Third-generation Synchrotron Facility Research Articles

Photoelectron Diffraction and Holography Studies on Dopant Local Structures

Photoelectron holography (PEH) is an experimental technique that can be used to study the three-dimensional (3D) local structure around a focused atom. Recent advancements in reconstruction algorithm and the utilization of high-intensity soft X-rays generated from third-generation synchrotron facilities have made it possible to reveal detailed dopant local structures of less than 1% concentrations, with element and chemical site selectivities. Moreover, recent PEH studies have demonstrated that even the dopant occupancy for each crystal site of diamond and graphene can be estimated and that the orientation of a dopant vacancy complex can be determined. The information obtained by this technique is valuable for understanding and improving the physical properties of doped materials and also sheds light on how dopants are taken up in a crystal during synthesis. Here, photoelectron diffraction (PED) studies on dopant locations and recent PEH studies reporting detailed dopant local structures are reviewed, emphasizing the unique local structure information that can be obtained by this technique.

ゴム破壊現象の高速3D観察

X-ray computed tomography (CT) is a non-destructive three-dimensional visualization method that uses the high penetrating power of hard X-rays with energy of 10 keV or higher to visualize the inside of a sample. We realized 4D (3D＋time) X-ray CT with a temporal resolution of 10 ms and a pixel size of 4.2 μm using a white synchrotron beam from a bending magnet source of the third-generation synchrotron facility. Real-time observation of the tensile fracture process of a tire rubber sample was successfully achieved for the first time. It is expected that our approach has various applications, such as mechanical fracture of soft materials, adhesive interface fracture, friction, and wear mechanisms.

Accurate high-resolution single-crystal diffraction data from a Pilatus3 X CdTe detector.

Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb2, and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing (SAINT-Plus, SADABS and SORTAV), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements.

GigaFRoST: the gigabit fast readout system for tomography.

Owing to recent developments in CMOS technology, it is now possible to exploit tomographic microscopy at third-generation synchrotron facilities with unprecedented speeds. Despite this rapid technical progress, one crucial limitation for the investigation of realistic dynamic systems has remained: a generally short total acquisition time at high frame rates due to the limited internal memory of available detectors. To address and solve this shortcoming, a new detection and readout system, coined GigaFRoST, has been developed based on a commercial CMOS sensor, acquiring and streaming data continuously at 7.7 GB s-1 directly to a dedicated backend server. This architecture allows for dynamic data pre-processing as well as data reduction, an increasingly indispensable step considering the vast amounts of data acquired in typical fast tomographic experiments at synchrotron beamlines (up to several tens of TByte per day of raw data).

Mini-beam modes on standard MX beamline BL17U at SSRF.

The macromolecular crystallography beamlines at third-generation synchrotron facilities play a central role in solving macromolecular crystal structures and also in understanding the biological function at molecular levels. The MX beamline BL17U at Shanghai Synchrotron Radiation Facility is a typical standard MX beamline with a focused beam size (H × V) of FWHM around 80 μm × 45 μm. However the protein samples brought to the beamline are down to 5-10 m from the important and challenging science project now. These samples require smaller size beam. In order to achieve the mini-size beamline, two mini-beam modes have been developed on BL17U: the pinhole-based mini-beam and the focused mini-beam by compound refractive lens (CRL). Compared to the pinhole-based mode, three times increase in flux is obtained by the CRL mode at a similar beam size. The flux gain obtained by the CRL needs to be considered for data collection strategies. It takes few minutes to switch the beamline from the normal to CRL mini-beam mode.

Serial Synchrotron X-Ray Crystallography (SSX).

Prompted by methodological advances in measurements with X-ray free electron lasers, it was realized in the last two years that traditional (or conventional) methods for data collection from crystals of macromolecular specimens can be complemented by synchrotron measurements on microcrystals that would individually not suffice for a complete data set. Measuring, processing, and merging many partial data sets of this kind requires new techniques which have since been implemented at several third-generation synchrotron facilities, and are described here. Among these, we particularly focus on the possibility of in situ measurements combined with in meso crystal preparations and data analysis with the XDS package and auxiliary programs.

In situ characterization of liquid network structures at high pressure and temperature using X-ray absorption spectroscopy coupled with the Paris-Edinburgh press

ABSTRACTWe review recent progress in studying structural properties of liquids using X-ray absorption spectroscopy coupled with the Paris-Edinburgh press at third-generation synchrotron facilities. This experimental method allows for detecting subtle changes in atomic arrangements of melts over a wide pressure–temperature range. It has been also employed to monitor variations of the local coordination environment of diluted species contained in glasses, liquids and crystalline phases as a function of the pressure and temperature. Such information is of great importance for gaining deeper insights into the physico-chemical properties of liquids at extreme condition, including the understanding of such phenomena as liquid–liquid phase transitions, viscosity drops and various transport properties of geological melts. Here, we describe the experimental approach and discuss its potential in structural characterization on selected scientific highlights. Finally, the current ongoing instrumental developments and future scientific opportunities are discussed.

High-pressure experimental studies on geo-liquids using synchrotron radiation at the Advanced Photon Source

We review recent progress in studying silicate, carbonate, and metallic liquids of geological and geophysical importance at high pressure and temperature, using the large-volume high-pressure devices at the third-generation synchrotron facility of the Advanced Photon Source, Argonne National Laboratory. These integrated high-pressure facilities now offer a unique combination of experimental techniques that allow researchers to investigate structure, density, elasticity, viscosity, and interfacial tension of geo-liquids under high pressure, in a coordinated and systematic fashion. Experimental techniques are described, along with scientific highlights. Future developments are also discussed.

Demonstration of osmotically dependent promotion of aerenchyma formation at different levels in the primary roots of rice using a ‘sandwich’ method and X-ray computed tomography

The effect of environmental factors on the regulation of aerenchyma formation in rice roots has been discussed for a long time, because aerenchyma is constitutively formed under aerated conditions. To elucidate this problem, a unique method has been developed that enables sensitive detection of differences in the development of aerenchyma under two different environmental conditions. The method is tested to determine whether aerenchyma development in rice roots is affected by osmotic stress. To examine aerenchyma formation both with and without mannitol treatment in the same root, germinating rice (Oryza sativa) caryopses were sandwiched between two agar slabs, one of which contained 270 mm of mannitol. The roots were grown touching both slabs and were thereby exposed unilaterally to osmotic stress. As a non-invasive approach, refraction contrast X-ray computed tomography (CT) using a third-generation synchrotron facility, SPring-8 (Super photon ring 8 GeV, Japan Synchrotron Radiation Research Institute), was used to visualize the three-dimensional (3-D) intact structure of aerenchyma and its formation in situ in rice roots. The effects of unilateral mannitol treatment on the development of aerenchyma were quantitatively examined using conventional light microscopy. Structural continuity of aerenchyma was clearly visualized in 3-D in the primary root of rice and in situ using X-ray CT. Light microscopy and X-ray CT showed that the development of aerenchyma was promoted on the mannitol-treated side of the root. Detailed light microscopic analysis of cross-sections cut along the root axis from the tip to the basal region demonstrated that aerenchyma developed significantly closer to the root tip on the mannitol-treated side of the root. Continuity of the aerenchyma along the rice root axis was morphologically demonstrated using X-ray CT. By using this 'sandwich' method it was shown that mannitol promoted aerenchyma formation in the primary roots of rice.

Circular dichroism beamline B23 at the Diamond Light Source

Synchrotron radiation circular dichroism (SRCD) is a well established technique in structural biology. The first UV-VIS beamline, dedicated to circular dichroism, at Diamond Light Source Ltd, a third-generation synchrotron facility in south Oxfordshire, UK, has recently become operational and it is now available for the user community. Herein the main characteristics of the B23 SRCD beamline, the ancillary facilities available for users, and some of the recent advances achieved are summarized.

High-performance soft x-ray spectromicroscopy beamline at SSRF

The Shanghai Synchrotron Radiation Facility (SSRF) is the first third-generation synchrotron facility in China and operated at an electron energy of 3.5 GeV. One of the seven beamlines in the first construction phase is devoted to soft x-ray spectromicroscopy and is equipped with an elliptically polarized undulator light source, a plane grating monochromator, and a scanning transmission x-ray microscope end station. Initial results reveal the high performance of this beamline, with an energy resolving power estimated to be over 10,000 at the argon L-edge and a spatial resolution better than 30 nm.

B23 circular dichroism beamline at the Diamond Light Source

Circular dichroism spectroscopy is a useful and versatile tool to obtain low-resolution structural information about proteins, biopolymers and other chiral materials in solution. The first UV–VIS beamline dedicated to circular dichroism, B23, at Diamond Light Source Ltd., a third-generation synchrotron facility in the UK, has recently become operational and is now available for the user community. Herein we summarize the main characteristics of the beamline and some possible applications.

Negative (and very low) thermal expansion in ReO3from 5 to 300 K

This paper reports the accurate measurement of the ReO3cell parameter as a function of temperature. The thermal expansion is confirmed to be negative over most of the temperature range from 5 to 300 K. The main problems with the measurements are the very small variations (in the range of 10−5 Å) in the cell parameter at each temperature, requiring tight control of the stability and reliability of instrumental effects. In particular, achieving monochromator stability over time might be challenging with the high energy and high beam current variations of a third-generation synchrotron facility. On the other hand, such effects are usually checked by the addition of silicon as an internal standard, but the accuracy (and precision) of the published thermal expansion (which is not certified) might not be sufficient for its use when dealing with very small cell parameter variations.

Increasing Heart Rate Decreased Actin-Myosin Interaction in Isolated Beating Rat Whole Heart

Background: Heart rate (HR) is one of the determinant factors of cardiac performance. Failing human myocardium shows negative force frequency relation, whereas normal one shows positive relation. Purpose: To test the effect of HR on actin-myosin interaction (AMI) in beating rat hearts those have negative force-frequency relation by X-ray diffraction (XRD) analysis at third-generation synchrotron facility. Methods: Seven isolated isovolumically contracting rat hearts were paced at 120, 240, and 300bpm after complete heart block, mounted so that the X-ray beam (15.0keV) passed the left ventricular (LV) free wall, and perfused with Tyrode solution bubbled with 100% O2. LV volume were adjusted through water filled thin latex balloon inserted into LV cavity so that end-diastolic LV pressure (LVP) was 0 mmHg. The amount of AMI was evaluated by the minimum value of the intensity ratio of inner (1,0) and outer (1,1) equatorial reflections (Imin) provided by anaysis of XRD. Between three different HRs, we compared the amount of AMI and LVP. We also measured frequency-dependent changes in Ca2+ transient in sliced myocardial preparations at 0.5, 1.0, and 2.0Hz. Results: In all hearts, we did not observe incomplete relaxations. As increasing HR at 120, 240, and 300bpm, LVP significantly decreased (66±18, 51±16, and 47±18mmHg, respectively) and Imin also significantly increased (0.93±0.16, 1.20±0.11, and 1.56±0.18, respectively), indicating a significant decrease of the amount of AMI. The durations of Ca2+ transient at 20% developed level at stimulating frequency of 0.5, 1.0, and 2.0Hz were significantly shortened (233±25, 206±34, and 171±28ms, respectively). Conclusion: Increasing HR reduces the AMI. Absence of incomplete relaxations indicates intact intracellular Ca2+ handling. These results may derive from shortening the period of Ca2+-myofilament interaction with increasing HR.

Direct determination of Burgers vector sense and magnitude of elementary dislocations by synchrotron white x-ray topography

The x-ray topography by using highly coherent beam obtained at third-generation synchrotron facilities can provide higher spatial resolution and higher lattice-distortion sensitivity than those by former-generation facilities. Here, we report the direct determination of the Burgers vector senses and magnitudes of elementary dislocations in a high-quality silicon carbide single crystal using white x-ray section topography with a long sample-to-film distance. Our data strongly indicate that there are very weak but extraordinarily long-range elastic interactions between elementary screw dislocations. Those interactions govern dislocation-propagation behavior and the distribution of dislocations. Moreover, we found that white x-ray projection topography with a long sample-to-film distance can also be a powerful tool to effectively examine the detailed structure of elementary dislocations in single crystals.

Lower limits of detection of synchrotron radiation high-energy X-ray fluorescence spectrometry and its possibility for the forensic application for discrimination of glass fragments

Synchrotron radiation high-energy X-ray fluorescence (SR-XRF) analysis utilizing 75.5 keV X-ray radiation from beam-line BL37XU at Super Photon Ring 8 GeV (SPring-8), a third-generation synchrotron facility, was found to have advantages for forensic discrimination of glass samples. The lower limits of detection (LLD) for calibration curves were at the picogram level for Ba, Ce, and Sm and at the 10 pg level for Sr, Zr, Sn, and Hf. The spectrum of NIST SRM 612 glass reference material demonstrated K-line peaks of 31 elements including rare-earth elements, and the relative standard deviations (R.S.D.) of all the measured elements except Ca were less than 9.7%. Fragments of collected sheet glass were used as samples for investigating the application of this technique to forensic analysis. Several trace elements such as Pb, Rb, Sr, Zr, La, Ce, and Hf were detected in the spectra of the samples, and these elements could be used as indexes to characterize the glass samples. But the “lower limits of detection (LLD)” of each element were not examined enough. In this report, these limits by synchrotron radiation X-ray spectrometry were clarified. By these results, this technique should provide an effective approach to the nondestructive discrimination of small glass fragments in the field of forensic science.

Study on Iron Distribution and Electrical Activities at Grain Boundaries in Polycrystalline Silicon Substrate for Solar Cells

To clarify the role of grain boundaries in iron sinks and carrier recombination centers, iron distributions and their chemical states were studied before and after gettering. They were measured by the X-ray microprobe fluorescence and the X-ray absorption in the near-edge structure using the beamline 37XU at the SPring-8 third-generation synchrotron facility. To determine the crystallographic orientation of the grain boundaries, electron backscatter diffraction measurements were performed. The distribution of electric active defects was characterized by electron-beam-induced current measurements. Before gettering, the iron was distributed in the small grain and its chemical state was similar to that of iron oxide. After gettering, the iron was redistributed along the small angle grain boundary, and its chemical state was similar to the iron silicide complexed with the iron oxide. Regarding the electrical activity, high carrier recombination was observed along the small-angle grain boundary. On the contrary, Σ3 grain boundaries were relatively weak impurity sinks and showed low recombination activity.

Partial structure analysis of glassy As2Se3 using anomalous X-ray scattering

Anomalous X-ray scattering experiments have been performed on glassy As2Se3 at room temperature in order to clarify the role of each constituent for short- and intermediate-range order. The experiments were performed using intense X-rays from a third-generation synchrotron facility, ESRF. Differential structure factors, ΔiS(Q), close to the As and Se K edges were obtained from a detailed analysis. The prepeak around Q=12nm−1 in the total structure factor, S(Q), indicating evidence of intermediate-range order, is dominated by the As–As correlation around 12nm−1 and the Se–Se correlation around 14.5nm−1. The origin of the prepeak is carefully discussed.

High-resolution soft X-ray emission spectrograph at advanced light source

Abstract The progress of valence electronic spectroscopy with X-rays has been largely limited by the challenge of fine instrumentation. Relatively weak scattering cross-section and/or limited (coarse) energy resolution restrict X-ray spectroscopy to address fundamental issues in condensed-matter electron physics. Depending on the nature of excitations, high brightness photon beam from third-generation synchrotron facilities helps raise the count rates to a detectable limit over the noise level. Over the past decade, it has been realized that high-resolution resonant inelastic soft X-ray scattering has the potential to play an important role in understanding complex phenomena observed in highly correlated systems. Driven by such demand, we have developed a soft X-ray emission spectrograph based on variable line spacing (VLS) gratings to work in the soft X-ray and deep UV (the M edge of transition metals) regime. The slit-less design coupled with high quality optical elements and a high quantum efficiency (QE) in-vacuum CCD detector greatly improves the overall throughput. The M edge spectrograph has been demonstrated to have a resolving power better than 10,000 and will be used in conjunction with meV-resolution beamline (MERLIN) at the Advanced Light Source at Lawrence Berkeley National Laboratory.

The ALS on completion of its first decade

The Advanced Light Source (ALS), a third-generation synchrotron facility optimized for ultraviolet and soft X-rays, started operation in 1993. The current status of the facility will be described, and highlights of recent research in areas such as condensed-matter physics, EUV lithography, and nanomagnetism will be presented. A strategic vision for the ALS into its next decade and beyond will be outlined.