scholarly journals X-Ray Diffraction in Biology: How Can We See DNA and Proteins in Three Dimensions?

10.5772/64999 ◽  
2017 ◽  
Author(s):  
Claudine Mayer
Keyword(s):  
Three Dimensions ◽  
X Ray Diffraction ◽  
X Ray

In situ reactor to image catalysts at work in three-dimensions by Bragg coherent X-ray diffraction

2019 ◽  
Vol 336 ◽  
pp. 169-173 ◽  
Author(s):  
Amélie Rochet ◽  
Ana Flávia Suzana ◽  
Aline R. Passos ◽  
Tiago Kalile ◽  
Felisa Berenguer ◽  
...  
Keyword(s):  
Three Dimensions ◽  
X Ray Diffraction ◽  
X Ray

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

M3+(H2AsO4)(H2As2O7) (M3+= Al, Ga) and In2(H2AsO4)2(H2As2O7)2: a new layer structure type and a new framework structure type containing the rare H2As2O72−group

2017 ◽  
Vol 73 (8) ◽  
pp. 600-608 ◽  
Author(s):  
Karolina Schwendtner ◽  
Uwe Kolitsch
Keyword(s):  
Hydrogen Bonds ◽  
Room Temperature ◽  
Layer Structure ◽  
Structure Type ◽  
Three Dimensions ◽  
Framework Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Third ◽  
New Framework

The crystal structures of hydrothermally synthesized aluminium dihydrogen arsenate(V) dihydrogen diarsenate(V), Al(H2AsO4)(H2As2O7), gallium dihydrogen arsenate(V) dihydrogen diarsenate(V), Ga(H2AsO4)(H2As2O7), and diindium bis[dihydrogen arsenate(V)] bis[dihydrogen diarsenate(V)], In2(H2AsO4)2(H2As2O7)2, were determined from single-crystal X-ray diffraction data collected at room temperature. The first two compounds are representatives of a novel sheet structure type, whereas the third compound crystallizes in a novel framework structure. In all three structures, the basic building units areM3+O6octahedra (M= Al, Ga, In) that are connectedviaone H2AsO4−and two H2As2O72−groups into chains, and furtherviaH2As2O72−groups into layers. In Al/Ga(H2AsO4)(H2As2O7), these layers are interconnected by weak-to-medium–strong hydrogen bonds. In In2(H2AsO4)2(H2As2O7)2, the H2As2O72−groups link the chains in three dimensions, thus creating a framework topology, which is reinforced by weak-to-medium–strong hydrogen bonds. The three title arsenates represent the first compounds containing both H2AsO4−and H2As2O72−groups.

Three-dimensional plastic response in polycrystalline coppervianear-field high-energy X-ray diffraction microscopy

2012 ◽  
Vol 45 (6) ◽  
pp. 1098-1108 ◽  
Author(s):  
S. F. Li ◽  
J. Lind ◽  
C. M. Hefferan ◽  
R. Pokharel ◽  
U. Lienert ◽  
...  
Keyword(s):  
Goodness Of Fit ◽  
Polycrystalline Sample ◽  
High Energy ◽  
Three Dimensions ◽  
X Ray Diffraction ◽  
Orientation Field ◽  
X Ray ◽  
Alignment Procedure ◽  
Polycrystal Plasticity ◽  
Diffraction Microscopy

The evolution of the crystallographic orientation field in a polycrystalline sample of copper is mapped in three dimensions as tensile strain is applied. Using forward-modeling analysis of high-energy X-ray diffraction microscopy data collected at the Advanced Photon Source, the ability to track intragranular orientation variations is demonstrated on an ∼2 µm length scale with ∼0.1° orientation precision. Lattice rotations within grains are tracked between states with ∼1° precision. Detailed analysis is presented for a sample cross section before and after ∼6% strain. The voxel-based (0.625 µm triangular mesh) reconstructed structure is used to calculate kernel-averaged misorientation maps, which exhibit complex patterns. Simulated scattering from the reconstructed orientation field is shown to reproduce complex scattering patterns generated by the defected microstructure. Spatial variation of a goodness-of-fit or confidence metric associated with the optimized orientation field indicates regions of relatively high or low orientational disorder. An alignment procedure is used to match sample cross sections in the different strain states. The data and analysis methods point toward the ability to perform detailed comparisons between polycrystal plasticity computational model predictions and experimental observations of macroscopic volumes of material.

The effect of coordinated water on the connectivity of uranium(IV) sulfatex-hydrate: [U(SO4)2(H2O)5]·H2O and [U(SO4)2(H2O)6]·2H2O, and a comparison with other known structures

2014 ◽  
Vol 70 (7) ◽  
pp. 726-731 ◽  
Author(s):  
Alexander D. Burns ◽  
Brian O. Patrick ◽  
Anita E. Lam ◽  
David Dreisinger
Keyword(s):  
Raman Spectroscopy ◽  
Binding Mode ◽  
Three Dimensions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Anhydrous Compound ◽  
Coordinated Water ◽  
Ir And Raman ◽  
Sulfate Complexes

Two new solid-state uranium(IV) sulfatex-hydrate complexes (wherexis the total number of coordinated plus solvent waters), namelycatena-poly[[pentaaquauranium(IV)]-di-μ-sulfato-κ4O:O′] monohydrate], {[U(SO4)2(H2O)5]·H2O}n, and hexaaquabis(sulfato-κ2O,O′)uranium(IV) dihydrate, [U(SO4)2(H2O)6]·2H2O, have been synthesized, structurally characterized by single-crystal X-ray diffraction and analyzed by vibrational (IR and Raman) spectroscopy. By comparing these structures with those of four other known uranium(IV) sulfatex-hydrates, the effect of additional coordinated water molecules on their structures has been elucidated. As the number of coordinated water molecules increases, the sulfate bonds are displaced, thus changing the binding mode of the sulfate ligands to the uranium centre. As a result, uranium(IV) sulfatex-hydrate changes from being fully crosslinked in three dimensions in the anhydrous compound, through sheet and chain linking in the tetra- and hexahydrates, to fully unlinked molecules in the octa- and nonahydrates. It can be concluded that coordinated waters play an important role in determining the structure and connectivity of UIVsulfate complexes.

Three-dimensional grain resolved strain mapping using laboratory X-ray diffraction contrast tomography: theoretical analysis

2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Adam Lindkvist ◽  
Yubin Zhang
Keyword(s):  
Near Field ◽  
Three Dimensional ◽  
Simulated Data ◽  
Three Dimensions ◽  
X Ray Diffraction ◽  
Strain Mapping ◽  
X Ray ◽  
Microstructural Parameters ◽  
Diffraction Contrast ◽  
Sample Distance

Laboratory diffraction contrast tomography (LabDCT) is a recently developed technique to map crystallographic orientations of polycrystalline samples in three dimensions non-destructively using a laboratory X-ray source. In this work, a new theoretical procedure, named LabXRS, expanding LabDCT to include mapping of the deviatoric strain tensors on the grain scale, is proposed and validated using simulated data. For the validation, the geometries investigated include a typical near-field LabDCT setup utilizing Laue focusing with equal source-to-sample and sample-to-detector distances of 14 mm, a magnified setup where the sample-to-detector distance is increased to 200 mm, a far-field Laue focusing setup where the source-to-sample distance is also increased to 200 mm, and a near-field setup with a source-to-sample distance of 200 mm. The strain resolution is found to be in the range of 1–5 × 10−4, depending on the geometry of the experiment. The effects of other experimental parameters, including pixel binning, number of projections and imaging noise, as well as microstructural parameters, including grain position, grain size and grain orientation, on the strain resolution are examined. The dependencies of these parameters, as well as the implications for practical experiments, are discussed.

scholarly journals Electron crystallography: imaging and single-crystal diffraction from powders

2007 ◽  
Vol 64 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Xiaodong Zou ◽  
Sven Hovmöller
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction ◽  
Recent Developments

The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

scholarly journals The Calcite (104) Surface - Electrolyte Structure: A 3D Comparison of Surface X-Ray Diffraction and Simulations

2020 ◽  
Author(s):  
Sander Brugman ◽  
Paolo Raiteri ◽  
Paolo Accordini ◽  
Frank Megens ◽  
Julian Gale ◽  
...  
Keyword(s):  
State Of The Art ◽  
Interfacial Structure ◽  
Three Dimensions ◽  
Ion Adsorption ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Factors ◽  
First Time ◽  
Experimental Structure ◽  
Good Agreement

<div>Adsorption and incorporation of ions is known to influence the morphology and growth of calcite. Using surface X-ray diffraction, the interfacial structure of calcite in contact with CaCO3, MgCl2, CaCl2</div><div>and BaCl2 solutions was determined. All of these conditions yield a comparable interfacial structure,</div><div>meaning that there is no significant ion adsorption. This allows for the first time a thorough comparison in all three dimensions with state-of-the-art computer simulations, involving molecular dynamics</div><div>based on both DFT and two different force field models. Additionally, the simulated structures are</div><div>used to calculate the corresponding structure factors, which in turn are compared to those obtained</div><div>from experiment, thereby avoiding the need for fitting or subjective interpretation. In general, there</div><div>is a good agreement between experiment and the simulations, though there are some small discrepancies in the atomic positions, which lead to an inadequate fit of certain features characteristic of the</div><div>structure of water at the interface. Of the three simulation methods examined, the DFT results were</div><div>found to agree best with the experimental structure.</div>

scholarly journals Bonsu: the interactive phase retrieval suite

2012 ◽  
Vol 45 (4) ◽  
pp. 840-843 ◽  
Author(s):  
Marcus C. Newton ◽  
Yoshinori Nishino ◽  
Ian K. Robinson
Keyword(s):  
Phase Retrieval ◽  
Nondestructive Method ◽  
Three Dimensions ◽  
Material Structure ◽  
X Ray Diffraction ◽  
Data Manipulation ◽  
X Ray ◽  
Python Language ◽  
Real Time Visualization ◽  
Diffraction Imaging

Coherent X-ray diffraction imaging has received considerable attention as a nondestructive method for probing material structure at the nanoscale. However, tools for reconstructing and analysing data in both two and three dimensions have lagged somewhat behind.Bonsu, the interactive phase retrieval suite, is the first software package that allows real-time visualization of the reconstruction of phase information in both two and three dimensions. It comes complete with an inventory of algorithms and routines for data manipulation and reconstruction.Bonsuis open source, is designed around the Python language (with C++ bindings) and is largely platform independent.Bonsuis made available under version three of the GNU General Public License and can be found at https://code.google.com/p/bonsu/.

scholarly journals Towards a quantitative determination of strain in Bragg Coherent X-ray Diffraction Imaging: artefacts and sign convention in reconstructions

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jérôme Carnis ◽  
Lu Gao ◽  
Stéphane Labat ◽  
Young Yong Kim ◽  
Jan P. Hofmann ◽  
...  
Keyword(s):  
Displacement Field ◽  
Phase Retrieval ◽  
Dynamic Range ◽  
Surface Strain ◽  
Three Dimensions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Retrieval Algorithms ◽  
Diffraction Imaging

AbstractBragg coherent X-ray diffraction imaging (BCDI) has emerged as a powerful technique to image the local displacement field and strain in nanocrystals, in three dimensions with nanometric spatial resolution. However, BCDI relies on both dataset collection and phase retrieval algorithms that can induce artefacts in the reconstruction. Phase retrieval algorithms are based on the fast Fourier transform (FFT). We demonstrate how to calculate the displacement field inside a nanocrystal from its reconstructed phase depending on the mathematical convention used for the FFT. We use numerical simulations to quantify the influence of experimentally unavoidable detector deficiencies such as blind areas or limited dynamic range as well as post-processing filtering on the reconstruction. We also propose a criterion for the isosurface determination of the object, based on the histogram of the reconstructed modulus. Finally, we study the capability of the phasing algorithm to quantitatively retrieve the surface strain (i.e., the strain of the surface voxels). This work emphasizes many aspects that have been neglected so far in BCDI, which need to be understood for a quantitative analysis of displacement and strain based on this technique. It concludes with the optimization of experimental parameters to improve throughput and to establish BCDI as a reliable 3D nano-imaging technique.

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