Sample cell for studying liquid interfaces with an in situ electric field using X-ray reflectivity and application to clay particles at oil – oil interfaces
Commissioning results of a liquid sample cell for X-ray reflectivity studies with an in situ applied electrical field are presented. The cell consists of a Plexiglas container with lateral Kapton windows for air – liquid and liquid – liquid interface studies, and was constructed with grooves to accept plate electrodes on the walls parallel to the direction of the beam. Both copper and ITO plate electrodes have been used, the latter being useful for simultaneous optical studies. Commissioning tests were made at the I07 beamline of the Diamond Light Source. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Larsen, S.R. Hansteen, M. Pacakova, B. Theodor, K. Arnold, T. Rennie, A.R. Helgesen, G. Knudsen, K.D. Bordallo, H.N. Fossum, J.O. Cavalcanti, L.P. Tags: X ray reflectivity electrical field liquid surface oil – oil interface clay laboratory notes Source Type: research
A convolutional neural network-based screening tool for X-ray serial crystallography
A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Ke, T.-W. Brewster, A.S. Yu, S.X. Ushizima, D. Yang, C. Sauter, N.K. Tags: convolutional neural networks deep learning serial crystallography X-ray free-electron laser macromolecular structure research papers Source Type: research
Characterization of the surface contamination of deep X-ray lithography mirrors exposed to synchrotron radiation
In deep X-ray lithography (DXRL), synchrotron radiation is applied to pattern polymer microstructures. At the Synchrotron Laboratory for Micro and Nano Devices (SyLMAND), Canadian Light Source, a chromium-coated grazing-incidence X-ray double-mirror system is applied as a tunable low-pass filter. In a systematic study, the surface conditions of the two mirrors are analyzed to determine the mirror reflectivity for DXRL process optimization, without the need for spectral analysis or surface probing: PMMA resist foils were homogeneously exposed and developed to determine development rates for mirror angles between 6 mrad ...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Achenbach, S. Wells, G. Shen, C. Tags: mirror reflectivity oxidation carbon contamination development rate X-ray lithography research papers Source Type: research
Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources
Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic – plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spect...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Tang, M.X. Zhang, Y.Y. E, J.C. Luo, S.N. Tags: single-crystal tantalum molecular dynamics synchrotron undulator sources X-ray diffraction simulation lattice strain research papers Source Type: research
Synchrotron X-ray microbeam dosimetry with a 20 micrometre resolution scintillator fibre-optic dosimeter
Cancer is one of the leading causes of death worldwide. External beam radiation therapy is one of the most important modalities for the treatment of cancers. Synchrotron microbeam radiation therapy (MRT) is a novel pre-clinical therapy that uses highly spatially fractionated X-ray beams to target tumours, allowing doses much higher than conventional radiotherapies to be delivered. A dosimeter with a high spatial resolution is required to provide the appropriate quality assurance for MRT. This work presents a plastic scintillator fibre optic dosimeter with a one-dimensional spatial resolution of 20 µ m, an improve...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Archer, J. Li, E. Petasecca, M. Stevenson, A. Livingstone, J. Dipuglia, A. Davis, J. Rosenfeld, A. Lerch, M. Tags: microbeam radiation therapy scintillator dosimetry fibre-optic dosimeters research papers Source Type: research
High-speed tomography under extreme conditions at the PSICHE beamline of the SOLEIL Synchrotron
In situ microtomography at high pressure and temperature has developed rapidly in the last decade, driven by the development of new high-pressure apparatus. It is now routinely possible to characterize material under high pressure with acquisition times for tomograms of the order of tens of minutes. Here, advantage was taken of the possibility to combine the use of a pink beam projected through a standard Paris – Edinburgh press in order to demonstrate the possibility to perform high-speed synchrotron X-ray tomography at high pressure and temperature allowing complete high-resolution tomograms to be acquired in about...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Boulard, E. King, A. Guignot, N. Deslandes, J.-P. Le Godec, Y. Perrillat, J.-P. Clark, A. Morard, G. Iti é , J.-P. Tags: X-ray absorption tomography high pressure melt research papers Source Type: research
Wavelet processing and digital interferometric contrast to improve reconstructions from X-ray Gabor holograms
In this work, the application of an undecimated wavelet transformation together with digital interferometric contrast to improve the resulting reconstructions in a digital hard X-ray Gabor holographic microscope is shown. Specifically, the starlet transform is used together with digital Zernike contrast. With this contrast, the results show that only a small set of scales from the hologram are, in effect, useful, and it is possible to enhance the details of the reconstruction. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Aguilar, J.C. Misawa, M. Matsuda, K. Suzuki, Y. Takeuchi, A. Yasumoto, M. Tags: holography X-ray microscopy wavelet transformation research papers Source Type: research
Investigation of the multiplet features of SrTiO3 in X-ray absorption spectra based on configuration interaction calculations
Synchrotron-based L2,3-edge absorption spectra show strong sensitivities to the local electronic structure and chemical environment. However, detailed physical information cannot be extracted easily without computational aids. Here, using the experimental Ti L2,3-edges absorption spectrum of SrTiO3 as a fingerprint and considering full multiplet effects, calculations yield different energy parameters characterizing local ground state properties. The peak splitting and intensity ratios of the L3 and L2 set of peaks are carefully analyzed quantitatively, giving rise to a small hybridization energy around 1.2 eV, and the ...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Wu, M. Xin, H.L. Wang, J.O. Li, X.J. Yuan, X.B. Zeng, H. Zheng, J.-C. Wang, H.-Q. Tags: soft X-ray absorption configuration interaction cluster calculation 3d transition metal oxide crystal field effect research papers Source Type: research
Development of an X-ray imaging system to prevent scintillator degradation for white synchrotron radiation
The high flux of the white X-ray beams from third-generation synchrotron light sources can significantly benefit the development of high-speed X-ray imaging, but can also bring technical challenges to existing X-ray imaging systems. One prevalent problem is that the image quality deteriorates because of dust particles accumulating on the scintillator screen during exposure to intense X-ray radiation. Here, this problem has been solved by embedding the scintillator in a flowing inert-gas environment. It is also shown that the detector maintains the quality of the captured images even after days of X-ray exposure. This modif...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Zhou, T. Wang, H. Connolley, T. Scott, S. Baker, N. Sawhney, K. Tags: white-beam detector fast imaging phase contrast scintillators X-ray exposure inert gas research papers Source Type: research
SLS-2 – the upgrade of the Swiss Light Source
An upgrade of the Swiss Light Source (SLS) is planned for 2021 – 2024 and includes the exchange of the existing storage ring by a new one providing about 40 – 50 times lower emittance in user operation mode. This will extend the performance of SLS in particular in the fields of coherent imaging, full-field tomography, soft X-ray angle-resolved photoelectron spectroscopy and resonant inelastic X-ray scattering. A science case and a conceptual design for the machine have been established. As a summary of these reports, the novel lattice design, undulator developments and scientific highlights are presented. (Sour...
Source: Journal of Synchrotron Radiation - April 24, 2018 Category: Physics Authors: Streun, A. Garvey, T. Rivkin, L. Schlott, V. Schmidt, T. Willmott, P. Wrulich, A. Tags: synchrotron radiation facility electron storage ring low-emittance lattice undulator imaging molecular biology X-ray spectroscopy feature articles Source Type: research
Quick X-ray reflectivity using monochromatic synchrotron radiation for time-resolved applications
A new technique for the parallel collection of X-ray reflectivity (XRR) data, compatible with monochromatic synchrotron radiation and flat substrates, is described and applied to the in situ observation of thin-film growth. The method employs a polycapillary X-ray optic to produce a converging fan of radiation, incident onto a sample surface, and an area detector to simultaneously collect the XRR signal over an angular range matching that of the incident fan. Factors determining the range and instrumental resolution of the technique in reciprocal space, in addition to the signal-to-background ratio, are described in detail...
Source: Journal of Synchrotron Radiation - April 5, 2018 Category: Physics Authors: Joress, H. Brock, J.D. Woll, A.R. Tags: X-ray reflectivity time-resolved in situ quick XRR film growth research papers Source Type: research
The fractional Fourier transform as a simulation tool for lens-based X-ray microscopy
The fractional Fourier transform (FrFT) is introduced as a tool for numerical simulations of X-ray wavefront propagation. By removing the strict sampling requirements encountered in typical Fourier optics, simulations using the FrFT can be carried out with much decreased detail, allowing, for example, on-line simulation during experiments. Moreover, the additive index property of the FrFT allows the propagation through multiple optical components to be simulated in a single step, which is particularly useful for compound refractive lenses (CRLs). It is shown that it is possible to model the attenuation from the entire CRL ...
Source: Journal of Synchrotron Radiation - April 5, 2018 Category: Physics Authors: Pedersen, A.F. Simons, H. Detlefs, C. Poulsen, H.F. Tags: wavefront propagation compound refractive lens X-ray microscopy research papers Source Type: research
MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron
MX2 is an in-vacuum undulator-based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range 4.8 – 21 keV to a focal spot of 22 × 12 µ m FWHM (H × V). At 13 keV the flux at the sample is 3.4 × 1012 photons s − 1. The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard-to-crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic dru...
Source: Journal of Synchrotron Radiation - April 3, 2018 Category: Physics Authors: Arag ã o, D. Aishima, J. Cherukuvada, H. Clarken, R. Clift, M. Cowieson, N.P. Ericsson, D.J. Gee, C.L. Macedo, S. Mudie, N. Panjikar, S. Price, J.R. Riboldi-Tunnicliffe, A. Rostan, R. Williamson, R. Caradoc-Davies, T.T. Tags: microfocus beamlines apertures undulators macromolecular crystallography remote access anomalous scattering EIGER detector long wavelengths collimators Source Type: research
Magnetic assessment and modelling of the Aramis undulator beamline
Within the SwissFEL project at the Paul Scherrer Institute (PSI), the hard X-ray line (Aramis) has been equipped with short-period in-vacuum undulators, known as the U15 series. The undulator design has been developed within the institute itself, while the prototyping and the series production have been implemented through a close collaboration with a Swiss industrial partner, Max Daetwyler AG, and several subcontractors. The magnetic measurement system has been built at PSI, together with all the data analysis tools. The Hall probe has been designed for PSI by the Swiss company SENIS. In this paper the general concepts of...
Source: Journal of Synchrotron Radiation - April 3, 2018 Category: Physics Authors: Calvi, M. Camenzuli, C. Ganter, R. Sammut, N. Schmidt, Th. Tags: hard X-ray line in-vacuum undulator magnetic measurements research papers Source Type: research
Effects of soft X-ray radiation damage on paraffin-embedded rat tissues supported on ultralene: a chemical perspective
Radiation damage is an important aspect to be considered when analysing biological samples with X-ray techniques as it can induce chemical and structural changes in the specimens. This work aims to provide new insights into the soft X-ray induced radiation damage of the complete sample, including not only the biological tissue itself but also the substrate and embedding medium, and the tissue fixation procedure. Sample preparation and handling involves an unavoidable interaction with the sample matrix and could play an important role in the radiation-damage mechanism. To understand the influence of sample preparation and h...
Source: Journal of Synchrotron Radiation - April 3, 2018 Category: Physics Authors: Bedolla, D.E. Mantuano, A. Pickler, A. Mota, C.L. Braz, D. Salata, C. Almeida, C.E. Birarda, G. Vaccari, L. Barroso, R.C. Gianoncelli, A. Tags: soft X-ray microscopy radiation damage Fourier transform infrared (FTIR) paraffin ultralene fixation research papers Source Type: research
XFEL experiments: jitter of pump – probe time delays and pulse intensities
Jitter of XFEL signals due to fluctuations in shot-to-shot time delays and intensities are explored in the frame of a statistical theory of X-ray diffraction from liquids. Deformed signals are calculated at different levels of pump – probe jitter. A new method is proposed to eliminate these distortions. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - March 28, 2018 Category: Physics Authors: Bratos, S. Wulff, M. Leicknam, J.-C. Tags: X-ray free-electron lasers femtosecond time-sorting research papers Source Type: research
First-principles X-ray absorption dose calculation for time-dependent mass and optical density
A dose integral of time-dependent X-ray absorption under conditions of variable photon energy and changing sample mass is derived from first principles starting with the Beer – Lambert (BL) absorption model. For a given photon energy the BL dose integral D(e, t) reduces to the product of an effective time integral T(t) and a dose rate R(e). Two approximations of the time-dependent optical density, i.e. exponential A(t) = c + aexp( − bt) for first-order kinetics and hyperbolic A(t) = c + a/(b + t) for second-order kinetics, were considered for BL dose evaluation. For both models three methods of evaluating t...
Source: Journal of Synchrotron Radiation - March 28, 2018 Category: Physics Authors: Berejnov, V. Rubinstein, B. Melo, L.G.A. Hitchcock, A.P. Tags: X-ray absorption dose integral STXM radiation damage research papers Source Type: research
Pulse intensity characterization of the LCLS nanosecond double-bunch mode of operation
The recent demonstration of the `nanosecond double-bunch' operation mode, i.e. two X-ray pulses separated in time between 0.35 and hundreds of nanoseconds and by increments of 0.35 ns, offers new opportunities to investigate ultrafast dynamics in diverse systems of interest. However, in order to reach its full potential, this mode of operation requires the precise characterization of the intensity of each X-ray pulse within each pulse pair for any time separation. Here, a transmissive single-shot diagnostic that achieves this goal for time separations larger than 0.7 ns with a precision better than 5% is presented....
Source: Journal of Synchrotron Radiation - March 27, 2018 Category: Physics Authors: Sun, Y. Decker, F.-J. Turner, J. Song, S. Robert, A. Zhu, D. Tags: FEL X-ray XSVS speckle XPCS research papers Source Type: research
Hybrid modelling of a high-power X-ray attenuator plasma
X-ray gas attenuators act as stress-free high-pass filters for synchrotron and free-electron laser beamlines to reduce the heat load in downstream optical elements without affecting other properties of the X-ray beam. The absorption of the X-ray beam triggers a cascade of processes that ionize and heat up the gas locally, changing its density and therefore the X-ray absorption. Aiming to understand and predict the behaviour of the gas attenuator in terms of efficiency versus gas pressure, a hybrid model has been developed, combining three approaches: an analytical description of the X-ray absorption; Monte Carlo for the el...
Source: Journal of Synchrotron Radiation - March 27, 2018 Category: Physics Authors: Mart í n Ortega, Á . Lacoste, A. Minea, T. Tags: gas attenuator X-ray absorption plasma model fluid model Monte Carlo research papers Source Type: research
Quantitative study of the influence of swimming therapy on osteoporosis rat models based on synchrotron radiation computed tomogaphy
Osteoporosis is a bone disease with a variety of causes, leading to bone pain and fragility to fracture. Major treatment methods include nutrition therapy, exercise therapy, drug therapy and surgical treatment, among which exercise therapy, such as swimming, is the most effective. To investigate the optimal swimming therapy regime for postmenopausal women, the effects of eight weeks of different intensity swimming exercises were studied in rat models. After the swimming program, lumbar vertebrae were dissected from all the rats and scanned by synchrotron radiation computed tomography (SRCT). Histomorphometry analysis and f...
Source: Journal of Synchrotron Radiation - March 27, 2018 Category: Physics Authors: Huang, L. Xu, J. Guo, H. Wang, Y. Zhao, J. Sun, J. Tags: swimming different intensities bone strength research papers Source Type: research
A scanning transmission X-ray microscope at the Pohang Light Source
A scanning transmission X-ray microscope is operational at the 10A beamline at the Pohang Light Source. The 10A beamline provides soft X-rays in the photon energy range 100 – 2000 eV using an elliptically polarized undulator. The practically usable photon energy range of the scanning transmission X-ray microscopy (STXM) setup is from ∼ 150 to ∼ 1600 eV. With a zone plate of 25 nm outermost zone width, the diffraction-limited space resolution, ∼ 30 nm, is achieved in the photon energy range up to ∼ 850 eV. In transmission mode for thin samples, STXM provides the element, chemical st...
Source: Journal of Synchrotron Radiation - March 15, 2018 Category: Physics Authors: Shin, H.-J. Kim, N. Kim, H.-S. Lee, W.-W. Lee, C.-S. Kim, B. Tags: STXM spectronanoscopy spectromicroscopy soft X-ray fluorescence beamlines Source Type: research
X-ray beam-position feedback system with easy-to-use beam-position monitor
X-ray beam-position stability is indispensable in cutting-edge experiments using synchrotron radiation. Here, for the first time, a beam-position feedback system is presented that utilizes an easy-to-use X-ray beam-position monitor incorporating a diamond-fluorescence screen. The acceptable range of the monitor is above 500 µ m and the feedback system maintains the beam position within 3 µ m. In addition to being inexpensive, the system has two key advantages: it works without a scale factor for position calibration, and it has no dependence on X-ray energy, X-ray intensity, beam size or beam shape. (So...
Source: Journal of Synchrotron Radiation - March 14, 2018 Category: Physics Authors: Park, J.Y. Kim, Y. Lee, S. Lim, J. Tags: X-ray beam-position monitor diamond-fluorescence screen feedback system short communications Source Type: research
Influence of the core-hole effect on optical properties of magnesium oxide (MgO) near the Mg L-edge region
The influence of the core-hole effect on optical properties of magnesium oxide (MgO) is established through experimental determination of optical constants and first-principles density functional theory studies. Optical constants ( δ and β ) of MgO thin film are measured in the spectral region 40 – 300 eV using reflectance spectroscopy techniques at the Indus-1 synchrotron radiation source. The obtained optical constants show strong core exciton features near the Mg L-edge region, causing significant mismatch with Henke's tabulated values. On comparing the experimentally obtained optical constants with...
Source: Journal of Synchrotron Radiation - March 14, 2018 Category: Physics Authors: Sinha, M. Modi, M.H. Ghosh, H. Yadav, P.K. Gupta, R.K. Tags: synchrotron radiation soft X-ray magnesium compound core-hole effect optical property research papers Source Type: research
Beam-induced redox transformation of arsenic during As K-edge XAS measurements: availability of reducing or oxidizing agents and As speciation
In this study, the As species immobilized by poorly crystallized mackinawite (FeS) was assessed for the susceptibility to beam-induced redox reactions as a function of sample properties including the redox state of FeS and the solid-phase As speciation. The beam-induced oxidation of reduced As species was found to be mediated by the atmospheric O2 and the oxidation products of FeS [e.g. Fe(III) (oxyhydr)oxides and intermediate sulfurs]. Regardless of the redox state of FeS, both arsenic sulfide and surface-complexed As(III) readily underwent the photo-oxidation upon exposure to the atmospheric O2 during XAS measurements. W...
Source: Journal of Synchrotron Radiation - March 14, 2018 Category: Physics Authors: Han, Y.-S. Jeong, H.Y. Hyun, S.P. Hayes, K.F. Chon, C.-M. Tags: X-ray absorption spectroscopy photocatalytic transformation mackinawite arsenic linear combination fitting research papers Source Type: research
(Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - February 28, 2018 Category: Physics Authors: , Tags: current events Source Type: research
Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE. Erratum
Corrections to an equation and a figure in the paper by Paithankar et al. (2009). [J. Synchrotron Rad. 16, 152 – 162] are made. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - February 28, 2018 Category: Physics Authors: Paithankar, K.S. Owen, R.L. Garman, E.F. Tags: absorbed dose macromolecular crystallography experimental dose limit fluorescence escape photoelectric absorption addenda and errata Source Type: research
Commissioning of a multi-beamline femtoslicing facility at SOLEIL
The investigation of ultrafast dynamics, taking place on the few to sub-picosecond time scale, is today a very active research area pursued in a variety of scientific domains. With the recent advent of X-ray free-electron lasers (XFELs), providing very intense X-ray pulses of duration as short as a few femtoseconds, this research field has gained further momentum. As a consequence, the demand for access strongly exceeds the capacity of the very few XFEL facilities existing worldwide. This situation motivates the development of alternative sub-picosecond pulsed X-ray sources among which femtoslicing facilities at synchrotro...
Source: Journal of Synchrotron Radiation - February 28, 2018 Category: Physics Authors: Labat, M. Brubach, J.-B. Ciavardini, A. Couprie, M.-E. Elkaim, E. Fertey, P. Ferte, T. Hollander, P. Hubert, N. Jal, E. Laulh é , C. Luning, J. Marcouill é , O. Moreno, T. Morin, P. Polack, F. Prigent, P. Ravy, S. Ricaud, J.-P. Roy, P. Silly, M. Sirotti Tags: femtoslicing storage ring coherent THz research papers Source Type: research
An X-ray harmonic separator for next-generation synchrotron X-ray sources and X-ray free-electron lasers
An X-ray prism for the extraction of a specific harmonic of undulator radiation is proposed. By using the prism in a grazing incidence geometry, the beam axes of fundamental and harmonics of undulator radiation are separated with large angles over 10 µ rad, which enables the selection of a specific harmonic with the help of apertures, while keeping a high photon flux. The concept of the harmonic separation was experimentally confirmed using X-ray beams from the X-ray free-electron laser SACLA. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - February 28, 2018 Category: Physics Authors: Inoue, I. Osaka, T. Tamasaku, K. Ohashi, H. Yamazaki, H. Goto, S. Yabashi, M. Tags: harmonic radiation X-ray free-electron lasers diffraction-limited storage rings harmonic separation SACLA research papers Source Type: research
Hiromichi Kamitsubo (1933 – 2017)
(Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - February 28, 2018 Category: Physics Authors: Ishikawa, T. Hasnain, S. Tags: obituary SPring-8 RIKEN JASRI SACLA obituaries Source Type: research
Quantitative investigation of linear arbitrary polarization in an APPLE-II undulator
Insertion devices are utilized at synchrotron radiation facilities around the world for their capability to provide a high-brilliance X-ray beam. APPLE-II type undulators are especially important for their capacity to switch between a variety of photon beam polarization states. A high-precision soft X-ray polarimeter has been used to investigate the polarization calibration of an APPLE-II undulator (period length λ u = 64 mm) installed on beamline I06 at Diamond Light Source. Systematic measurement of the beam polarization state at a range of linear arbitrary angles has been compared with the expected result for...
Source: Journal of Synchrotron Radiation - February 22, 2018 Category: Physics Authors: Hand, M. Wang, H. Maccherozzi, F. Apollonio, M. Zhu, J. Dhesi, S.S. Sawhney, K. Tags: polarization multilayers synchrotron radiation undulators research papers Source Type: research
Real-space analysis of radiation-induced specific changes with independent component analysis
A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identif...
Source: Journal of Synchrotron Radiation - February 22, 2018 Category: Physics Authors: Borek, D. Bromberg, R. Hattne, J. Otwinowski, Z. Tags: independent component analysis (ICA) singular value decomposition (SVD) radiation damage tunnelling research papers Source Type: research
Evaluation of the UFXC32k photon-counting detector for pump – probe experiments using synchrotron radiation
This paper presents the performance of a single-photon-counting hybrid pixel X-ray detector with synchrotron radiation. The camera was evaluated with respect to time-resolved experiments, namely pump – probe – probe experiments held at SOLEIL. The UFXC camera shows very good energy resolution of around 1.5 keV and allows the minimum threshold setting to be as low as 3 keV keeping the high-count-rate capabilities. Measurements of a synchrotron characteristic filling mode prove the proper separation of an isolated bunch of photons and the usability of the detector in time-resolved experiments. (Source: Jo...
Source: Journal of Synchrotron Radiation - February 21, 2018 Category: Physics Authors: Koziol, A. Bordessoule, M. Ciavardini, A. Dawiec, A. Da Silva, P. Desjardins, K. Grybos, P. Kanoute, B. Laulhe, C. Maj, P. Menneglier, C. Mercere, P. Orsini, F. Szczygiel, R. Tags: pump – probe experiments UFXC32k single-photon counting pixel array detector high frame rate research papers Source Type: research
Automatic Debye – Scherrer elliptical ring extraction via a computer vision approach
The accurate calibration of powder diffraction data acquired from area detectors using calibration standards is a crucial step in the data reduction process to attain high-quality one-dimensional patterns. A novel algorithm has been developed for extracting Debye – Scherrer rings automatically using an approach based on computer vision and pattern recognition techniques. The presented technique requires no human intervention and, unlike previous approaches, makes no restrictive assumptions on the diffraction setup and/or rings. It can detect complete rings as well as portions of them, and works on several types of di...
Source: Journal of Synchrotron Radiation - February 21, 2018 Category: Physics Authors: Shahzad, S. Khan, N. Nawaz, Z. Ferrero, C. Tags: powder diffraction calibration 2D patterns computer vision research papers Source Type: research
A Li K-edge XANES study of salts and minerals
The first comprehensive Li K-edge XANES study of a varied suite of Li-bearing minerals is presented. Drastic changes in the bonding environment for lithium are demonstrated and this can be monitored using the position and intensity of the main Li K-absorption edge. The complex silicates confirm the assignment of the absorption edge to be a convolution of triply degenerate p-like states as previously proposed for simple lithium compounds. The Li K-edge position depends on the electronegativity of the element to which it is bound. The intensity of the first peak varies depending on the existence of a 2p electron and can be u...
Source: Journal of Synchrotron Radiation - February 21, 2018 Category: Physics Authors: O'Shaughnessy, C. Henderson, G.S. Moulton, B.J.A. Zuin, L. Neuville, D.R. Tags: XANES lithium silicates phosphates salts research papers Source Type: research
X-ray Raman spectroscopy of lithium-ion battery electrolyte solutions in a flow cell
The effects of varying LiPF6 salt concentration and the presence of lithium bis(oxalate)borate additive on the electronic structure of commonly used lithium-ion battery electrolyte solvents (ethylene carbonate – dimethyl carbonate and propylene carbonate) have been investigated. X-ray Raman scattering spectroscopy (a non-resonant inelastic X-ray scattering method) was utilized together with a closed-circle flow cell. Carbon and oxygen K-edges provide characteristic information on the electronic structure of the electrolyte solutions, which are sensitive to local chemistry. Higher Li+ ion concentration in the solvent ...
Source: Journal of Synchrotron Radiation - February 21, 2018 Category: Physics Authors: Ketenoglu, D. Spiekermann, G. Harder, M. Oz, E. Koz, C. Yagci, M.C. Yilmaz, E. Yin, Z. Sahle, C.J. Detlefs, B. Yava ş , H. Tags: non-resonant inelastic X-ray scattering lithium-ion battery electrolyte C and O K-edge spectra research papers Source Type: research
miXAFS: a program for X-ray absorption fine-structure data analysis
A new program called miXAFS for the analysis of X-ray absorption fine-structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X-ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R-factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and fr...
Source: Journal of Synchrotron Radiation - February 20, 2018 Category: Physics Authors: Ikemoto, H. Tags: XAFS analysis program multi-edge fitting computer programs Source Type: research
Real-time diffraction computed tomography data reduction
Diffraction imaging is an X-ray imaging method which uses the crystallinity information (cell parameter, orientation) as a signal to create an image pixel by pixel: a pencil beam is raster-scanned onto a sample and the (powder) diffraction signal is recorded by a large area detector. With the flux provided by third-generation synchrotrons and the speed of hybrid pixel detectors, the acquisition speed of these experiments is now limited by the transfer rate to the local storage as the data reduction can hardly be performed in real time. This contribution presents the benchmarking of a typical data analysis pipeline for a di...
Source: Journal of Synchrotron Radiation - February 20, 2018 Category: Physics Authors: Kieffer, J. Petitdemange, S. Vincent, T. Tags: powder diffraction diffraction imaging Pilatus detector image compression azimuthal integration pyFAI FabIO silx computer programs Source Type: research
Solid energy calibration standards for P K-edge XANES: electronic structure analysis of PPh4Br
P K-edge X-ray absorption near-edge structure (XANES) spectroscopy is a powerful method for analyzing the electronic structure of organic and inorganic phosphorus compounds. Like all XANES experiments, P K-edge XANES requires well defined and readily accessible calibration standards for energy referencing so that spectra collected at different beamlines or under different conditions can be compared. This is especially true for ligand K-edge X-ray absorption spectroscopy, which has well established energy calibration standards for Cl (Cs2CuCl4) and S (Na2S2O3 · 5H2O), but not neighboring P. This paper presents a revi...
Source: Journal of Synchrotron Radiation - February 20, 2018 Category: Physics Authors: Blake, A.V. Wei, H. Donahue, C.M. Lee, K. Keith, J.M. Daly, S.R. Tags: P K-edge XANES energy calibration standards ligand K-edge XAS time-dependent density functional theory research papers Source Type: research
Characterization of a quadrant diamond transmission X-ray detector including a precise determination of the mean electron – hole pair creation energy
Precise monitoring of the incoming photon flux is crucial for many experiments using synchrotron radiation. For photon energies above a few keV, thin semiconductor photodiodes can be operated in transmission for this purpose. Diamond is a particularly attractive material as a result of its low absorption. The responsivity of a state-of-the art diamond quadrant transmission detector has been determined, with relative uncertainties below 1% by direct calibration against an electrical substitution radiometer. From these data and the measured transmittance, the thickness of the involved layers as well as the mean electron &nda...
Source: Journal of Synchrotron Radiation - February 20, 2018 Category: Physics Authors: Keister, J.W. Cibik, L. Schreiber, S. Krumrey, M. Tags: X-ray detectors diamond calibration scattering quadrant diamond transmission X-ray detector research papers Source Type: research
A high-energy-resolution resonant inelastic X-ray scattering spectrometer at ID20 of the European Synchrotron Radiation Facility
An end-station for resonant inelastic X-ray scattering and (resonant) X-ray emission spectroscopy at beamline ID20 of ESRF – The European Synchrotron is presented. The spectrometer hosts five crystal analysers in Rowland geometry for large solid angle collection and is mounted on a rotatable arm for scattering in both the horizontal and vertical planes. The spectrometer is optimized for high-energy-resolution applications, including partial fluorescence yield or high-energy-resolution fluorescence detected X-ray absorption spectroscopy and the study of elementary electronic excitations in solids. In addition, it can ...
Source: Journal of Synchrotron Radiation - February 20, 2018 Category: Physics Authors: Moretti Sala, M. Martel, K. Henriquet, C. Al Zein, A. Simonelli, L. Sahle, C. Gonzalez, H. Lagier, M.-C. Ponchut, C. Huotari, S. Verbeni, R. Krisch, M. Monaco, G. Tags: resonant inelastic X-ray scattering X-ray emission ID20 beamline RIXS spectrometer ESRF research papers Source Type: research
Time-resolved ion imaging at free-electron lasers using TimepixCam
The application of a novel fast optical-imaging camera, TimepixCam, to molecular photoionization experiments using the velocity-map imaging technique at a free-electron laser is described. TimepixCam is a 256 × 256 pixel CMOS camera that is able to detect and time-stamp ion hits with 20 ns timing resolution, thus making it possible to record ion momentum images for all fragment ions simultaneously and avoiding the need to gate the detector on a single fragment. This allows the recording of significantly more data within a given amount of beam time and is particularly useful for pump – probe experime...
Source: Journal of Synchrotron Radiation - February 20, 2018 Category: Physics Authors: Fisher-Levine, M. Boll, R. Ziaee, F. Bomme, C. Erk, B. Rompotis, D. Marchenko, T. Nomerotski, A. Rolles, D. Tags: time-stamping camera velocity map imaging VMI free-electron laser FEL ultrafast laser pump – probe experiments mass spectrometry research papers Source Type: research
Finite lifetime broadening of calculated X-ray absorption spectra: possible artefacts close to the edge
X-ray absorption spectra calculated within an effective one-electron approach have to be broadened to account for the finite lifetime of the core hole. For methods based on Green's function this can be achieved either by adding a small imaginary part to the energy or by convoluting the spectra on the real axis with a Lorentzian. By analyzing the Fe K- and L2,3-edge spectra it is demonstrated that these procedures lead to identical results only for energies higher than a few core-level widths above the absorption edge. For energies close to the edge, spurious spectral features may appear if too much weight is put on broaden...
Source: Journal of Synchrotron Radiation - February 19, 2018 Category: Physics Authors: Š ipr, O. Vack á r, J. Min á r, J. Tags: X-ray absorption spectroscopy core hole lifetime multiple-scattering formalism research papers Source Type: research
Tris-amidoximate uranyl complexes via η 2 binding mode coordinated in aqueous solution shown by X-ray absorption spectroscopy and density functional theory methods
The present study sheds some light on the long-standing debate concerning the coordination properties between uranyl ions and the amidoxime ligand, which is a key ingredient for achieving efficient extraction of uranium. Using X-ray absorption fine structure combined with theoretical simulation methods, the binding mode and bonding nature of a uranyl – amidoxime complex in aqueous solution were determined for the first time. The results show that in a highly concentrated amidoxime solution the preferred binding mode between UO22+ and the amidoxime ligand is η 2 coordination with tris-amidoximate species. In such ...
Source: Journal of Synchrotron Radiation - February 19, 2018 Category: Physics Authors: Zhang, L. Qie, M. Su, J. Zhang, S. Zhou, J. Li, J. Wang, Y. Yang, S. Wang, S. Li, J. Wu, G. Wang, J.-Q. Tags: uranyl speciation X-ray absorption near-edge structure XANES extended X-ray absorption fine structure EXAFS local coordination structure amidoxime ligand DFT calculations research papers Source Type: research
Counting-loss correction for X-ray spectroscopy using unit impulse pulse shaping
High-precision measurement of X-ray spectra is affected by the statistical fluctuation of the X-ray beam under low-counting-rate conditions. It is also limited by counting loss resulting from the dead-time of the system and pile-up pulse effects, especially in a high-counting-rate environment. In this paper a detection system based on a FAST-SDD detector and a new kind of unit impulse pulse-shaping method is presented, for counting-loss correction in X-ray spectroscopy. The unit impulse pulse-shaping method is evolved by inverse deviation of the pulse from a reset-type preamplifier and a C-R shaper. It is applied to obtain...
Source: Journal of Synchrotron Radiation - February 19, 2018 Category: Physics Authors: Hong, X. Zhou, J. Ni, S. Ma, Y. Yao, J. Zhou, W. Liu, Y. Wang, M. Tags: counting loss correction X-ray spectroscopy unit impulse pulse shaping FAST-SDD detector research papers Source Type: research
Compact coherence enhancement by subharmonic self-seeding in X-ray free-electron laser facilities
X-ray free-electron lasers (FELs) are cutting-edge scientific tools able to generate transversely coherent radiation with very high power and ultra-short pulse durations. The self-seeding mechanism has been proven to increase the longitudinal coherence of the FEL radiation but its efficiency could be significantly improved, especially for soft X-rays. This paper proposes the enhancement of the performance of self-seeding by combining it with the harmonic generation mechanism. In particular, by starting the process with a subharmonic of the wavelength of interest, the coherence of the produced radiation is improved, the und...
Source: Journal of Synchrotron Radiation - February 19, 2018 Category: Physics Authors: Prat, E. Reiche, S. Tags: free-electron laser self-seeding X-ray coherence simulations research papers Source Type: research
Multifarious injection chamber for molecular structure study (MICOSS) system: development and application for serial femtosecond crystallography at Pohang Accelerator Laboratory X-ray Free-Electron Laser
The multifarious injection chamber for molecular structure study (MICOSS) experimental system has been developed at the Pohang Accelerator Laboratory X-ray Free-Electron Laser for conducting serial femtosecond crystallography. This system comprises several instruments such as a dedicated sample chamber, sample injectors, sample environment diagnostic system and detector stage for convenient distance manipulation. Serial femtosecond crystallography experiments of lysozyme crystals have been conducted successfully. The diffraction peaks have reached to ∼ 1.8 Å resolution at the photon energy of 9.785 keV. (...
Source: Journal of Synchrotron Radiation - February 19, 2018 Category: Physics Authors: Park, J. Kim, S. Kim, S. Nam, K.H. Tags: serial femtosecond crystallography PAL-XFEL lysozyme NCI sample injector MICOSS research papers Source Type: research
X-ray reflectivity from curved liquid interfaces
X-ray reflectivity studies of the structure of liquid – vapour and liquid – liquid interfaces at modern sources, such as free-electron lasers, are currently impeded by the lack of dedicated liquid surface diffractometers. It is shown that this obstacle can be overcome by an alternative experimental approach that uses the natural curvature of a liquid drop for variation of the angle of incidence. Two modes of operation are shown: (i) sequential reflectivity measurements by a nanometre beam and (ii) parallel acquisition of large ranges of a reflectivity curve by micrometre beams. The feasibility of the two method...
Source: Journal of Synchrotron Radiation - February 16, 2018 Category: Physics Authors: Festersen, S. Hrkac, S.B. Koops, C.T. Runge, B. Dane, T. Murphy, B.M. Magnussen, O.M. Tags: X-ray reflectivity liquid interfaces methods free-elecron laser synchrotron research papers Source Type: research
Small-angle scattering of polychromatic X-rays: effects of bandwidth, spectral shape and high harmonics
Polychromatic X-ray sources can be useful for photon-starved small-angle X-ray scattering given their high spectral fluxes. Their bandwidths, however, are 10 – 100 times larger than those using monochromators. To explore the feasibility, ideal scattering curves of homogeneous spherical particles for polychromatic X-rays are calculated and analyzed using the Guinier approach, maximum entropy and regularization methods. Monodisperse and polydisperse systems are explored. The influence of bandwidth and asymmetric spectra shape are explored via Gaussian and half-Gaussian spectra. Synchrotron undulator spectra represented...
Source: Journal of Synchrotron Radiation - February 16, 2018 Category: Physics Authors: Chen, S. Luo, S.-N. Tags: SAXS polychromatic size distribution undulator light source research papers Source Type: research
Energy-dependent dead-time correction in digital pulse processors applied to silicon drift detector's X-ray spectra
Dead-time effects in X-ray spectra taken with a digital pulse processor and a silicon drift detector were investigated when the number of events at the low-energy end of the spectrum was more than half of the total, at counting rates up to 56 kHz. It was found that dead-time losses in the spectra are energy dependent and an analytical correction for this effect, which takes into account pulse pile-up, is proposed. This and the usual models have been applied to experimental measurements, evaluating the dead-time fraction either from the calculations or using the value given by the detector acquisition system. The energy...
Source: Journal of Synchrotron Radiation - February 15, 2018 Category: Physics Authors: Barros, S.F. Vanin, V.R, Malafronte, A.A. Maidana, N.L. Martins, M.N. Tags: dead-time correction Si drift detector pile up research papers Source Type: research
Transmission of an X-ray beam through a two-dimensional photonic crystal and the Talbot effect
Results of computer simulations of the transmission of an X-ray beam through a two-dimensional photonic crystal as well as the propagation of an X-ray beam in free space behind the photonic crystal are reported. The photonic crystal consists of a square lattice of silicon cylinders of diameter 0.5 µ m. The amount of matter in the path of the X-ray beam rapidly decreases at the sides of the cylinder projections. Therefore the transmission is localized near the boundaries, and appears like a channeling effect. The iterative method of computer simulations is applied. This method is similar to the multi-slice method ...
Source: Journal of Synchrotron Radiation - February 15, 2018 Category: Physics Authors: Kohn, V.G. Tags: X-ray transmission two-dimensional photonic crystal Talbot effect computer simulations iterative algorithm research papers Source Type: research