scholarly journals Analysis Strategies for MHz XPCS at the European XFEL

2021 ◽  
Vol 11 (17) ◽  
pp. 8037
Author(s):  
Francesco Dallari ◽  
Mario Reiser ◽  
Irina Lokteva ◽  
Avni Jain ◽  
Johannes Möller ◽  
...  
Keyword(s):  
New Technologies ◽  
Soft Condensed Matter ◽  
Pixel Detector ◽  
Analysis Pipeline ◽  
X Ray ◽  
X Ray Scattering ◽  
Analysis Strategies ◽  
Scientific Questions ◽  
Sophisticated Analysis ◽  
Data Analysis Pipeline

The nanometer length-scale holds precious information on several dynamical processes that develop from picoseconds to seconds. In the past decades, X-ray scattering techniques have been developed to probe the dynamics at such length-scales on either ultrafast (sub-nanosecond) or slow ((milli-)second) time scales. With the start of operation of the European XFEL, thanks to the MHz repetition rate of its X-ray pulses, even the intermediate μs range have become accessible. Measuring dynamics on such fast timescales requires the development of new technologies such as the Adaptive Gain Integrating Pixel Detector (AGIPD). μs-XPCS is a promising technique to answer many scientific questions regarding microscopic structural dynamics, especially for soft condensed matter systems. However, obtaining reliable results with complex detectors at free-electron laser facilities is challenging and requires more sophisticated analysis methods compared to experiments at storage rings. Here, we discuss challenges and possible solutions to perform XPCS experiments with the AGIPD at European XFEL; in particular, at the Materials Imaging and Dynamics (MID) instrument. We present our data analysis pipeline and benchmark the results obtained at the MID instrument with a well-known sample composed by silica nanoparticles dispersed in water.

scholarly journals Automated Pipeline for Purification, Biophysical and X-Ray Analysis of Biomacromolecular Solutions

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Melissa A. Graewert ◽  
Daniel Franke ◽  
Cy M. Jeffries ◽  
Clement E. Blanchet ◽  
Darja Ruskule ◽  
...  
Keyword(s):  
Biological Macromolecules ◽  
Analysis Pipeline ◽  
X Ray ◽  
X Ray Scattering ◽  
Automated Pipeline ◽  
Automated Data Analysis ◽  
Sample Component ◽  
Data Analysis Pipeline ◽  
Line Sample

Abstract Small angle X-ray scattering (SAXS), an increasingly popular method for structural analysis of biological macromolecules in solution, is often hampered by inherent sample polydispersity. We developed an all-in-one system combining in-line sample component separation with parallel biophysical and SAXS characterization of the separated components. The system coupled to an automated data analysis pipeline provides a novel tool to study difficult samples at the P12 synchrotron beamline (PETRA-3, EMBL/DESY, Hamburg).

scholarly journals ASAXS study of CaF2nanoparticles embedded in a silicate glass matrix

2014 ◽  
Vol 47 (1) ◽  
pp. 60-66 ◽  
Author(s):  
Armin Hoell ◽  
Zoltan Varga ◽  
Vikram Singh Raghuwanshi ◽  
Michael Krumrey ◽  
Christian Bocker ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Spatial Distribution ◽  
Glass Matrix ◽  
Structural Parameters ◽  
Pixel Detector ◽  
Oxyfluoride Glass ◽  
X Ray ◽  
X Ray Scattering ◽  
Silicate Glass Matrix

The formation and growth of nanosized CaF2crystallites by heat treatment of an oxyfluoride glass of composition 7.65Na2O–7.69K2O–10.58CaO–12.5CaF2–5.77Al2O3–55.8SiO2(wt%) was investigated using anomalous small-angle X-ray scattering (ASAXS). A recently developed vacuum version of the hybrid pixel detector Pilatus 1M was used for the ASAXS measurements below the CaK-edge of 4038 eV down to 3800 eV. ASAXS investigation allows the determination of structural parameters such as size and size distribution of nanoparticles and characterizes the spatial distribution of the resonant element, Ca. The method reveals quantitatively that the growing CaF2crystallites are surrounded by a shell of lower electron density. This depletion shell of growing thickness hinders and finally limits the growth of CaF2crystallites. Moreover, in samples that were annealed for 10 h and more, additional very small heterogeneities (1.6 nm diameter) were found.

scholarly journals Improved data acquisition in grazing-incidence X-ray scattering experiments using a pixel detector

2005 ◽  
Vol 61 (4) ◽  
pp. 418-425 ◽  
Author(s):  
C. M. Schlepütz ◽  
R. Herger ◽  
P. R. Willmott ◽  
B. D. Patterson ◽  
O. Bunk ◽  
...  
Keyword(s):  
Data Acquisition ◽  
Grazing Incidence ◽  
Pixel Detector ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals A diffraction effect in X-ray area detectors

2014 ◽  
Vol 47 (1) ◽  
pp. 378-383 ◽  
Author(s):  
Christian Gollwitzer ◽  
Michael Krumrey
Keyword(s):  
Bragg Reflection ◽  
Energy Calibration ◽  
Diffraction Effect ◽  
Pixel Detector ◽  
Sensor Layer ◽  
X Ray ◽  
Area Detector ◽  
X Ray Scattering ◽  
Detector Surface ◽  
Individual Detector

When an X-ray area detector based on a single-crystalline material, for instance a state-of-the-art hybrid pixel detector, is illuminated from a point source by monochromatic radiation, a pattern of lines appears which overlays the detected image. These lines are easily seen in scattering experiments with smooth patterns, such as small-angle X-ray scattering. The origin of this effect is Bragg reflection within the sensor layer of the detector. Experimental images are presented over a photon energy range from 3.4 to 10 keV, together with a theoretical analysis. The intensity of the detected signal is decreased by up to 20% on this pattern, which can affect the evaluation of scattering and diffraction experiments. The patterns can be exploited to check the alignment of the detector surface with the direct beam, and the alignment of individual detector modules with each other in the case of modular detectors, as well as for energy calibration of the radiation.

A pixel detector with large dynamic range for high photon counting rates

2002 ◽  
Vol 35 (4) ◽  
pp. 471-476 ◽  
Author(s):  
J.-F. Bérar ◽  
L. Blanquart ◽  
N. Boudet ◽  
P. Breugnon ◽  
B. Caillot ◽  
...  
Keyword(s):  
Room Temperature ◽  
Dynamic Range ◽  
Photon Counting ◽  
Pixel Detector ◽  
Pixel Size ◽  
Large Dynamic Range ◽  
X Ray ◽  
Photon Counting Detector ◽  
X Ray Scattering ◽  
Diffraction Patterns

In this paper, results obtained from a prototype photon counting detector are presented. The pixel size is 330 µm × 330 µm for a total area of 16 µm × 40 mm. The detector works at room temperature and its dynamic response ranges from 0.01 up to 106photons pixel−1s−1. An energy resolution of about 1.5 keV has been measured. Very encouraging small-angle X-ray scattering (SAXS) and diffraction patterns were obtained, demonstrating the success of the prototype. Plans for future developments based on this study are presented.

scholarly journals Opportunities and challenges in neutron crystallography

2020 ◽  
Vol 236 ◽  
pp. 02001
Author(s):  
Nathan Richard Zaccai ◽  
Nicolas Coquelle
Keyword(s):  
X Rays ◽  
Hydrogen Atoms ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Nuclei ◽  
X Ray Scattering ◽  
Data Collection And Analysis ◽  
Analysis Strategies ◽  
Structural Insights ◽  
Neutron Crystallography

Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.

scholarly journals Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130318 ◽  
Author(s):  
Richard Neutze
Keyword(s):  
Structural Dynamics ◽  
Free Electron ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Protein Structural Dynamics ◽  
Structural Biochemistry ◽  
Scientific Questions ◽  
Serial Femtosecond Crystallography

X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 10 12 X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

Time-Resolved Cryo-Electron Microscopy of Oscillating Microtubules

1990 ◽  
Vol 48 (1) ◽  
pp. 502-503
Author(s):  
Eva-Maria Mandelkow ◽  
Ron Milligan
Keyword(s):  
Electron Microscopy ◽  
Dynamic Instability ◽  
Entire Solution ◽  
Reaction Scheme ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
A Chain ◽  
Ray Scattering

Microtubules form part of the cytoskeleton of eukaryotic cells. They are hollow libers of about 25 nm diameter made up of 13 protofilaments, each of which consists of a chain of heterodimers of α-and β-tubulin. Microtubules can be assembled in vitro at 37°C in the presence of GTP which is hydrolyzed during the reaction, and they are disassembled at 4°C. In contrast to most other polymers microtubules show the behavior of “dynamic instability”, i.e. they can switch between phases of growth and phases of shrinkage, even at an overall steady state [1]. In certain conditions an entire solution can be synchronized, leading to autonomous oscillations in the degree of assembly which can be observed by X-ray scattering (Fig. 1), light scattering, or electron microscopy [2-5]. In addition such solutions are capable of generating spontaneous spatial patterns [6].In an earlier study we have analyzed the structure of microtubules and their cold-induced disassembly by cryo-EM [7]. One result was that disassembly takes place by loss of protofilament fragments (tubulin oligomers) which fray apart at the microtubule ends. We also looked at microtubule oscillations by time-resolved X-ray scattering and proposed a reaction scheme [4] which involves a cyclic interconversion of tubulin, microtubules, and oligomers (Fig. 2). The present study was undertaken to answer two questions: (a) What is the nature of the oscillations as seen by time-resolved cryo-EM? (b) Do microtubules disassemble by fraying protofilament fragments during oscillations at 37°C?

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