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.

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

High-resolution electron microscopy study of a Si-Mo x-ray mirror

1987 ◽  
Vol 45 ◽  
pp. 400-401
Author(s):  
R. Gronsky ◽  
J. Punglia
Keyword(s):  
Materials Science ◽  
High Resolution Electron Microscopy ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Thin Layers ◽  
Light Sources ◽  
X Rays ◽  
Optical Elements ◽  
X Ray ◽  
Resolution Electron

The science of x-ray optics has undergone rapid growth in recent years, spurned by the availability of high intensity light sources with tunable optical characteristics in the XUV spectral region which includes soft x-rays and ultraviolet radiation. The development of optical elements for use with XUV radiation has followed a parallel path of development with most recent emphasis being placed upon multilayer coatings that enhance the reflectivity of x-ray mirrors and at the same time provide spectral selectivity. In their simplest form, these coatings consist of alternating thin layers of two materials with different refractive indices that yield both the desired high reflectivity and a relatively broad wavelength bandpass. Additional considerations are based on their materials science: the multilayers must have atomically smooth interfaces and be resistant to interdiffusion or chemical reaction. A summary of their preparation and utilization is given in reference 3.

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 NSLS-II MX beamlines FMX for micro-crystallography & AMX for highly automated MX

2014 ◽  
Vol 70 (a1) ◽  
pp. C1733-C1733
Author(s):  
Martin Fuchs ◽  
Robert Sweet ◽  
Lonny Berman ◽  
Dileep Bhogadi ◽  
Wayne Hendrickson ◽  
...  
Keyword(s):  
Energy Range ◽  
Structure Determination ◽  
Optical Systems ◽  
Photon Flux ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Binding Studies ◽  
X Ray ◽  
Array Detectors ◽  
Broad Energy Range

We present the final design of the x-ray optical systems and experimental stations of the two macromolecular crystallography (MX) beamlines, FMX and AMX, at the National Synchrotron Light Source-II (NSLS-II). Along with its companion x-ray scattering beamline, LIX, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX, [1]) will begin user operation in 2016. The pair of MX beamlines with complementary and overlapping capabilities is located at canted undulators (IVU21) in sector 17-ID. The Frontier Microfocusing Macromolecular Crystallography beamline (FMX) will deliver a photon flux of ~5x10^12 ph/s at a wavelength of 1 Å into a spot of 1 - 50 µm size. It will cover a broad energy range from 5 - 30 keV, corresponding to wavelengths from 0.4 - 2.5 Å. The highly Automated Macromolecular Crystallography beamline (AMX) will be optimized for high throughput applications, with beam sizes from 4 - 100 µm, an energy range of 5 - 18 keV (0.7 - 2.5 Å), and a flux at 1 Å of ~10^13 ph/s. Central components of the in-house-developed experimental stations are a 100 nm sphere of confusion goniometer with a horizontal axis, piezo-slits to provide dynamic beam size changes during diffraction experiments, a dedicated secondary goniometer for crystallization plates, and sample- and plate-changing robots. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and data collection of crystals in trays, for instance to characterize membrane protein crystals and to conduct ligand-binding studies. Together with the solution scattering program at LIX, the new beamlines will offer unique opportunities for advanced diffraction experiments with micro- and mini-beams, with next generation hybrid pixel array detectors and emerging crystal delivery methods such as acoustic droplet ejection. This work is supported by the US National Institutes of Health.

2D real space visualization of d values in polycrystalline bulk materials of different hardness

2021 ◽  
Vol 54 (2) ◽  
pp. 597-603
Author(s):  
Mari Mizusawa ◽  
Kenji Sakurai
Keyword(s):  
Lattice Distortion ◽  
Structural Information ◽  
Hardness Test ◽  
Real Space ◽  
Polycrystalline Materials ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
D Values

Conventional X-ray diffraction measurements provide some average structural information, mainly on the crystal structure of the whole area of the given specimen, which might not be very uniform and may include different crystal structures, such as co-existing crystal phases and/or lattice distortion. The way in which the lattice plane changes due to strain also might depend on the position in the sample, and the average information might have some limits. Therefore, it is important to analyse the sample with good lateral spatial resolution in real space. Although various techniques for diffraction topography have been developed for single crystals, it has not always been easy to image polycrystalline materials. Since the late 1990s, imaging technology for fluorescent X-rays and X-ray absorption fine structure has been developed via a method that does not scan either a sample or an X-ray beam. X-ray diffraction imaging can be performed when this technique is applied to a synchrotron radiation beamline with a variable wavelength. The present paper reports the application of X-ray diffraction imaging to bulk steel materials with varying hardness. In this study, the distribution of lattice distortion of hardness test blocks with different hardness was examined. Via this 2D visualization method, the grains of the crystals with low hardness are large enough to be observed by X-ray diffraction contrast in real space. The change of the d value in the vicinity of the Vickers mark has also been quantitatively evaluated.

Accelerator-based X-ray sources: synchrotron radiation, X-ray free electron lasers and beyond

2019 ◽  
Vol 377 (2147) ◽  
pp. 20180231 ◽  
Author(s):  
Tetsuya Ishikawa
Keyword(s):  
Synchrotron Radiation ◽  
Storage Ring ◽  
Free Electron ◽  
Continuous Wave ◽  
Transitional Period ◽  
Light Sources ◽  
X Rays ◽  
Free Electron Lasers ◽  
Beam Emittance ◽  
X Ray

The evolution of synchrotron radiation (SR) sources and related sciences is discussed to explain the ‘generation’ of the SR sources. Most of the contemporary SR sources belong to the third generation, where the storage rings are optimized for the use of undulator radiation. The undulator development allowed to reduction of the electron energy of the storage ring necessary for delivering 10 keV X-rays from the initial 6–8 GeV to the current 3 Gev. Now is the transitional period from the double-bend-achromat lattice-based storage ring to the multi-bend-achromat lattice to achieve much smaller electron beam emittance. Free electron lasers are the other important accelerator-based light sources which recently reached hard X-ray regime by using self-amplified spontaneous emission scheme. Future accelerator-based X-ray sources should be continuous wave X-ray free electron lasers and pulsed X-ray free electron lasers. Some pathways to reach the future case are discussed. This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

scholarly journals Future developments for macromolecular crystallography at the CLS

2014 ◽  
Vol 70 (a1) ◽  
pp. C1737-C1737
Author(s):  
Pawel Grochulski ◽  
Miroslaw Cygler ◽  
Michel Fodje ◽  
Shaunivan Labiuk ◽  
James Gorin ◽  
...  
Keyword(s):  
High Efficiency ◽  
Single Photon ◽  
Temporal Stability ◽  
Small Samples ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Optical Elements ◽  
X Ray ◽  
Small Crystals ◽  
Reported Data

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source (CLS) is a suite of fully automated beamlines, 08ID-1 and 08B1-1 [1]. It serves over 60 Canadian groups plus academic and commercial users in the US. Besides remote data collection, we offer Mail-In service where data are collected by CMCF staff. Beamline 08B1-1 has been in operation since 2011 and beamline 08ID-1 since 2006. When beamline 08ID-1 was designed, over 10 years ago, small crystals were defined as having sizes of 50-100 μm. Today, the most challenging experiments require more intense X-ray beams that can be focused to accommodate much smaller crystal sizes of less than 5 μm with flux on the order of 10^11 photons/s. To reach these stringent parameters, a new more powerful source of X-rays will be required, which will be provided by a longer small-gap in-vacuum undulator (SGU). To accommodate the higher power levels and to focus X-rays to a smaller focal spot with a high degree of spatial and temporal stability, the existing X-ray optical elements need to be upgraded. The remaining components of the project include a 5-axis alignment table for improving alignment of small samples with the microbeam, a high-efficiency robotic sample-changer and a single-photon X-ray detector. Several options for the new design will be discussed. These developments are consistent with the current direction of structural biology research at the CLS [2]. Since 2006 over 225 (240) papers and 400 (444) PDB deposits reported data collected at beamline 08ID-1. Parentheses indicate the total number for the CMCF. Many of these have been published in very high impact journals such as N. Engl. J. Med., Nature, Cell, Science, PNAS, among others (http://cmcf.lightsource.ca/publications/).

GENERATION OF X-RAYS WITH A HIGH DEGREE OF LONGITUDINAL COHERENCE

2007 ◽  
Vol 21 (03n04) ◽  
pp. 513-518
Author(s):  
ROBERT ROSSMANITH
Keyword(s):  
Synchrotron Radiation ◽  
Storage Rings ◽  
Light Sources ◽  
X Rays ◽  
X Ray ◽  
Electron Accelerators ◽  
Longitudinal Coherence ◽  
High Degree

Synchrotron radiation produced either in storage rings or SASE-FELs is longitudinally incoherent. In this paper a way to produce short longitudinally coherent X-ray pulses is discussed. In addition it is investigated if these sources can be modified to use them as light sources for vacuum electron accelerators.

scholarly journals All Femtosecond Optical Pump and X-Ray Probe: Holey-Axicon for Free Electron Laser

2020 ◽  
Author(s):  
Vijayakumar Anand ◽  
Jovan Maksimovic ◽  
Tomas Katkus ◽  
Soon Hock Ng ◽  
Orestas Ulcinas ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Optical Axis ◽  
Bessel Beam ◽  
X Rays ◽  
Temporal Dimension ◽  
Optical Elements ◽  
Optical Pump ◽  
X Ray ◽  
Fs Laser

We put forward a co-axial pump(optical)-probe(X-rays) experimental concept and show performance of the optical component. A Bessel beam generator with a central 100 micrometers-diameter hole (on the optical axis) was fabricated using femtosecond (fs) laser structuring inside a silica plate. This flat-axicon optical element produces a needle-like axial intensity distribution which can be used for the optical pump pulse. The fs-X-ray free electron laser (X-FEL) beam of sub-1 micrometer diameter can be introduced through the central hole along the optical axis onto a target as a probe. Different realisations of optical pump are discussed. Such optical elements facilitate alignment of ultra-short fs-pulses in space and time and can be used in light-matter interaction experiments at extreme energy densities on the surface and in the volume of targets. Full advantage of ultra-short 10 fs X-FEL probe pulses with fs-pump(optical) opens an unexplored temporal dimension of phase transitions and the fastest laser-induced rates of material heating and quenching. A wider field of applications of fs-laser-enabled structuring of materials and design of specific optical elements for astrophotonics is presented.

scholarly journals Reconstruction of the two-dimensional gravitational potential of galaxy clusters from X-ray and Sunyaev-Zel’dovich measurements

2018 ◽  
Vol 614 ◽  
pp. A38 ◽  
Author(s):  
C. Tchernin ◽  
M. Bartelmann ◽  
K. Huber ◽  
A. Dekel ◽  
G. Hurier ◽  
...  
Keyword(s):  
Covariance Matrix ◽  
Galaxy Clusters ◽  
Gravitational Potential ◽  
Gravitational Lensing ◽  
Simulated Data ◽  
Forthcoming Paper ◽  
X Rays ◽  
Two Dimensional ◽  
X Ray ◽  
Joint Reconstruction

Context. The mass of galaxy clusters is not a direct observable, nonetheless it is commonly used to probe cosmological models. Based on the combination of all main cluster observables, that is, the X-ray emission, the thermal Sunyaev–Zel’dovich (SZ) signal, the velocity dispersion of the cluster galaxies, and gravitational lensing, the gravitational potential of galaxy clusters can be jointly reconstructed. Aims. We derive the two main ingredients required for this joint reconstruction: the potentials individually reconstructed from the observables and their covariance matrices, which act as a weight in the joint reconstruction. We show here the method to derive these quantities. The result of the joint reconstruction applied to a real cluster will be discussed in a forthcoming paper. Methods. We apply the Richardson-Lucy deprojection algorithm to data on a two-dimensional (2D) grid. We first test the 2D deprojection algorithm on a β-profile. Assuming hydrostatic equilibrium, we further reconstruct the gravitational potential of a simulated galaxy cluster based on synthetic SZ and X-ray data. We then reconstruct the projected gravitational potential of the massive and dynamically active cluster Abell 2142, based on the X-ray observations collected with XMM-Newton and the SZ observations from the Planck satellite. Finally, we compute the covariance matrix of the projected reconstructed potential of the cluster Abell 2142 based on the X-ray measurements collected with XMM-Newton. Results. The gravitational potentials of the simulated cluster recovered from synthetic X-ray and SZ data are consistent, even though the potential reconstructed from X-rays shows larger deviations from the true potential. Regarding Abell 2142, the projected gravitational cluster potentials recovered from SZ and X-ray data reproduce well the projected potential inferred from gravitational-lensing observations. We also observe that the covariance matrix of the potential for Abell 2142 reconstructed from XMM-Newton data sensitively depends on the resolution of the deprojected grid and on the smoothing scale used in the deprojection. Conclusions. We show that the Richardson-Lucy deprojection method can be effectively applied on a grid and that the projected potential is well recovered from real and simulated data based on X-ray and SZ signal. The comparison between the reconstructed potentials from the different observables provides additional information on the validity of the assumptions as function of the projected radius.

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