scholarly journals Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission

IUCrJ ◽  
2017 ◽  
Vol 4 (6) ◽  
pp. 778-784 ◽  
Author(s):  
H. Olof Jönsson ◽  
Carl Caleman ◽  
Jakob Andreasson ◽  
Nicuşor Tîmneanu

Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Ivus L. O. Matos ◽  
Adriano B. Andrade ◽  
Zélia S. Macedo ◽  
Mário E. G. Valerio

The production of high-density bismuth germanate (Bi3Ge4O12) ceramic scintillators by uniaxial hot pressing was investigated as a function of different applied pressure conditions. The X-ray diffraction showed that the sintering process was able to eliminate the undesirable secondary phase present in the nonsintered samples. The height changes from samples with higher applied pressure rate and applied pressure duration lead to a better relative density value, >95% for samples sintered under a pressure of 0.14 and 0.18 MPa. The radioluminescence results showed that all samples have the characteristic emission spectra of Bi3Ge4O12 and that the hot-pressed samples have higher radioluminescence emission efficiency.


2006 ◽  
Vol 514-516 ◽  
pp. 1638-1642
Author(s):  
Ana J. López ◽  
Alberto Ramil ◽  
Gines Nicolas ◽  
Mari Paz Mateo ◽  
Victor Piñon ◽  
...  

Archaeological ceramics Terra Sigillata manufactured in different production centres have been studied by “laser induced plasma spectroscopy” (LIPS). The aim of this work is to demonstrate the capability of LIPS for the classification of pottery shreds in function of their provenance. Characteristic emission spectra of different pottery groups were obtained and simple linear correlation methods were used for grouping samples. In addition, complementary scanning electron microscopy coupled with energy-dispersive X-ray spectrometry (SEM-EDX) analysis were performed to obtain morphological features and to confirm chemical results


2019 ◽  
Vol 89 (9) ◽  
pp. 1412
Author(s):  
К.Н. Орехова ◽  
Ю.М. Серов ◽  
П.А. Дементьев ◽  
Е.В. Иванова ◽  
В.А. Кравец ◽  
...  

During the study of materials on electron probe devices in the field of the electron beam, a contamination hydrocarbon film is formed, which influences the results of experiments. In this paper, we studied the effect of a contamination film formed on carbon-coated dielectric samples on the intensity of cathodoluminescence and X-ray characteristic emission lines. The absorption coefficient of the film for the visible and UV ranges was determined. The mechanism of film formation for various parameters of the electron beam is discussed.


2016 ◽  
Vol 72 (8) ◽  
pp. 944-955 ◽  
Author(s):  
Saeed Oghbaey ◽  
Antoine Sarracini ◽  
Helen M. Ginn ◽  
Olivier Pare-Labrosse ◽  
Anling Kuo ◽  
...  

The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means ofin situspectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.


1965 ◽  
Vol 9 ◽  
pp. 471-486 ◽  
Author(s):  
R. A. Mattson ◽  
R. C. Ehlert

AbstractResults are shown for O and F K emission lines from several oxide and fluoride compounds. The spectra are examined for both structure and wavelength. Excitation of the spectra is by both electrons and X-rays. The emission spectra from several oxygen- and fluorine-bearing gases and the influence of the composition of the diffracting crystal on the shape of the observed oxygen spectra are also discussed. Curved crystals of potassium acid phthalate and lead stearate, and a thin-window flow proportional counter, are used to obtain the results.


2012 ◽  
Vol 502 ◽  
pp. 312-315 ◽  
Author(s):  
Jia Yue Sun ◽  
Jun Hui Zeng ◽  
Ji Cheng Zhu ◽  
Yi Ning Sun ◽  
Hai Yan Du

A new red-emitting Rare-earth silicon carbonitrides phosphor, Y2Si4N6C, was prepared by a carbothermal reduction and nitridation method. X-ray powder diffraction (XRD), the photoluminescence excitation and emission spectra, temperature dependent was measured. The emission spectrum obtained by excitation into 410 nm contains exclusively the characteristic emission of Sm3+ at 568, 607 and 654 nm which correspond to the transitions from4G5/2to6H5/2,6H7/2, and6H9/2of Sm3+, respectively. The strongest one is located at 606 nm due to4G5/2to6H7/2transition of Sm3+.


Author(s):  
Y. Y. Wang ◽  
H. Zhang ◽  
V. P. Dravid ◽  
H. Zhang ◽  
L. D. Marks ◽  
...  

Azuma et al. observed planar defects in a high pressure synthesized infinitelayer compound (i.e. ACuO2 (A=cation)), which exhibits superconductivity at ~110 K. It was proposed that the defects are cation deficient and that the superconductivity in this material is related to the planar defects. In this report, we present quantitative analysis of the planar defects utilizing nanometer probe xray microanalysis, high resolution electron microscopy, and image simulation to determine the chemical composition and atomic structure of the planar defects. We propose an atomic structure model for the planar defects.Infinite-layer samples with the nominal chemical formula, (Sr1-xCax)yCuO2 (x=0.3; y=0.9,1.0,1.1), were prepared using solid state synthesized low pressure forms of (Sr1-xCax)CuO2 with additions of CuO or (Sr1-xCax)2CuO3, followed by a high pressure treatment.Quantitative x-ray microanalysis, with a 1 nm probe, was performed using a cold field emission gun TEM (Hitachi HF-2000) equipped with an Oxford Pentafet thin-window x-ray detector. The probe was positioned on the planar defects, which has a 0.74 nm width, and x-ray emission spectra from the defects were compared with those obtained from vicinity regions.


1997 ◽  
Vol 7 (C2) ◽  
pp. C2-515-C2-516
Author(s):  
H. Agren ◽  
L. G.M. Pettersson ◽  
V. Carravetta ◽  
Y. Luo ◽  
L. Yang ◽  
...  

1987 ◽  
Vol 48 (C9) ◽  
pp. C9-1059-C9-1062
Author(s):  
P. J. DURHAM ◽  
C. F. HAGUE ◽  
J.-M. MARIOT ◽  
W. M. TEMMERMAN

2008 ◽  
Author(s):  
Yuzo Shigesato ◽  
Kento Hirohata ◽  
Yasutaka Nishi ◽  
Nobuto Oka ◽  
Yasushi Sato ◽  
...  

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