Accelerated X-Ray Diffraction (Tensor) Tomography Simulation Using OptiX GPU Ray-Tracing Engine

Numerical calculations of the effect of the finite dimensions and orientations of source and crystal are presented for plane and von Hamos Bragg crystal spectrometers for PIXE analysis, combined with a position sensitive (X-ray) detector. Analytical studies of all effects are provided. It is shown that some parameters can produce line shifts and asymmetries. A numerical model for an X-ray diffraction ray-tracing procedure for a crystal Bragg spectrometer is described.

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Ray-tracing analysis of capillary concentrators for macromolecular crystallography

Journal of Synchrotron Radiation ◽

10.1107/s0909049597035607 ◽

1998 ◽

Vol 5 (3) ◽

pp. 820-822 ◽

Cited By ~ 6

Author(s):

Daniel J. Thiel

Keyword(s):

Synchrotron Radiation ◽

Ray Tracing ◽

Macromolecular Crystallography ◽

X Ray Diffraction ◽

X Ray

The use of capillary concentrators as X-ray condensers specifically for macromolecular X-ray diffraction experiments using synchrotron radiation is evaluated. Monocapillary and polycapillary designs are assessed by ray-tracing analysis to evaluate how effectively these capillary concentrators can increase the X-ray intensity onto a 50 µm crystal.

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A RAY TRACING METHOD TO DESCRIBE THE ANGULAR PROFILES OF DIFFRACTION RODS IN SURFACE X RAY EXPERIMENTS

Surface Review and Letters ◽

10.1142/s0218625x97001243 ◽

1997 ◽

Vol 04 (05) ◽

pp. 1035-1038 ◽

Cited By ~ 2

Author(s):

X. TORRELLES ◽

J. ALVAREZ ◽

S. FERRER

Keyword(s):

Ray Tracing ◽

Accurate Determination ◽

X Ray Diffraction ◽

Ray Tracing Method ◽

X Ray ◽

Ewald Sphere ◽

Geometrical Effects ◽

Tracing Method

The accurate determination of the coordinates normal to the surface in X ray diffraction experiments requires measuring up to high exit angles. Under these conditions some instrumental and geometrical effects related to the dimensions of the detector slits and the location in the Ewald sphere of the outgoing beam may complicate the analysis of the data. We have developed a method based on the ray tracing technique to investigate the appropriate corrections. Examples for Ge(001)-(2×1) are presented.

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Quantifying the hydroxyapatite orientation near the ossification front in a piglet femoral condyle using X-ray diffraction tensor tomography

Scientific Reports ◽

10.1038/s41598-020-80615-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Fredrik K. Mürer ◽

Basab Chattopadhyay ◽

Aldritt Scaria Madathiparambil ◽

Kim Robert Tekseth ◽

Marco Di Michiel ◽

...

Keyword(s):

Subchondral Bone ◽

Bone Growth ◽

Femoral Condyle ◽

Large Field ◽

Detailed Knowledge ◽

X Ray Diffraction ◽

X Ray ◽

Tensor Tomography ◽

Computed Tomography Images ◽

Orientation Maps

AbstractWhile a detailed knowledge of the hierarchical structure and morphology of the extracellular matrix is considered crucial for understanding the physiological and mechanical properties of bone and cartilage, the orientation of collagen fibres and carbonated hydroxyapatite (HA) crystallites remains a debated topic. Conventional microscopy techniques for orientational imaging require destructive sample sectioning, which both precludes further studies of the intact sample and potentially changes the microstructure. In this work, we use X-ray diffraction tensor tomography to image non-destructively in 3D the HA orientation in a medial femoral condyle of a piglet. By exploiting the anisotropic HA diffraction signal, 3D maps showing systematic local variations of the HA crystallite orientation in the growing subchondral bone and in the adjacent mineralized growth cartilage are obtained. Orientation maps of HA crystallites over a large field of view (~ 3 × 3 × 3 mm3) close to the ossification (bone-growth) front are compared with high-resolution X-ray propagation phase-contrast computed tomography images. The HA crystallites are found to predominantly orient with their crystallite c-axis directed towards the ossification front. Distinct patterns of HA preferred orientation are found in the vicinity of cartilage canals protruding from the subchondral bone. The demonstrated ability of retrieving 3D orientation maps of bone-cartilage structures is expected to give a better understanding of the physiological properties of bones, including their propensity for bone-cartilage diseases.

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Orientational mapping of minerals in Pierre shale using X-ray diffraction tensor tomography

IUCrJ ◽

10.1107/s205225252100587x ◽

2021 ◽

Vol 8 (5) ◽

Author(s):

Fredrik K. Mürer ◽

Aldritt Scaria Madathiparambil ◽

Kim Robert Tekseth ◽

Marco Di Michiel ◽

Pierre Cerasi ◽

...

Keyword(s):

Orientation Distribution ◽

Bedding Plane ◽

Structural Features ◽

Spatial Density ◽

Structural Description ◽

X Ray Diffraction ◽

Crystallite Orientation ◽

X Ray ◽

Tensor Tomography ◽

Pierre Shale

Shales have a complex mineralogy with structural features spanning several length scales, making them notoriously difficult to fully understand. Conventional attenuation-based X-ray computed tomography (CT) measures density differences, which, owing to the heterogeneity and sub-resolution features in shales, makes reliable interpretation of shale images a challenging task. CT based on X-ray diffraction (XRD-CT), rather than intensity attenuation, is becoming a well established technique for non-destructive 3D imaging, and is especially suited for heterogeneous and hierarchical materials. XRD patterns contain information about the mineral crystal structure, and crucially also crystallite orientation. Here, we report on the use of orientational imaging using XRD-CT to study crystallite-orientation distributions in a sample of Pierre shale. Diffraction-contrast CT data for a shale sample measured with its bedding-plane normal aligned parallel to a single tomographic axis perpendicular to the incoming X-ray beam are discussed, and the spatial density and orientation distribution of clay minerals in the sample are described. Finally, the scattering properties of highly attenuating inclusions in the shale bulk are studied, which are identified to contain pyrite and clinochlore. A path forward is then outlined for systematically improving the structural description of shales.

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A new model for the description of X-ray diffraction from mosaic crystals for ray-tracing calculations

Journal of Applied Crystallography ◽

10.1107/s1600576717012626 ◽

2017 ◽

Vol 50 (5) ◽

pp. 1490-1497 ◽

Cited By ~ 2

Author(s):

Christopher Schlesiger ◽

Lars Anklamm ◽

Wolfgang Malzer ◽

Richard Gnewkow ◽

Birgit Kanngießer

Keyword(s):

Ray Tracing ◽

X Ray Diffraction ◽

Multiple Reflections ◽

New Model ◽

X Ray ◽

Additional Information ◽

Diffraction Model ◽

Reflection Model ◽

Mosaic Crystals ◽

Ray Tracing Simulation

This paper presents the development of a new reflection model for describing X-ray diffraction from mosaic crystals. In contrast to the well established diffraction model of Zachariasen [Zachariasen (1994),Theory of X-ray Diffraction in Crystals. Mineola: Dover Publications], it gives additional information on the spatial reflection behaviour and not just on the depth-integrated reflectivity of the crystal material. The new reflection model enables a concrete description of mosaic crystal performance in an arbitrary X-ray spectrometer configuration. Multiple reflections inside the crystal are described by splitting the calculation into a discrete number of reflections. Hence, the influence of each number of reflections is investigated, leading to a laterally resolved solution for the reflectivity. In addition, the model can use a mosaicity of arbitrary shape. This is important because the present work uses a Lorentzian-shaped mosaicity instead of a Gaussian one, which is usually the case in the most widely used simulation programs. A comparison between the new model and that of Zachariasen is performed, and it predicts a similar integrated reflectivity with a deviation lower than 0.7%. Further, a ray-tracing simulation with multiple reflections based on the new model is compared with a measurement, showing a deviation of lower than 5%.

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The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071107 ◽

1973 ◽

Vol 31 ◽

pp. 132-133 ◽

Cited By ~ 1

Author(s):

R. E. Herfert

Keyword(s):

Surface Characterization ◽

Analytical Techniques ◽

X Ray Diffraction ◽

Depth Of Penetration ◽

X Ray ◽

The Past ◽

Transmission Electron ◽

Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

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Ribosome Structural Organization

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051670 ◽

1974 ◽

Vol 32 ◽

pp. 332-333

Author(s):

James A. Lake

Keyword(s):

Ribosomal Proteins ◽

Structural Organization ◽

Three Dimensional ◽

Small Subunit ◽

Structural Studies ◽

X Ray Diffraction ◽

Specific Antibodies ◽

X Ray ◽

E Coli ◽

Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

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Electron Microscopy of Human Gallstones

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100065523 ◽

1971 ◽

Vol 29 ◽

pp. 296-297

Author(s):

C. Wolpers ◽

R. Blaschke

Keyword(s):

Electron Microscopy ◽

Room Temperature ◽

Bile Pigment ◽

X Ray Diffraction ◽

Triclinic Crystal System ◽

X Ray ◽

Follow Up Study ◽

Infra Red ◽

Main Components

Scanning microscopy was used to study the surface of human gallstones and the surface of fractures. The specimens were obtained by operation, washed with water, dried at room temperature and shadowcasted with carbon and aluminum. Most of the specimens belong to patients from a series of X-ray follow-up study, examined during the last twenty years. So it was possible to evaluate approximately the age of these gallstones and to get information on the intensity of growing and solving.Cholesterol, a group of bile pigment substances and different salts of calcium, are the main components of human gallstones. By X-ray diffraction technique, infra-red spectroscopy and by chemical analysis it was demonstrated that all three components can be found in any gallstone. In the presence of water cholesterol crystallizes in pane-like plates of the triclinic crystal system.

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High Resolution Replication of Organoclay Surfaces

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100055126 ◽

1982 ◽

Vol 40 ◽

pp. 576-577

Author(s):

W. W. Barker ◽

W. E. Rigsby ◽

V. J. Hurst ◽

W. J. Humphreys

Keyword(s):

Clay Mineral ◽

Organic Molecule ◽

Organic Molecules ◽

X Ray Diffraction ◽

Xrd Pattern ◽

X Ray ◽

Naturally Occurring ◽

Silicate Layers ◽

Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

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