science and technology Progress in HAXPES performance combining full-field k-imaging with time-of-flight recording By scripts.iucr.org Published On :: 2019-11-01 An alternative approach to hard-X-ray photoelectron spectroscopy (HAXPES) has been established. The instrumental key feature is an increase of the dimensionality of the recording scheme from 2D to 3D. A high-energy momentum microscope detects electrons with initial kinetic energies up to 8 keV with a k-resolution of 0.025 Å−1, equivalent to an angular resolution of 0.034°. A special objective lens with k-space acceptance up to 25 Å−1 allows for simultaneous full-field imaging of many Brillouin zones. Combined with time-of-flight (ToF) parallel energy recording this yields maximum parallelization. Thanks to the high brilliance (1013 hν s−1 in a spot of <20 µm diameter) of beamline P22 at PETRA III (Hamburg, Germany), the microscope set a benchmark in HAXPES recording speed, i.e. several million counts per second for core-level signals and one million for d-bands of transition metals. The concept of tomographic k-space mapping established using soft X-rays works equally well in the hard X-ray range. Sharp valence band k-patterns of Re, collected at an excitation energy of 6 keV, correspond to direct transitions to the 28th repeated Brillouin zone. Measured total energy resolutions (photon bandwidth plus ToF-resolution) are 62 meV and 180 meV FWHM at 5.977 keV for monochromator crystals Si(333) and Si(311) and 450 meV at 4.0 keV for Si(111). Hard X-ray photoelectron diffraction (hXPD) patterns with rich fine structure are recorded within minutes. The short photoelectron wavelength (10% of the interatomic distance) `amplifies' phase differences, making full-field hXPD a sensitive structural tool. Full Article text
science and technology Coherence properties of the high-energy fourth-generation X-ray synchrotron sources By scripts.iucr.org Published On :: 2019-11-01 An analysis of the coherence properties of the fourth-generation high-energy storage rings with emittance values of 10 pm rad is performed. It is presently expected that a storage ring with these low emittance values will reach diffraction limit at hard X-rays. Simulations of coherence properties were performed with the XRT software and an analytical approach for different photon energies from 500 eV to 50 keV. It was demonstrated that a minimum photon emittance (diffraction limit) reached at such storage rings is λ/2π. Using mode decomposition it is shown that, for the parameters of the storage ring considered in this work, the diffraction limit will be reached for soft X-ray energies of 500 eV. About ten modes will contribute to the radiation field at 12 keV photon energy and even more modes give a contribution at higher photon energies. Energy spread effects of the electron beam in a low-emittance storage ring were analysed in detail. Simulations were performed at different relative energy spread values from zero to 2 × 10−3. A decrease of the degree of coherence with an increase of the relative energy spread value was observed. This analysis shows that, to reach the diffraction limit for high photon energies, electron beam emittance should go down to 1 pm rad and below. Full Article text
science and technology Transmission measurement at the Bernina branch of the Aramis Beamline of SwissFEL By scripts.iucr.org Published On :: 2019-10-23 The transmission of the optical components of the Bernina branch of the Aramis beamline at SwissFEL has been measured with an X-ray gas monitor from DESY and compared with a PSI gas detector upstream of the optical components. The transmission efficiencies of the Mo, Si and SiC mirror coatings of the Aramis beamline and the various other in-beam components were evaluated and compared with theoretical calculations, showing an agreement of 6% or better in all cases. The experiment has also shown the efficacy of the high-harmonic rejection mirrors at the Bernina branch of the Aramis beamline at SwissFEL, and characterized the transmission efficiency of the on-line spectrometer in the Aramis beamline. The theoretical transmission of the mirror coatings match the experimental data to within 7%. The accuracy of these measurements was checked against a radiative bolometer from a Japanese collaboration and found to agree to a level of 4% or better. Further comparisons with a diamond detector from a US-based inter-institute collaboration demonstrated a good agreement for the attenuator settings of the beamline. Full Article text
science and technology Improved calibration of area detectors using multiple placements By scripts.iucr.org Published On :: 2019-10-23 Calibration of area detectors from powder diffraction standards is widely used at synchrotron beamlines. From a single diffraction image, it is not possible to determine both the sample-to-detector distance and the wavelength, but, with images taken from multiple positions along the beam direction and where the relative displacement is known, the sample-to-detector distance and wavelength can both be determined with good precision. An example calibration using the GSAS-II software package is presented. Full Article text
science and technology A von Hamos-type hard X-ray spectrometer at the PETRA III beamline P64 By scripts.iucr.org Published On :: 2020-01-01 The design and performance of the high-resolution wavelength-dispersive multi-crystal von Hamos-type spectrometer at PETRA III beamline P64 are described. Extended analyzer crystal collection available at the beamline allows coverage of a broad energy range from 5 keV to 20 keV with an energy resolution of 0.35–1 eV. Particular attention was paid to enabling two-color measurements by a combination of two types of analyzer crystals and two two-dimensional detectors. The performance of the spectrometer is demonstrated by elastic-line and emission-line measurements on various compounds. Full Article text
science and technology X-ray fluorescence analysis of metal distributions in cryogenic biological samples using large-acceptance-angle SDD detection and continuous scanning at the Hard X-ray Micro/Nano-Probe beamline P06 at PETRA III By scripts.iucr.org Published On :: 2020-01-01 A new Rococo 2 X-ray fluorescence detector was implemented into the cryogenic sample environment at the Hard X-ray Micro/Nano-Probe beamline P06 at PETRA III, DESY, Hamburg, Germany. A four sensor-field cloverleaf design is optimized for the investigation of planar samples and operates in a backscattering geometry resulting in a large solid angle of up to 1.1 steradian. The detector, coupled with the Xspress 3 pulse processor, enables measurements at high count rates of up to 106 counts per second per sensor. The measured energy resolution of ∼129 eV (Mn Kα at 10000 counts s−1) is only minimally impaired at the highest count rates. The resulting high detection sensitivity allows for an accurate determination of trace element distributions such as in thin frozen hydrated biological specimens. First proof-of-principle measurements using continuous-movement 2D scans of frozen hydrated HeLa cells as a model system are reported to demonstrate the potential of the new detection system. Full Article text
science and technology XUV-driven plasma switch for THz: new spatio-temporal overlap tool for XUV–THz pump–probe experiments at FELs By scripts.iucr.org Published On :: 2020-01-01 A simple and robust tool for spatio-temporal overlap of THz and XUV pulses in in-vacuum pump–probe experiments is presented. The technique exploits ultrafast changes of the optical properties in semiconductors (i.e. silicon) driven by ultrashort XUV pulses that are probed by THz pulses. This work demonstrates that this tool can be used for a large range of XUV fluences that are significantly lower than when probing by visible and near-infrared pulses. This tool is mainly targeted at emerging X-ray free-electron laser facilities, but can be utilized also at table-top high-harmonics sources. Full Article text
science and technology Characterization of the soft X-ray spectrometer PEAXIS at BESSY II By scripts.iucr.org Published On :: 2020-01-01 The performance of the recently commissioned spectrometer PEAXIS for resonant inelastic soft X-ray scattering (RIXS) and X-ray photoelectron spectroscopy and its hosting beamline U41-PEAXIS at the BESSY II synchrotron are characterized. The beamline provides linearly polarized light from 180 eV to 1600 eV allowing for RIXS measurements in the range 200–1200 eV. The monochromator optics can be operated in different configurations to provide either high flux with up to 1012 photons s−1 within the focal spot at the sample or high energy resolution with a full width at half maximum of <40 meV at an incident photon energy of ∼400 eV. The measured total energy resolution of the RIXS spectrometer is in very good agreement with theoretically predicted values obtained by ray-tracing simulations. PEAXIS features a 5 m-long RIXS spectrometer arm that can be continuously rotated about the sample position by 106° within the horizontal photon scattering plane, thus enabling the study of momentum-transfer-dependent excitations. Selected scientific examples are presented to demonstrate the instrument capabilities, including measurements of excitations in single-crystalline NiO and in liquid acetone employing a fluid cell sample manipulator. Planned upgrades of the beamline and the RIXS spectrometer to further increase the energy resolution to ∼100 meV at 1000 eV incident photon energy are discussed. Full Article text
science and technology Methods for dynamic synchrotron X-ray respiratory imaging in live animals By scripts.iucr.org Published On :: 2020-01-01 Small-animal physiology studies are typically complicated, but the level of complexity is greatly increased when performing live-animal X-ray imaging studies at synchrotron and compact light sources. This group has extensive experience in these types of studies at the SPring-8 and Australian synchrotrons, as well as the Munich Compact Light Source. These experimental settings produce unique challenges. Experiments are always performed in an isolated radiation enclosure not specifically designed for live-animal imaging. This requires equipment adapted to physiological monitoring and test-substance delivery, as well as shuttering to reduce the radiation dose. Experiment designs must also take into account the fixed location, size and orientation of the X-ray beam. This article describes the techniques developed to overcome the challenges involved in respiratory X-ray imaging of live animals at synchrotrons, now enabling increasingly sophisticated imaging protocols. Full Article text
science and technology Full-field spectroscopic measurement of the X-ray beam from a multilayer monochromator using a hyperspectral X-ray camera By scripts.iucr.org Published On :: 2020-01-01 Multilayer monochromator devices are commonly used at (imaging) beamlines of synchrotron facilities to shape the X-ray beam to relatively small bandwidth and high intensity. However, stripe artefacts are often observed and can deteriorate the image quality. Although the intensity distribution of these artefacts has been described in the literature, their spectral distribution is currently unknown. To assess the spatio-spectral properties of the monochromated X-ray beam, the direct beam has been measured for the first time using a hyperspectral X-ray detector. The results show a large number of spectral features with different spatial distributions for a [Ru, B4C] strip monochromator, associated primarily with the higher-order harmonics of the undulator and monochromator. It is found that their relative contributions are sufficiently low to avoid an influence on the imaging data. The [V, B4C] strip suppresses these high-order harmonics even more than the former, yet at the cost of reduced efficiency. Full Article text
science and technology White beam diagnostics using X-ray back-scattering from a CVD diamond vacuum window By scripts.iucr.org Published On :: 2020-01-01 Collecting back-scattered X-rays from vacuum windows using a pinhole X-ray camera provides an efficient and reliable method of measuring the beam shape and position of the white synchrotron beam. In this paper, measurements are presented that were conducted at ESRF beamline ID6 which uses an in-vacuum cryogenically cooled permanent-magnet undulator (CPMU18) and a traditional U32 undulator as its radiation sources, allowing tests to be performed at very high power density levels that were adjusted by changing the gap of the undulators. These measurements show that it is possible to record beam shape and beam position using a simple geometry without having to place any further items in the beam path. With this simple test setup it was possible to record the beam position with a root-mean-square noise figure of 150 nm. Full Article text
science and technology Picosecond pump–probe X-ray scattering at the Elettra SAXS beamline By scripts.iucr.org Published On :: 2020-01-01 A new setup for picosecond pump–probe X-ray scattering at the Austrian SAXS beamline at Elettra-Sincrotrone Trieste is presented. A high-power/high-repetion-rate laser has been installed on-site, delivering UV/VIS/IR femtosecond-pulses in-sync with the storage ring. Data acquisition is achieved by gating a multi-panel detector, capable of discriminating the single X-ray pulse in the dark-gap of the Elettra hybrid filling mode. Specific aspects of laser- and detection-synchronization, on-line beam steering as well protocols for spatial and temporal overlap of laser and X-ray beam are also described. The capabilities of the setup are demonstrated by studying transient heat-transfer in an In/Al/GaAs superlattice structure and results are confirmed by theoretical calculations. Full Article text
science and technology A semi-analytical approach for the characterization of ordered 3D nanostructures using grazing-incidence X-ray fluorescence By scripts.iucr.org Published On :: 2020-02-11 Following the recent demonstration of grazing-incidence X-ray fluorescence (GIXRF)-based characterization of the 3D atomic distribution of different elements and dimensional parameters of periodic nanoscale structures, this work presents a new computational scheme for the simulation of the angular-dependent fluorescence intensities from such periodic 2D and 3D nanoscale structures. The computational scheme is based on the dynamical diffraction theory in many-beam approximation, which allows a semi-analytical solution to the Sherman equation to be derived in a linear-algebraic form. The computational scheme has been used to analyze recently published GIXRF data measured on 2D Si3N4 lamellar gratings, as well as on periodically structured 3D Cr nanopillars. Both the dimensional and structural parameters of these nanostructures have been reconstructed by fitting numerical simulations to the experimental GIXRF data. Obtained results show good agreement with nominal parameters used in the manufacturing of the structures, as well as with reconstructed parameters based on the previously published finite-element-method simulations, in the case of the Si3N4 grating. Full Article text
science and technology X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector By scripts.iucr.org Published On :: 2020-02-07 Detection of heavy elements, such as metals, in macromolecular crystallography (MX) samples by X-ray fluorescence is a function traditionally covered at synchrotron MX beamlines by silicon drift detectors, which cannot be used at X-ray free-electron lasers because of the very short duration of the X-ray pulses. Here it is shown that the hybrid pixel charge-integrating detector JUNGFRAU can fulfill this function when operating in a low-flux regime. The feasibility of precise position determination of micrometre-sized metal marks is also demonstrated, to be used as fiducials for offline prelocation in serial crystallography experiments, based on the specific fluorescence signal measured with JUNGFRAU, both at the synchrotron and at SwissFEL. Finally, the measurement of elemental absorption edges at a synchrotron beamline using JUNGFRAU is also demonstrated. Full Article text
science and technology AP-XPS beamline, a platform for operando science at Pohang Accelerator Laboratory By scripts.iucr.org Published On :: 2020-01-28 Beamline 8A (BL 8A) is an undulator-based soft X-ray beamline at Pohang Accelerator Laboratory. This beamline is aimed at high-resolution ambient-pressure X-ray photoelectron spectroscopy (AP-XPS), soft X-ray absorption spectroscopy (soft-XAS) and scanning photoemission microscopy (SPEM) experiments. BL 8A has two branches, 8A1 SPEM and 8A2 AP-XPS, that share a plane undulator, the first mirror (M1) and the monochromator. The photon beam is switched between the two branches by changing the refocusing mirrors after the monochromator. The acceptance angle of M1 is kept glancing at 1.2°, and Pt is coated onto the mirrors to achieve high reflectance, which ensures a wide photon energy range (100–2000 eV) with high resolution at a photon flux of ∼1013 photons s−1. In this article, the main properties and performance of the beamline are reported, together with selected experiments performed on the new beamline and experimental system. Full Article text
science and technology The HXD95: a modified Bassett-type hydrothermal diamond-anvil cell for in situ XRD experiments up to 5 GPa and 1300 K By scripts.iucr.org Published On :: 2020-01-29 A new diamond-anvil cell apparatus for in situ synchrotron X-ray diffraction measurements of liquids and glasses, at pressures from ambient to 5 GPa and temperatures from ambient to 1300 K, is reported. This portable setup enables in situ monitoring of the melting of complex compounds and the determination of the structure and properties of melts under moderately high pressure and high temperature conditions relevant to industrial processes and magmatic processes in the Earth's crust and shallow mantle. The device was constructed according to a modified Bassett-type hydrothermal diamond-anvil cell design with a large angular opening (θ = 95°). This paper reports the successful application of this device to record in situ synchrotron X-ray diffraction of liquid Ga and synthetic PbSiO3 glass to 1100 K and 3 GPa. Full Article text
science and technology A five-axis parallel kinematic mirror unit for soft X-ray beamlines at MAX IV By scripts.iucr.org Published On :: 2020-01-29 With the introduction of the multi-bend achromats in the new fourth-generation storage rings the emittance has decreased by an order of magnitude resulting in increased brightness. However, the higher brightness comes with smaller beam sizes and narrower radiation cones. As a consequence, the requirements on mechanical stability regarding the beamline components increases. Here an innovative five-axis parallel kinematic mirror unit for use with soft X-ray beamlines using off-axis grazing-incidence optics is presented. Using simulations and measurements from the HIPPIE beamline at the MAX IV Laboratory it is shown that it has no Eigen frequencies below 90 Hz. Its positioning accuracy is better than 25 nm linearly and 17–35 µrad angularly depending on the mirror chamber dimensions. Full Article text
science and technology A lathe system for micrometre-sized cylindrical sample preparation at room and cryogenic temperatures By scripts.iucr.org Published On :: 2020-01-29 A simple two-spindle based lathe system for the preparation of cylindrical samples intended for X-ray tomography is presented. The setup can operate at room temperature as well as under cryogenic conditions, allowing the preparation of samples down to 20 and 50 µm in diameter, respectively, within minutes. Case studies are presented involving the preparation of a brittle biomineral brachiopod shell and cryogenically fixed soft brain tissue, and their examination by means of ptychographic X-ray computed tomography reveals the preparation method to be mainly free from causing artefacts. Since this lathe system easily yields near-cylindrical samples ideal for tomography, a usage for a wide variety of otherwise challenging specimens is anticipated, in addition to potential use as a time- and cost-saving tool prior to focused ion-beam milling. Fast sample preparation becomes especially important in relation to shorter measurement times expected in next-generation synchrotron sources. Full Article text
science and technology A portable on-axis laser-heating system for near-90° X-ray spectroscopy: application to ferropericlase and iron silicide By scripts.iucr.org Published On :: 2020-02-13 A portable IR fiber laser-heating system, optimized for X-ray emission spectroscopy (XES) and nuclear inelastic scattering (NIS) spectroscopy with signal collection through the radial opening of diamond anvil cells near 90°with respect to the incident X-ray beam, is presented. The system offers double-sided on-axis heating by a single laser source and zero attenuation of incoming X-rays other than by the high-pressure environment. A description of the system, which has been tested for pressures above 100 GPa and temperatures up to 3000 K, is given. The XES spectra of laser-heated Mg0.67Fe0.33O demonstrate the potential to map the iron spin state in the pressure–temperature range of the Earth's lower mantle, and the NIS spectra of laser-heated FeSi give access to the sound velocity of this candidate of a phase inside the Earth's core. This portable system represents one of the few bridges across the gap between laser heating and high-resolution X-ray spectroscopies with signal collection near 90°. Full Article text
science and technology ProQEXAFS: a highly optimized parallelized rapid processing software for QEXAFS data By scripts.iucr.org Published On :: 2020-02-07 The high temporal resolution in data acquisition, possible in the quick-scanning EXAFS (QEXAFS) mode of operation, provides new challenges in efficient data processing methods. Here a new approach is developed that combines an easy to use interactive graphical interface with highly optimized and fully parallelized Python-based routines for extracting, normalizing and interpolating oversampled time-resolved XAS spectra from a raw binary stream of data acquired during operando QEXAFS studies. The programs developed are freely available via a Github repository. Full Article text
science and technology X-ray free-electron laser wavefront sensing using the fractional Talbot effect By scripts.iucr.org Published On :: 2020-02-12 Wavefront sensing at X-ray free-electron lasers is important for quantitatively understanding the fundamental properties of the laser, for aligning X-ray instruments and for conducting scientific experimental analysis. A fractional Talbot wavefront sensor has been developed. This wavefront sensor enables measurements over a wide range of energies, as is common on X-ray instruments, with simplified mechanical requirements and is compatible with the high average power pulses expected in upcoming X-ray free-electron laser upgrades. Single-shot measurements were performed at 500 eV, 1000 eV and 1500 eV at the Linac Coherent Light Source. These measurements were applied to study both mirror alignment and the effects of undulator tapering schemes on source properties. The beamline focal plane position was tracked to an uncertainty of 0.12 mm, and the source location for various undulator tapering schemes to an uncertainty of 1 m, demonstrating excellent sensitivity. These findings pave the way to use the fractional Talbot wavefront sensor as a routine, robust and sensitive tool at X-ray free-electron lasers as well as other high-brightness X-ray sources. Full Article text
science and technology IRIXS: a resonant inelastic X-ray scattering instrument dedicated to X-rays in the intermediate energy range By scripts.iucr.org Published On :: 2020-02-26 A new resonant inelastic X-ray scattering (RIXS) instrument has been constructed at beamline P01 of the PETRA III synchrotron. This instrument has been named IRIXS (intermediate X-ray energy RIXS) and is dedicated to X-rays in the tender-energy regime (2.5–3.5 keV). The range covers the L2,3 absorption edges of many of the 4d elements (Mo, Tc, Ru, Rh, Pd and Ag), offering a unique opportunity to study their low-energy magnetic and charge excitations. The IRIXS instrument is currently operating at the Ru L3-edge (2840 eV) but can be extended to the other 4d elements using the existing concept. The incoming photons are monochromated with a four-bounce Si(111) monochromator, while the energy analysis of the outgoing photons is performed by a diced spherical crystal analyzer featuring (102) lattice planes of quartz (SiO2). A total resolution of 100 meV (full width at half-maximum) has been achieved at the Ru L3-edge, a number that is in excellent agreement with ray-tracing simulations. Full Article text
science and technology Limited angle tomography for transmission X-ray microscopy using deep learning By scripts.iucr.org Published On :: 2020-02-13 In transmission X-ray microscopy (TXM) systems, the rotation of a scanned sample might be restricted to a limited angular range to avoid collision with other system parts or high attenuation at certain tilting angles. Image reconstruction from such limited angle data suffers from artifacts because of missing data. In this work, deep learning is applied to limited angle reconstruction in TXMs for the first time. With the challenge to obtain sufficient real data for training, training a deep neural network from synthetic data is investigated. In particular, U-Net, the state-of-the-art neural network in biomedical imaging, is trained from synthetic ellipsoid data and multi-category data to reduce artifacts in filtered back-projection (FBP) reconstruction images. The proposed method is evaluated on synthetic data and real scanned chlorella data in 100° limited angle tomography. For synthetic test data, U-Net significantly reduces the root-mean-square error (RMSE) from 2.55 × 10−3 µm−1 in the FBP reconstruction to 1.21 × 10−3 µm−1 in the U-Net reconstruction and also improves the structural similarity (SSIM) index from 0.625 to 0.920. With penalized weighted least-square denoising of measured projections, the RMSE and SSIM are further improved to 1.16 × 10−3 µm−1 and 0.932, respectively. For real test data, the proposed method remarkably improves the 3D visualization of the subcellular structures in the chlorella cell, which indicates its important value for nanoscale imaging in biology, nanoscience and materials science. Full Article text
science and technology X-ray absorption linear dichroism at the Ti K-edge of rutile (001) TiO2 single crystal By scripts.iucr.org Published On :: 2020-02-14 X-ray absorption linear dichroism of rutile TiO2 at the Ti K-edge provides information about the electronic states involved in the pre-edge transitions. Here, linear dichroism with high energy resolution is analyzed in combination with ab initio finite difference method calculations and spherical tensor analysis. It provides an assignment of the three pre-edge peaks beyond the octahedral crystal field splitting approximation and estimates the spatial extension of the corresponding final states. It is then discussed for the first time the X-ray absorption (XAS) of pentacoordinated titanium atoms due to oxygen vacancies and it is found that, similarly to anatase TiO2, rutile is expected to exhibit a transition on the low-energy side of peak A3. Its apparent absence in the experiment is related to the degree of p–d orbital mixing which is small in rutile due to its centrosymmetric point group. A recent XAS linear dichroism study on anatase TiO2 single crystals has shown that peak A2 has an intrinsic origin and is due to a quadrupolar transition to the 3d energy levels. In rutile, due to its centrosymmetric point group, the corresponding peak A2 has a small dipole moment explaining the weak transition. The results are confronted with recent picosecond X-ray absorption spectroscopy on rutile TiO2 nanoparticles. Full Article text
science and technology The HARE chip for efficient time-resolved serial synchrotron crystallography By scripts.iucr.org Published On :: 2020-02-27 Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided. Full Article text
science and technology Understanding the mechanical limitations of the performance of soft X-ray monochromators at MAX IV laboratory By scripts.iucr.org Published On :: 2020-02-19 MAX IV is a fourth-generation, or diffraction-limited, synchrotron light source with a number of state-of-the-art beamlines. The performance of a beamline is, to a high degree, set by the energy resolution it can achieve, which in turn is governed to a large extent by the monochromator. During the design phase of a monochromator, the mechanical requirements must be fully understood and met with margin. During commissioning, the performance must be verified and optimized. In this paper, six soft X-ray monochromators at MAX IV beamlines (Bloch, Veritas, HIPPIE, SPECIES, FinEstBeAMS and SoftiMAX) are examined with a focus on their resolving power, energy range and the time required to change measurement range, as those parameters are dependent on each other. The monochromators have a modern commercial design, planned and developed in close collaboration with the vendors. This paper aims to present the current status of the commissioning at MAX IV with emphasis on elucidating the mechanical limitations on the performance of the monochromators. It contains analysis of the outcome and our approach to achieve fast and high-resolution monochromators. Full Article text
science and technology Tomographic reconstruction with a generative adversarial network By scripts.iucr.org Published On :: 2020-02-18 This paper presents a deep learning algorithm for tomographic reconstruction (GANrec). The algorithm uses a generative adversarial network (GAN) to solve the inverse of the Radon transform directly. It works for independent sinograms without additional training steps. The GAN has been developed to fit the input sinogram with the model sinogram generated from the predicted reconstruction. Good quality reconstructions can be obtained during the minimization of the fitting errors. The reconstruction is a self-training procedure based on the physics model, instead of on training data. The algorithm showed significant improvements in the reconstruction accuracy, especially for missing-wedge tomography acquired at less than 180° rotational range. It was also validated by reconstructing a missing-wedge X-ray ptychographic tomography (PXCT) data set of a macroporous zeolite particle, for which only 51 projections over 70° could be collected. The GANrec recovered the 3D pore structure with reasonable quality for further analysis. This reconstruction concept can work universally for most of the ill-posed inverse problems if the forward model is well defined, such as phase retrieval of in-line phase-contrast imaging. Full Article text
science and technology Foreword to the special virtual issue dedicated to the proceedings of the PhotonDiag2018 workshop on FEL Photon Diagnostics, Instrumentation, and Beamlines Design By scripts.iucr.org Published On :: 2020-03-01 Full Article text
science and technology Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse By journals.iucr.org Published On :: The time evolution of the electron density and the resulting time dependence of the X-ray polarizability of a crystal irradiated by highly intense XFEL femtosecond pulses is investigated theoretically. Rate equations for bound electrons and the Boltzmann equation for the unbound electron gas are used in calculations. Full Article text
science and technology Contributions of charge-density research to medicinal chemistry By journals.iucr.org Published On :: Contributions of experimental and selected theoretical charge-density research to medicinal chemistry are reviewed; combining experimental methods from high-resolution small-molecule and macromolecular crystallography with theory proves to be fruitful. Full Article text
science and technology Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments By journals.iucr.org Published On :: Possibilities in auxiliary technique combinations with small- and wide-angle X ray scattering are described, as well as more complicated sample environments used in X-ray and neutron scattering. Full Article text
science and technology Correlated changes in structure and viscosity during gelatinization and gelation of tapioca starch granules By journals.iucr.org Published On :: Melting of the semicrystalline structure of native tapioca starch granules is correlated to solution viscosity for elucidating gelatinization and gelation processes. Full Article text
science and technology Automated nucleic acid chain tracing in real time By journals.iucr.org Published On :: A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software. Likely nucleotides lying in the vicinity of the current view are located and then grown into connected chains in a fraction of a second. When this development is combined with existing tools, assisted manual model building is as simple as or simpler than for proteins. Full Article text
science and technology Pressure effects on lipids and bio-membrane assemblies By journals.iucr.org Published On :: Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the structure of membranes and recent developments in high-pressure instrumentation. Full Article text
science and technology Viruses and viral proteins By journals.iucr.org Published On :: The X-ray structures of viruses and viral proteins currently available are providing high-resolution snapshots of viral molecular machineries, expanding our vision of the virus world and giving crucial information on potential targets for future antiviral therapies. Full Article text
science and technology Molecular self-assembly of nylon-12 nanorods cylindrically confined to nanoporous alumina By journals.iucr.org Published On :: It has been revealed that in cylindrical nano-confinement, the hydrogen-bonding direction of nylon-12 crystals in the rod could self-assemble to be parallel to the long axis of the rod. The dominant growth direction and hydrogen-bonding direction of the γ-form crystal in the long axis of the rod has been revealed by TEM–SAED and WAXD. Full Article text
science and technology Location of Cu2+ in CHA zeolite investigated by X-ray diffraction using the Rietveld/maximum entropy method By journals.iucr.org Published On :: Rietveld/MEM analysis applied to synchrotron powder X-ray diffraction data of dehydrated CHA zeolites with catalytically active Cu2+ reveals Cu2+ in both the six- and eight-membered rings in the CHA framework, providing the first complete structural model that accounts for all Cu2+. Density functional theory calculations are used to corroborate the experimental structure and to discuss the Cu2+ coordination in terms of the Al distribution in the framework. Full Article text
science and technology The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm By journals.iucr.org Published On :: An expectation maximization algorithm is implemented to resolve the indexing ambiguity which arises when merging data from many crystals in protein crystallography, especially in cases where partial reflections are recorded in serial femtosecond crystallography (SFX) at XFELs. Full Article text
science and technology Reconciling the regulatory role of Munc18 proteins in SNARE-complex assembly By journals.iucr.org Published On :: Mammalian Munc18 proteins are essential for membrane fusion and human health. Here, we review the literature describing structural and in vitro data, and identify a possible explanation for the conflicting functional roles that have been reported. Full Article text
science and technology Diffuse scattering and partial disorder in complex structures By journals.iucr.org Published On :: This review discusses the state of the field of single-crystal diffuse scattering (SCDS), including detectors, data collection and the modelling techniques. High quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing increasingly detailed and quantitative analyses to be undertaken. Full Article text
science and technology Nanocrystalline materials: recent advances in crystallographic characterization techniques By journals.iucr.org Published On :: This feature article reviews the control and understanding of nanoparticle shape from their crystallography and growth. Particular emphasis is placed on systems relevant for plasmonics and catalysis. Full Article text
science and technology Investigating increasingly complex macromolecular systems with small-angle X-ray scattering By journals.iucr.org Published On :: A review of recent and ongoing development and results within the field of biological solution small-angle X-ray scattering (BioSAXS), with a focus on the increasing complexity of biological samples, data collection and data evaluation strategies. Full Article text
science and technology Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation By journals.iucr.org Published On :: The structure and function of dioxygenases in histone demethylation and DNA/RNA dimethylation are discussed. Full Article text
science and technology EXAFS and XANES analysis of oxides at the nanoscale By journals.iucr.org Published On :: This work presents a discussion of the possibilities offered by X-ray absorption spectroscopy (XAS) to study the local structure of nanomaterials. The current state of the art for the interpretation of extended X-ray absorption fine structure (EXAFS), including an advanced approach based on the use of classical molecular dynamics, is described and exemplified in the case of NiO nanoparticles. In addition, the limits and possibilities of X-ray absorption near-edge spectroscopy (XANES) in determining several effects associated with the nanocrystalline nature of materials are also discussed in connection with the development of ZnO-based dilute magnetic semiconductors and iron oxide nanoparticles. Full Article text
science and technology Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein By journals.iucr.org Published On :: A neutron crystallographic study of perdeuterated transthyretin reveals important aspects of the structure relating to its stability and its propensity to form fibrils, as well as evidence of a single water molecule that affects the symmetry of the two binding pockets. Full Article text
science and technology The first X-ray diffraction measurements on Mars By journals.iucr.org Published On :: The X-ray diffraction/X-ray fluorescence instrument CheMin on the Curiosity rover is a shoebox-sized device using transmission geometry and an energy-discriminating CCD detector. The instrument has returned the first X-ray diffraction data for soil and drilled samples from Mars outcrops, revealing a suite of primary basaltic minerals, amorphous components and varied hydrous alteration products including phyllosilicates. Full Article text
science and technology X-ray techniques for innovation in industry By journals.iucr.org Published On :: Are synchrotrons needed for innovation in industry? What can scientists at large-scale facilities offer for R&D in industry? Is the comfort of life profiting from research? Full Article text
science and technology Capability of X-ray diffraction for the study of microstructure of metastable thin films By journals.iucr.org Published On :: PLEASE REDUCE TO 1-2 SENTENCES. The capability of X-ray diffraction for the microstructure investigations of metastable systems is illustrated on the example of thin films of titanium aluminium nitrides with high aluminium content, which are supersaturated and partially decomposed. In addition to the chemical composition, the surface mobility of the deposited species was employed as a factor influencing the microstructure of the thin films. It is shown how the micromechanical properties of the partially decomposed (Ti,Al)N thin films, which were deduced from the synchrotron diffraction experiments, are related to the thin film microstructure and to the decomposition mechanism. The prominent role of the crystallographic anisotropy of the macroscopic and microscopic lattice deformations in the understanding of the micromechanical properties is addressed. Full Article text
science and technology Chemical crystallography and crystal engineering By journals.iucr.org Published On :: Today, there is very little doubt that chemistry owes as much to crystallography as crystallography does to chemistry. This mutual synergy defines modern chemical crystallography. Full Article text
science and technology In-depth analysis of subclass-specific conformational preferences of IgG antibodies By journals.iucr.org Published On :: An extended analysis of structural ensembles obtained from small-angle X-ray scattering data reveals subclass-specific conformational preferences of IgG antibodies, which are largely determined by the hinge-region structure. Full Article text