io Device for source position stabilization and beam parameter monitoring at inverse Compton X-ray sources By scripts.iucr.org Published On :: 2019-08-07 Compact X-ray sources based on inverse Compton scattering provide brilliant and partially coherent X-rays in a laboratory environment. The cross section for inverse Compton scattering is very small, requiring high-power laser systems as well as small laser and electron beam sizes at the interaction point to generate sufficient flux. Therefore, these systems are very sensitive to distortions which change the overlap between the two beams. In order to monitor X-ray source position, size and flux in parallel to experiments, the beam-position monitor proposed here comprises a small knife edge whose image is acquired with an X-ray camera specifically designed to intercept only a very small fraction of the X-ray beam. Based on the source position drift recorded with the monitor, a closed-loop feedback stabilizes the X-ray source position by adjusting the laser beam trajectory. A decrease of long-term source position drifts by more than one order of magnitude is demonstrated with this device. Consequently, such a closed-loop feedback system which enables stabilization of source position drifts and flux of inverse Compton sources in parallel to experiments has a significant impact on the performance of these sources. Full Article text
io Scientific instrument Femtosecond X-ray Experiments (FXE): instrumentation and baseline experimental capabilities By scripts.iucr.org Published On :: 2019-08-09 The European X-ray Free-Electron Laser (EuXFEL) delivers extremely intense (>1012 photons pulse−1 and up to 27000 pulses s−1), ultrashort (<100 fs) and transversely coherent X-ray radiation, at a repetition rate of up to 4.5 MHz. Its unique X-ray beam parameters enable novel and groundbreaking experiments in ultrafast photochemistry and material sciences at the Femtosecond X-ray Experiments (FXE) scientific instrument. This paper provides an overview of the currently implemented experimental baseline instrumentation and its performance during the commissioning phase, and a preview of planned improvements. FXE's versatile instrumentation combines the simultaneous application of forward X-ray scattering and X-ray spectroscopy techniques with femtosecond time resolution. These methods will eventually permit exploitation of wide-angle X-ray scattering studies and X-ray emission spectroscopy, along with X-ray absorption spectroscopy, including resonant inelastic X-ray scattering and X-ray Raman scattering. A suite of ultrafast optical lasers throughout the UV–visible and near-IR ranges (extending up to mid-IR in the near future) with pulse length down to 15 fs, synchronized to the X-ray source, serve to initiate dynamic changes in the sample. Time-delayed hard X-ray pulses in the 5–20 keV range are used to probe the ensuing dynamic processes using the suite of X-ray probe tools. FXE is equipped with a primary monochromator, a primary and secondary single-shot spectrometer, and a timing tool to correct the residual timing jitter between laser and X-ray pulses. Full Article text
io Fast identification of mineral inclusions in diamond at GSECARS using synchrotron X-ray microtomography, radiography and diffraction By scripts.iucr.org Published On :: 2019-07-19 Mineral inclusions in natural diamond are widely studied for the insight that they provide into the geochemistry and dynamics of the Earth's interior. A major challenge in achieving thorough yet high rates of analysis of mineral inclusions in diamond derives from the micrometre-scale of most inclusions, often requiring synchrotron radiation sources for diffraction. Centering microinclusions for diffraction with a highly focused synchrotron beam cannot be achieved optically because of the very high index of refraction of diamond. A fast, high-throughput method for identification of micromineral inclusions in diamond has been developed at the GeoSoilEnviro Center for Advanced Radiation Sources (GSECARS), Advanced Photon Source, Argonne National Laboratory, USA. Diamonds and their inclusions are imaged using synchrotron 3D computed X-ray microtomography on beamline 13-BM-D of GSECARS. The location of every inclusion is then pinpointed onto the coordinate system of the six-circle goniometer of the single-crystal diffractometer on beamline 13-BM-C. Because the bending magnet branch 13-BM is divided and delivered into 13-BM-C and 13-BM-D stations simultaneously, numerous diamonds can be examined during coordinated runs. The fast, high-throughput capability of the methodology is demonstrated by collecting 3D diffraction data on 53 diamond inclusions from Juína, Brazil, within a total of about 72 h of beam time. Full Article text
io Microfluidic electrochemical cell for in situ structural characterization of amorphous thin-film catalysts using high-energy X-ray scattering By scripts.iucr.org Published On :: 2019-08-09 Porous, high-surface-area electrode architectures are described that allow structural characterization of interfacial amorphous thin films with high spatial resolution under device-relevant functional electrochemical conditions using high-energy X-ray (>50 keV) scattering and pair distribution function (PDF) analysis. Porous electrodes were fabricated from glass-capillary array membranes coated with conformal transparent conductive oxide layers, consisting of either a 40 nm–50 nm crystalline indium tin oxide or a 100 nm–150 nm-thick amorphous indium zinc oxide deposited by atomic layer deposition. These porous electrodes solve the problem of insufficient interaction volumes for catalyst thin films in two-dimensional working electrode designs and provide sufficiently low scattering backgrounds to enable high-resolution signal collection from interfacial thin-film catalysts. For example, PDF measurements were readily obtained with 0.2 Å spatial resolution for amorphous cobalt oxide films with thicknesses down to 60 nm when deposited on a porous electrode with 40 µm-diameter pores. This level of resolution resolves the cobaltate domain size and structure, the presence of defect sites assigned to the domain edges, and the changes in fine structure upon redox state change that are relevant to quantitative structure–function modeling. The results suggest the opportunity to leverage the porous, electrode architectures for PDF analysis of nanometre-scale surface-supported molecular catalysts. In addition, a compact 3D-printed electrochemical cell in a three-electrode configuration is described which is designed to allow for simultaneous X-ray transmission and electrolyte flow through the porous working electrode. Full Article text
io Linear array detector for online diagnostics of spectral distributions at MHz repetition rates By scripts.iucr.org Published On :: 2019-09-01 Free-electron lasers (FELs) based on superconducting accelerator technology and storage ring facilities operate with bunch repetition rates in the MHz range, and the need arises for bunch-by-bunch electron and photon diagnostics. For photon-pulse-resolved measurements of spectral distributions, fast one-dimensional profile monitors are required. The linear array detector KALYPSO (KArlsruhe Linear arraY detector for MHz-rePetition rate SpectrOscopy) has been developed for electron bunch or photon pulse synchronous read-out with frame rates of up to 2.7 MHz. At the FLASH facility at DESY, a current version of KALYPSO with 256 pixels has been installed at a grating spectrometer as online diagnostics to monitor the pulse-resolved spectra of the high-repetition-rate FEL pulses. Application-specific front-end electronics based on MicroTCA standard have been developed for data acquisition and processing. Continuous data read-out with low latency in the microsecond range enables the integration into fast feedback applications. In this paper, pulse-resolved FEL spectra recorded at 1.0 MHz repetition rate for various operation conditions at FLASH are presented, and the first application of an adaptive feedback for accelerator control based on photon beam diagnostics is demonstrated. Full Article text
io Microsecond time-resolved X-ray diffraction for the investigation of fatigue behavior during ultrasonic fatigue loading By scripts.iucr.org Published On :: 2019-08-20 A new method based on time-resolved X-ray diffraction is proposed in order to measure the elastic strain and stress during ultrasonic fatigue loading experiments. Pure Cu was chosen as an example material for the experiments using a 20 kHz ultrasonic fatigue machine mounted on the six-circle diffractometer available at the DiffAbs beamline on the SOLEIL synchrotron facility in France. A two-dimensional hybrid pixel X-ray detector (XPAD3.2) was triggered by the strain gage signal in a synchronous data acquisition scheme (pump–probe-like). The method enables studying loading cycles with a period of 50 µs, achieving a temporal resolution of 1 µs. This allows a precise reconstruction of the diffraction patterns during the loading cycles. From the diffraction patterns, the position of the peaks, their shifts and their respective broadening can be deduced. The diffraction peak shift allows the elastic lattice strain to be estimated with a resolution of ∼10−5. Stress is calculated by the self-consistent scale-transition model through which the elastic response of the material is estimated. The amplitudes of the cyclic stresses range from 40 to 120 MPa and vary linearly with respect to the displacement applied by the ultrasonic machine. Moreover, the experimental results highlight an increase of the diffraction peak broadening with the number of applied cycles. Full Article text
io BioStruct-Africa: empowering Africa-based scientists through structural biology knowledge transfer and mentoring – recent advances and future perspectives By scripts.iucr.org Published On :: 2019-08-28 Being able to visualize biology at the molecular level is essential for our understanding of the world. A structural biology approach reveals the molecular basis of disease processes and can guide the design of new drugs as well as aid in the optimization of existing medicines. However, due to the lack of a synchrotron light source, adequate infrastructure, skilled persons and incentives for scientists in addition to limited financial support, the majority of countries across the African continent do not conduct structural biology research. Nevertheless, with technological advances such as robotic protein crystallization and remote data collection capabilities offered by many synchrotron light sources, X-ray crystallography is now potentially accessible to Africa-based scientists. This leap in technology led to the establishment in 2017 of BioStruct-Africa, a non-profit organization (Swedish corporate ID: 802509-6689) whose core aim is capacity building for African students and researchers in the field of structural biology with a focus on prevalent diseases in the African continent. The team is mainly composed of, but not limited to, a group of structural biologists from the African diaspora. The members of BioStruct-Africa have taken up the mantle to serve as a catalyst in order to facilitate the information and technology transfer to those with the greatest desire and need within Africa. BioStruct-Africa achieves this by organizing workshops onsite at our partner universities and institutions based in Africa, followed by post-hoc online mentoring of participants to ensure sustainable capacity building. The workshops provide a theoretical background on protein crystallography, hands-on practical experience in protein crystallization, crystal harvesting and cryo-cooling, live remote data collection on a synchrotron beamline, but most importantly the links to drive further collaboration through research. Capacity building for Africa-based researchers in structural biology is crucial to win the fight against the neglected tropical diseases, e.g. ascariasis, hookworm, trichuriasis, lymphatic filariasis, active trachoma, loiasis, yellow fever, leprosy, rabies, sleeping sickness, onchocerciasis, schistosomiasis, etc., that constitute significant health, social and economic burdens to the continent. BioStruct-Africa aims to build local and national expertise that will have direct benefits for healthcare within the continent. Full Article text
io Generating three-color pulses in high-gain harmonic-generation free-electron lasers with a tilted electron bunch By scripts.iucr.org Published On :: 2019-08-12 A multi-color light source is a significant tool for nonlinear optics experiments, pump–dump/repump–probe experiments and in other fields. Here, a novel method is proposed to create three-color pulses based on a high-gain harmonic-generation (HGHG) free-electron laser with a tilted electron bunch. In this method, the initial bunch tilt is created by transverse wakefields after the bunch passes through a corrugated structure with an off-axis orbit, and is further enlarged in a following drift section. Then the tilted bunch experiences the off-axis field of a quadrupole magnet to cool down the large transverse velocity induced before. After that, it enters an HGHG configuration adopting a transverse gradient undulator (TGU) as the radiator, where only three separated fractions of the tilted bunch will resonate at three adjacent harmonics of the seed wavelength and are enabled to emit three-color pulses simultaneously. In addition, the use of the natural transverse gradient of a normal planar undulator instead of the TGU radiator to emit three-color pulses is also studied in detail. Numerical simulations including the generation of the tilted bunch and the free-electron laser radiation confirm the validity and feasibility of this scheme both for the TGU radiator and the natural gradient in the extreme-ultraviolet waveband. Full Article text
io Reducing sample consumption for serial crystallography using acoustic drop ejection By scripts.iucr.org Published On :: 2019-08-16 Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry. Full Article text
io X-ray radiation damage to biological samples: recent progress By scripts.iucr.org Published On :: 2019-07-01 With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below. Full Article text
io An enlightening procedure to explain the extreme power of synchrotron radiation By scripts.iucr.org Published On :: 2019-10-10 A simple approach exploits quantum properties to justify the dependence on γ4 of the total synchrotron emitted power. It also clarifies some apparent puzzles and brings to light the underlying, multiple relativistic phenomena. Full Article text
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io 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
io Rochelle salt – a structural reinvestigation with improved tools. I. The high-T paraelectric phase at 308 K By journals.iucr.org Published On :: A novel sample cell with control of temperature and relative humidity permitted collection of data of excellent quality, enabling unrestrained refinement of all atomic parameters. One of the K atoms in the structure is disordered; very strong anisotropy in three of the four water O atoms indicates partial static disorder, which does not involve the bonded H atoms. Full Article text
io Precession electron diffraction – a topical review By journals.iucr.org Published On :: This topical review highlights progress made recently in the development and application of precession electron diffraction (PED) and its scanning variant for the determination of unknown crystal structures and the mapping of orientations at the nanoscale. Full Article text
io A modulation wave approach to the order hidden in disorder By journals.iucr.org Published On :: A modulation wave approach is used to interpret the coupled longer range as well as truly short range order hidden in the highly structured diffuse intensity distributions of three representative such systems. The longer range as well as the truly short range order simultaneously encoded in such highly structured diffuse intensity distributions is highlighted. Full Article text
io UK government's fracking 'ban' has a convenient loophole - The Conversation UK By theconversation.com Published On :: Fri, 08 Nov 2019 08:00:00 GMT UK government's fracking 'ban' has a convenient loophole The Conversation UK Full Article
io Leading scientists set out resource challenge of meeting net zero emissions in the UK by 2050 - The Natural History Museum By www.nhm.ac.uk Published On :: Wed, 05 Jun 2019 07:00:00 GMT Leading scientists set out resource challenge of meeting net zero emissions in the UK by 2050 The Natural History Museum Full Article
io Fracking in the UK was doomed a decade ago – Tories have wasted precious time on a fossil fuel fantasy - The Conversation UK By theconversation.com Published On :: Tue, 12 Nov 2019 08:00:00 GMT Fracking in the UK was doomed a decade ago – Tories have wasted precious time on a fossil fuel fantasy The Conversation UK Full Article
io Decision day looms over Ellesmere Port shale gas plan - Cheshire Live By www.cheshire-live.co.uk Published On :: Fri, 24 Jan 2020 08:00:00 GMT Decision day looms over Ellesmere Port shale gas plan Cheshire Live Full Article
io Fast trashion: Exhibition of garments made from street-litter opens at Imperial | Imperial News - Imperial College London By www.imperial.ac.uk Published On :: Tue, 07 Jan 2020 08:00:00 GMT Fast trashion: Exhibition of garments made from street-litter opens at Imperial | Imperial News Imperial College London Full Article
io London soil pollution worst on former Blitz bomb sites - Chemistry World By www.chemistryworld.com Published On :: Mon, 15 Jan 2018 08:00:00 GMT London soil pollution worst on former Blitz bomb sites Chemistry World Full Article
io 'Surrey swarm' quakes 'not caused by oil extraction' - BBC News By www.bbc.com Published On :: Tue, 27 Aug 2019 07:00:00 GMT 'Surrey swarm' quakes 'not caused by oil extraction' BBC News Full Article
io British Geological Survey submits application for geoenergy observatory in Cheshire - ThinkGeoEnergy By www.thinkgeoenergy.com Published On :: Fri, 04 Jan 2019 08:00:00 GMT British Geological Survey submits application for geoenergy observatory in Cheshire ThinkGeoEnergy Full Article
io Dr Tim Gregory Works with a Meteorite That's Older Than The Earth - LeftLion By www.leftlion.co.uk Published On :: Wed, 14 Aug 2019 07:00:00 GMT Dr Tim Gregory Works with a Meteorite That's Older Than The Earth LeftLion Full Article