scholarly journals Single-particle structure determination by correlations of snapshot X-ray diffraction patterns

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
D. Starodub ◽  
A. Aquila ◽  
S. Bajt ◽  
M. Barthelmess ◽  
A. Barty ◽  
...  
Keyword(s):  
Structure Determination ◽  
Single Particle ◽  
X Ray Diffraction ◽  
Particle Structure ◽  
X Ray ◽  
Diffraction Patterns

scholarly journals Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges

2015 ◽  
Vol 2 (4) ◽  
pp. 041601 ◽  
Author(s):  
A. Hosseinizadeh ◽  
A. Dashti ◽  
P. Schwander ◽  
R. Fung ◽  
A. Ourmazd
Keyword(s):  
Structure Determination ◽  
Single Particle ◽  
Free Electron ◽  
Free Electron Lasers ◽  
Particle Structure ◽  
X Ray

scholarly journals Start-to-End XFEL experiment simulation:A framework and coherent imaging example

2014 ◽  
Vol 70 (a1) ◽  
pp. C290-C290
Author(s):  
Adrian Mancuso ◽  
Chun Hong Yoon ◽  
Mikhail Yurkov ◽  
Evgeny Schneidmiller ◽  
Liubov Samoylova ◽  
...  
Keyword(s):  
Structure Determination ◽  
Single Particle ◽  
Source Parameters ◽  
Simulated Data ◽  
Real Space ◽  
Light Sources ◽  
X Rays ◽  
Particle Structure ◽  
Optical Elements ◽  
X Ray

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. We present a framework for Start-to-End (S2E) simulations of a coherent X-ray experiment, including source parameters, propagation of the coherent X-rays though optical elements, interaction of the photons with matter, and their subsequent detection and analysis. To demonstrate this framework, we show a single-particle structure determination example using parameters of the Single Particles, Clusters and Biomolecules (SPB) instrument [1] at the under-construction European XFEL [2, 3]. We use cross platform wave optics software [4] for the propagation of the coherent beams, a molecular dynamics treatment of real space dynamics of atoms, ions and free electrons to account for radiation damage [5], and the Expansion-Maximization-Compression (EMC) algorithm [6] for assembling the simulated data before subsequent phasing and structure determination. It is hoped such simulations can provide an insight into the critical regions of parameter space for the single-particle imaging problem, and hence direct efforts to best utilize these next generation light sources.

FOX: Modular Approach to Crystal Structure Determination from Powder Diffraction

2004 ◽  
Vol 443-444 ◽  
pp. 35-38 ◽  
Author(s):  
V. Favre-Nicolin ◽  
R. Černý
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Structure Determination ◽  
Building Blocks ◽  
Adaptive Method ◽  
Crystal Structure Determination ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neighboring Building ◽  
Diffraction Patterns

Program FOX for ab initio crystal structure determination from powder diffraction uses global optimization algorithms to find the correct structure by making trials in the direct space. It is a modular program, capable of using several criteria for evaluating each trial configuration, e.g. combining neutron and X-ray diffraction patterns. The program describes the structural building blocks (polyhedrons, molecules etc.) with their internal coordinates (Z-matrices), thus allowing natural constraints on interatomic distances and angles. Identical atoms shared between neighboring building blocks, and special positions are handled with an automatic, adaptive method (Dynamical Occupancy Correction). Several algorithms (Simulated Annealing, Parallel Tempering) are currently available. The program is based on an object-oriented crystallographic library ObjCryst++(programming language c++). The program and the library are available for Linux and Windows on http://objcryst.sourceforge.net. Inorganic and organic structures with the complexity up to 26 independents atoms are routinely solved from laboratory X-ray, synchrotron or neutron data.

Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

1977 ◽  
Vol 35 ◽  
pp. 330-333
Author(s):  
T. Gulik-Krzywicki ◽  
M.J. Costello
Keyword(s):  
Biological Materials ◽  
Molecular Organization ◽  
X Ray Diffraction ◽  
Glass Capillary ◽  
X Ray ◽  
Rate Dependent ◽  
Before And After ◽  
Freeze Etching ◽  
Diffraction Patterns ◽  
Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

Examination of Rabbit Fc Crystals

1968 ◽  
Vol 26 ◽  
pp. 140-141
Author(s):  
J. P. Robinson ◽  
P. G. Lenhert
Keyword(s):  
Molecular Weight ◽  
Flat Plate ◽  
Phosphate Buffer ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutral Ph ◽  
Small Crystals ◽  
Carbon Coated ◽  
Diffraction Patterns

Crystallographic studies of rabbit Fc using X-ray diffraction patterns were recently reported. The unit cell constants were reported to be a = 69. 2 A°, b = 73. 1 A°, c = 60. 6 A°, B = 104° 30', space group P21, monoclinic, volume of asymmetric unit V = 148, 000 A°3. The molecular weight of the fragment was determined to be 55, 000 ± 2000 which is in agreement with earlier determinations by other methods.Fc crystals were formed in water or dilute phosphate buffer at neutral pH. The resulting crystal was a flat plate as previously described. Preparations of small crystals were negatively stained by mixing the suspension with equal volumes of 2% silicotungstate at neutral pH. A drop of the mixture was placed on a carbon coated grid and allowed to stand for a few minutes. The excess liquid was removed and the grid was immediately put in the microscope.

Control of the phase composition of advanced calcium phosphates using an x-ray diffractometer with a curved position-sensitive detector

2020 ◽  
Vol 86 (6) ◽  
pp. 29-35
Author(s):  
V. P. Sirotinkin ◽  
O. V. Baranov ◽  
A. Yu. Fedotov ◽  
S. M. Barinov
Keyword(s):  
Phase Composition ◽  
Calcium Phosphates ◽  
Position Sensitive Detector ◽  
Sensitive Detector ◽  
X Ray Diffraction ◽  
X Ray ◽  
Impurity Phases ◽  
Position Sensitive ◽  
Diffraction Peaks ◽  
Diffraction Patterns

The results of studying the phase composition of advanced calcium phosphates Ca10(PO4)6(OH)2, β-Ca3(PO4)2, α-Ca3(PO4)2, CaHPO4 · 2H2O, Ca8(HPO4)2(PO4)4 · 5H2O using an x-ray diffractometer with a curved position-sensitive detector are presented. Optimal experimental conditions (angular positions of the x-ray tube and detector, size of the slits, exposure time) were determined with allowance for possible formation of the impurity phases during synthesis. The construction features of diffractometers with a position-sensitive detector affecting the profile characteristics of x-ray diffraction peaks are considered. The composition for calibration of the diffractometer (a mixture of sodium acetate and yttrium oxide) was determined. Theoretical x-ray diffraction patterns for corresponding calcium phosphates are constructed on the basis of the literature data. These x-ray diffraction patterns were used to determine the phase composition of the advanced calcium phosphates. The features of advanced calcium phosphates, which should be taken into account during the phase analysis, are indicated. The powder of high-temperature form of tricalcium phosphate strongly adsorbs water from the environment. A strong texture is observed on the x-ray diffraction spectra of dicalcium phosphate dihydrate. A rather specific x-ray diffraction pattern of octacalcium phosphate pentahydrate revealed the only one strong peak at small angles. In all cases, significant deviations are observed for the recorded angular positions and relative intensity of the diffraction peaks. The results of the study of experimentally obtained mixtures of calcium phosphate are presented. It is shown that the graphic comparison of experimental x-ray diffraction spectra and pre-recorded spectra of the reference calcium phosphates and possible impurity phases is the most effective method. In this case, there is no need for calibration. When using this method, the total time for analysis of one sample is no more than 10 min.

Infrared spectroscopic study of the YPO4-YCrO4 system

1985 ◽  
Vol 50 (10) ◽  
pp. 2139-2145
Author(s):  
Alexander Muck ◽  
Eva Šantavá ◽  
Bohumil Hájek
Keyword(s):  
Spectroscopic Study ◽  
Infrared Spectra ◽  
Point Of View ◽  
Mixed Crystals ◽  
Crystal Symmetry ◽  
Infrared Spectroscopic Study ◽  
X Ray Diffraction ◽  
X Ray ◽  
Infrared Spectroscopic ◽  
Diffraction Patterns

The infrared spectra and powder X-ray diffraction patterns of polycrystalline YPO4-YCrO4 samples are studied from the point of view of their crystal symmetry. Mixed crystals of the D4h19 symmetry are formed over the region of 0-30 mol.% YPO4 in YCrO4. The Td → D2d → D2 or C2v(GS eff) correlation is appropriate for both PO43- and CrO43- anions.

scholarly journals Deep learning for visualization and novelty detection in large X-ray diffraction datasets

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Lars Banko ◽  
Phillip M. Maffettone ◽  
Dennis Naujoks ◽  
Daniel Olds ◽  
Alfred Ludwig
Keyword(s):  
Thin Film ◽  
Crystal Structure ◽  
Artificial Intelligence ◽  
Deep Learning ◽  
Novelty Detection ◽  
Structural Similarity ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Post Hoc

AbstractWe apply variational autoencoders (VAE) to X-ray diffraction (XRD) data analysis on both simulated and experimental thin-film data. We show that crystal structure representations learned by a VAE reveal latent information, such as the structural similarity of textured diffraction patterns. While other artificial intelligence (AI) agents are effective at classifying XRD data into known phases, a similarly conditioned VAE is uniquely effective at knowing what it doesn’t know: it can rapidly identify data outside the distribution it was trained on, such as novel phases and mixtures. These capabilities demonstrate that a VAE is a valuable AI agent for aiding materials discovery and understanding XRD measurements both ‘on-the-fly’ and during post hoc analysis.

scholarly journals Simultaneous Multi-Bragg Peak Coherent X-ray Diffraction Imaging

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 312
Author(s):  
Florian Lauraux ◽  
Stéphane Labat ◽  
Sarah Yehya ◽  
Marie-Ingrid Richard ◽  
Steven J. Leake ◽  
...  
Keyword(s):  
Bragg Reflection ◽  
Volume Ratio ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystal Substrate ◽  
In Series ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Lattice Planes ◽  
Oriented Parallel

The simultaneous measurement of two Bragg reflections by Bragg coherent X-ray diffraction is demonstrated on a twinned Au crystal, which was prepared by the solid-state dewetting of a 30 nm thin gold film on a sapphire substrate. The crystal was oriented on a goniometer so that two lattice planes fulfill the Bragg condition at the same time. The Au 111 and Au 200 Bragg peaks were measured simultaneously by scanning the energy of the incident X-ray beam and recording the diffraction patterns with two two-dimensional detectors. While the former Bragg reflection is not sensitive to the twin boundary, which is oriented parallel to the crystal–substrate interface, the latter reflection is only sensitive to one part of the crystal. The volume ratio between the two parts of the twinned crystal is about 1:9, which is also confirmed by Laue microdiffraction of the same crystal. The parallel measurement of multiple Bragg reflections is essential for future in situ and operando studies, which are so far limited to either a single Bragg reflection or several in series, to facilitate the precise monitoring of both the strain field and defects during the application of external stimuli.

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