scholarly journals XFEL diffraction: developing processing methods to optimize data quality

2015 ◽  
Vol 22 (2) ◽  
pp. 239-248 ◽  
Author(s):  
Nicholas K. Sauter
Keyword(s):  
Approximate Model ◽  
Difficult Problem ◽  
Integration Step ◽  
X Rays ◽  
Experimental Conditions ◽  
Structural Details ◽  
Laser Sources ◽  
Serial Crystallography ◽  
Difference Fourier ◽  
Damage Processes

Serial crystallography, using either femtosecond X-ray pulses from free-electron laser sources or short synchrotron-radiation exposures, has the potential to reveal metalloprotein structural details while minimizing damage processes. However, deriving a self-consistent set of Bragg intensities from numerous still-crystal exposures remains a difficult problem, with optimal protocols likely to be quite different from those well established for rotation photography. Here several data processing issues unique to serial crystallography are examined. It is found that the limiting resolution differs for each shot, an effect that is likely to be due to both the sample heterogeneity and pulse-to-pulse variation in experimental conditions. Shots with lower resolution limits produce lower-quality models for predicting Bragg spot positions during the integration step. Also, still shots by their nature record only partial measurements of the Bragg intensity. An approximate model that corrects to the full-spot equivalent (with the simplifying assumption that the X-rays are monochromatic) brings the distribution of intensities closer to that expected from an ideal crystal, and improves the sharpness of anomalous difference Fourier peaks indicating metal positions.

scholarly journals Crystallographic data processing for free-electron laser sources

2013 ◽  
Vol 69 (7) ◽  
pp. 1231-1240 ◽  
Author(s):  
Thomas A. White ◽  
Anton Barty ◽  
Francesco Stellato ◽  
James M. Holton ◽  
Richard A. Kirian ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Incident Beam ◽  
Crystallographic Analysis ◽  
Monte Carlo Integration ◽  
Laser Source ◽  
Integration Scheme ◽  
X Rays ◽  
Laser Sources ◽  
Serial Crystallography

A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suiteCrystFELand the pre-processing programCheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.

scholarly journals Closed Fractures of the Distal Part of the Shin Bones. Different Types and Methods of the Treatment in Adolescence. Short Period Results

2021 ◽  
Vol 3 (1) ◽  
pp. 11-23
Author(s):  
Alexander I. Dorokhin ◽  
Alexander I. Krupatkin ◽  
Anastasia A. Adrianova ◽  
Vladimir I. Khudik ◽  
Dmitriy S. Sorokin ◽  
...  
Keyword(s):  
Distal Part ◽  
Clinical Investigation ◽  
Morphological Changes ◽  
Treatment Algorithm ◽  
Age Groups ◽  
Growth Zone ◽  
Difficult Problem ◽  
Pathological Process ◽  
X Rays ◽  
Short Period

Background.Fractures of the distal leg bones in children, due to the peculiarities of localization, the presence of a growth zone, the proximity of the joint and the involvement of the ligamentous apparatus in the pathological process, present a difficult problem in the choice of treatment and rehabilitation.Aims:In order to our aims we create the diagnostic and treatment algorithm in the system of early rehabilitation after fractures in the distal part of the shin bone in adolescence.Methods.Our clinical investigation based on the treatment of 56 patients in the age 817 years. Cohort of patients consist from three age groups: 811 years (n=13), 1214 years (n=28) and 1517 years (n=15). Examination was done with X-rays, CT and Ultrasound, specialy in the cases where the damage of ligamentous apparatus was suspicious. The main method of treatment was surgical osteosynthesis by pins, plates and screws. In the rehabilitation period the legs were immobilized by Plaster of Paris for 46 weeks.Results.In majority of cases the outcomes in the period of 68 weeks after trauma were good and satisfactory. The method of laser Doppler fluometry was performed in 16 cases in follow up period after trauma for examination of the regional blood circulation as a argumentation of regeneration process.Conclusion.The different choice in treatment of compound fractures of the distal part of the shin bones according to morphological changes in adolescence permits to aid good results in majority of caces.

scholarly journals X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules

2019 ◽  
Vol 88 (1) ◽  
pp. 35-58 ◽  
Author(s):  
Henry N. Chapman
Keyword(s):  
Free Electron ◽  
Conformational Dynamics ◽  
Cryogenic Cooling ◽  
X Rays ◽  
Free Electron Lasers ◽  
X Ray ◽  
Virus Particles ◽  
Structure And Dynamics ◽  
Small Crystals ◽  
Serial Crystallography

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

POSITRON FACILITIES TESTS OF THE X-RAYS PRODUCED BY CRYSTALLINE UNDULATORS

2005 ◽  
Vol 19 (03) ◽  
pp. 85-98 ◽  
Author(s):  
S. BELLUCCI
Keyword(s):  
Positron Beam ◽  
Precise Determination ◽  
X Rays ◽  
Experimental Conditions ◽  
X Ray ◽  
Accelerated Particles

One of the main involvements of the INFN-Laboratori Nazionali di Frascati group in channeling researches is described, i.e. the crystal undulator R & D, with the characterization of the crystal undulator prototypes with SEM and the positron beam. We consider a precise determination of the optimal experimental conditions for channeling of this kind of accelerated particles through such microstructured crystals, as promising candidates for producing X-ray beams.

scholarly journals THE INACTIVATION OF DILUTE SOLUTIONS OF CRYSTALLINE TRYPSIN BY X-RADIATION

1955 ◽  
Vol 38 (5) ◽  
pp. 581-598 ◽  
Author(s):  
Margaret R. McDonald
Keyword(s):  
Sulfuric Acid ◽  
Nitric Acid ◽  
Hydrochloric Acid ◽  
Radiation Effects ◽  
Reaction Yield ◽  
X Rays ◽  
Dilute Solutions ◽  
Experimental Conditions ◽  
Ph Range ◽  
Ph Curve

The proteolytic activity of dilute solutions of clystalline trypsin is destroyed by x-rays, the amount of inactivation being an exponential function of the radiation dose. The reaction yield increases steadily with increasing concentration of trypsin, varying, as the concentration of enzyme is increased from 1 to 300 µM, from 0.068 to 0.958 micromole of trypsin per liter inactivated per 1000 r with 0.005 N hydrochloric acid as the solvent, from 0.273 to 0.866 with 0.005 N sulfuric acid as the solvent, and from 0.343 to 0.844 with 0.005 N nitric acid as the solvent. When the reaction yields are plotted as a function of the initial concentration of trypsin, they fall on a curve given by the expression Y α XK, in which Y is the reaction yield, X is the concentration of trypsin, and K is a constant equal to 0.46, 0.20, and 0.16, respectively, with 0.005 N hydrochloric, sulfuric, and nitric acids as solvents. The differences between the reaction yields found with chloride and sulfate ions in I to 10 µM trypsin solutions are significant only in the pH range from 2 to 4. The amount of inactivation obtained with a given dose of x-rays depends on the pH of the solution being irradiated and the nature of the solvent. The reaction yield-pH curve is a symmetrical one, with minimum yields at about pH 7. Buffers such as acetate, citrate, borate and barbiturate, and other organic molecules such as ethanol and glucose, in concentrations as low as 20 µM, inhibit the inactivation of trypsin by x-radiation. Sigmoid inactivation-dose curves instead of exponential ones are obtained in the presence of ethanol. The reaction yields for the inactivation of trypsin solutions by x-rays are approximately 1.5 times greater when the irradiation is done at 26°C. than when it is done at 5°C., when 0.005 N hydrochloric acid is the solvent. The dependence on temperature is less when 0.005 N sulfuric acid is used, and is negligible with 0.005 N nitric acid. The difficulties involved in interpreting radiation effects in aqueous systems, and in comparing the results obtained under different experimental conditions, are discussed.

A Study on Parameter Determination Method of Large-Scale and Complex Dynamic Systems With Judgment Functions (No. 1)—Theory

1983 ◽  
Vol 105 (2) ◽  
pp. 64-69
Author(s):  
Osamu Furukawa ◽  
Hideomi Ikeshoji ◽  
Satoshi Iida
Keyword(s):  
Dynamic Systems ◽  
Large Scale ◽  
Optimization Methods ◽  
Approximate Model ◽  
Difficult Problem ◽  
Parameter Determination ◽  
Design Parameters ◽  
Dynamic Relationships ◽  
Complex Mechanical Systems ◽  
Selection Of

In the design of large-scale and complex mechanical systems, determination of design parameters is a very difficult problem. This study deals with parameter satisfaction problems of large-scale, complex, and dynamic systems with judgment functions. In order to solve these problems, a new method is proposed which sequentially exchanges the original mathematical model to an analyzable approximate model by means of the identification method and which improves a lot of parameters simultaneously. First, criteria of selection of attributes to build up approximate model are clarified. Moreover, as tools for selection of attributes, two analysis charts are proposed which express dynamic relationships among the attributes. Second, a general condition to determine the structure of approximate models and a statistical method to linearize the original model with judgment functions are derived. Finally, a combinatorial method of statistical identification and parameter optimization methods are proposed. By this method, some shortcomings of sensitivity analysis, decomposition technique (enormous calculations of partial derivatives) and statistical methods such as Monte Carlo method (bad convergency of solutions) can be avoided. As a result of this, it becomes possible to search satisfactory parameters efficiently.

scholarly journals Sample delivery using capillary and delivery medium for serial crystallography

2019 ◽  
Author(s):  
Ki Hyun Nam
Keyword(s):  
Capillary Tube ◽  
Low Flow ◽  
Innovative Technology ◽  
X Rays ◽  
Delivery Method ◽  
Interaction Point ◽  
Crystal Sample ◽  
X Ray ◽  
Serial Crystallography ◽  
Delivery Medium

AbstractSerial crystallography (SX) is an innovative technology in structural biology that enables the visualization of molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques and drastically reducing sample consumption. This simple but highly efficient sample delivery method can allow researchers to deliver crystals precisely to X-rays in SX experiments.

scholarly journals A computational–experimental approach for automated crystal structure solution

2014 ◽  
Vol 70 (a1) ◽  
pp. C131-C131
Author(s):  
Chris Wolverton
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Hydrogen Storage ◽  
First Principles ◽  
Materials Science ◽  
Hybrid Approach ◽  
X Rays ◽  
Experimental Conditions ◽  
Algorithmic Optimization ◽  
Structure Solution

Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li–air batteries; and high-pressure silane, SiH4.

scholarly journals Pattern-matching indexing of Laue and monochromatic serial crystallography data for applications in materials science

2020 ◽  
Vol 53 (3) ◽  
pp. 824-836
Author(s):  
Catherine Dejoie ◽  
Nobumichi Tamura
Keyword(s):  
Pattern Matching ◽  
Materials Science ◽  
Reciprocal Lattice ◽  
Unit Cell ◽  
Crystallographic Structure ◽  
Experimental Conditions ◽  
Lattice Vector ◽  
Small Unit ◽  
Orientation Matrix ◽  
Serial Crystallography

Serial crystallography data can be challenging to index, as each frame is processed individually, rather than being processed as a whole like in conventional X-ray single-crystal crystallography. An algorithm has been developed to index still diffraction patterns arising from small-unit-cell samples. The algorithm is based on the matching of reciprocal-lattice vector pairs, as developed for Laue microdiffraction data indexing, combined with three-dimensional pattern matching using a nearest-neighbors approach. As a result, large-bandpass data (e.g. 5–24 keV energy range) and monochromatic data can be processed, the main requirement being prior knowledge of the unit cell. Angles calculated in the vicinity of a few theoretical and experimental reciprocal-lattice vectors are compared, and only vectors with the highest number of common angles are selected as candidates to obtain the orientation matrix. Global matching on the entire pattern is then checked. Four indexing options are available, two for the ranking of the theoretical reciprocal-lattice vectors and two for reducing the number of possible candidates. The algorithm has been used to index several data sets collected under different experimental conditions on a series of model samples. Knowing the crystallographic structure of the sample and using this information to rank the theoretical reflections based on the structure factors helps the indexing of large-bandpass data for the largest-unit-cell samples. For small-bandpass data, shortening the candidate list to determine the orientation matrix should be based on matching pairs of reciprocal-lattice vectors instead of triplet matching.

The Kinetics and Equilibrium Thermodynamics Study on the Removal of Direct Blue and Titan Yellow Dyes from Aqueous Media by Modified Rice Husk Char

2020 ◽  
Vol 234 (3) ◽  
pp. 485-503
Author(s):  
Abdul Malik ◽  
Abbas Khan ◽  
Nasrullah Shah ◽  
Muhammad Sufaid Khan
Keyword(s):  
Rice Husk ◽  
Adsorption Process ◽  
Aqueous Media ◽  
Isotherm Models ◽  
Maximum Adsorption Capacity ◽  
Order Kinetic ◽  
X Rays ◽  
Experimental Conditions ◽  
Titan Yellow ◽  
Direct Blue

AbstractThe use of indigenous natural materials and their modification toward fruitful application is one of the important subjects. Thermal modification of Rice Husk at 400 oC resulted into Rice Husk Char (RHC) which was chemically modified with KOH and was labeled as KOH Modified Rice Husk Char (KMRHC). Both RHC and KMRHC were characterized by using, Fourier transformed infrared (FTIR), scanning electron microscopy (SEM), energy dispersive X-rays (EDX) and X-ray diffraction (XRD) before and after their use as adsorbents. The prepared material was applied for the removal of toxic dyes, Direct Blue (DB) and Titan Yellow (TY) from aqueous media. The maximum adsorption capacity of DB and TY dyes on KMRHC were inspected as 30.9 mg/g and 28.6 mg/g, respectively at pH 4 using initial dye concentrations of 80 mg/L containing 2500 mg/L of the adsorbent dose with agitation speed of 240 rpm at 303 K. At the same experimental conditions the highest percentage removal of DB and TY on the adsorbent were observed as 96.6% and 89.3%, respectively. Thermodynamics studies of the adsorption of DB and TY dyes on KMRHC inferred for exothermic and spontaneous process. The value of ΔS is negative which suggested that randomness decreases at the interface of adsorbent-adsorbate during the adsorption. The kinetics study indicated that the experimental data of the adsorption process for both dyes, best fits to pseudo-second order kinetic model. The equilibrium data was tested on Langmuir, Freundlich and Temkin adsorption isotherm models. It was observed that the data are best fit to the Langmuir isotherm model (R2 > 0.99), which suggested that the adsorption process is dominated by chemisorption approach. The overall results suggest that various parameters of the adsorption process were not only affected by the variation in experimental conditions but also by the chemical structure of the adsorbate molecules for the same adsorbent.

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