1-A resolution. The second method assumes there is sufficient amplitude scatter from images recorded in focus which can be utilized with a sensitive densitometer and computer contrast stretching to yield fine structure image details. Cancer virus characterization is discussed as an illustrative example. Numerous photographs supplement the text.

Nathan, R.↗