Micro-focused Beam Research Articles

Micro PIXE mapping proves a differential distribution and concentration of trace elements in fungal structures of Rhizophagus intraradices

Arbuscular mycorrhizal (AM) fungi can sequester different potentially toxic elements, such as trace elements (TEs), within their structures to alleviate the toxicity for its host plant and themselves. To elucidate the role of AM fungi in TEs immobilization in the rhizosphere of host plants, it is important to know the TEs distribution in AM fungal structures. In the present study, we investigated the distribution and concentration of TEs within extraradical spores and mycelium of the AM fungus Rhizophagus intraradices, collected from the rhizosphere of Senecio bonariensis plants grown in a soil polluted with multiple TEs, by using Particle-Induced X-ray Emission with a micro-focused beam (micro PIXE). This technique enabled the simultaneous micrometric mapping of elements in a sample. The calculated values were compared with those in the polluted substrate, measured by the Wavelength Dispersive X-ray Fluorescence technique. The highest concentrations of Fe, P, Ti, Mn, Cr, Cu and Zn were found in AM fungal spores, where they were accumulated, while extraradical mycelium was enriched in Cu. Finally, we demonstrated that AM fungi can simultaneously accumulate high amounts of different TEs in their structures, thus reducing the toxicity of these elements to its host plant.

Observation of edge states derived from topological helix chains.

Introducing the concept of topology has revolutionized materials classification, leading to the discovery of topological insulators and Dirac-Weyl semimetals1-3. One of the most fundamental theories underpinning topological materials is the Su-Schrieffer-Heeger (SSH) model4,5, which was developed in 1979-decades before the recognition of topological insulators-to describe conducting polymers. Distinct from the vast majority of known topological insulators with two and three dimensions1-3, the SSH model predicts a one-dimensional analogue of topological insulators, which hosts topological bound states at the endpoints of a chain4-8. To establish this unique and pivotal state, it is crucial to identify the low-energy excitations stemming from bound states, but this has remained unknown in solids because of the absence of suitable platforms. Here we report unusual electronic states that support the emergent bound states in elemental tellurium, the single helix of which was recently proposed to realize an extended version of the SSH chain9,10. Using spin- and angle-resolved photoemission spectroscopy with a micro-focused beam, we have shown spin-polarized in-gap states confined to the edges of the (0001) surface. Our densityfunctional theory calculations indicate that these states are attributed to the interacting bound states originating from the one-dimensional array of SSH tellurium chains. Helices in solids offer a promising experimental platform for investigating exotic properties associated with the SSH chain and exploring topological phases through dimensionality control.

Monoclinic Pleysteinite and Hochleitnerite from the Hagendorf-Süd Pegmatite: Synchrotron Microfocus Diffraction Studies on Twinned Members of Paulkerrite-Group Minerals

Abstract Single-crystal X-ray diffraction data sets for pleysteinite, [(H2O)K]Mn2Al3(PO4)4F2(H2O)10·4H2O, and hochleitnerite, [(H2O)K]Mn2(Ti2Fe)(PO4)4O2(H2O)10·4H2O, collected using a synchrotron microfocus beam, gave monoclinic unit cells, in contrast to previously reported orthorhombic cells obtained using laboratory-based sealed-tube diffractometer data. The differences are attributed to twinning in crystals of the two minerals. As the laboratory diffractometer beam diameter of the sealed-tube SXRD is larger than the crystals that were analyzed, the diffraction results were averaged over the different twin domains, whereas those obtained with the synchrotron microfocus beam gave diffraction data wholly or predominantly from a single domain. Data from the synchrotron datasets give a = 10.440(5) Å, b = 20.588(5) Å, c = 12.234(2) Å, β = 90.38(1)° for pleysteinite and a = 10.547(2) Å, b = 20.577(4) Å, c = 12.373(2) Å, β = 90.09(3)° for hochleitnerite. The crystal structures for both minerals were refined in P21/c, giving Robs = 0.059, 0.058 for 5951, 6718 reflections with I > 3σ(I), respectively. The ideal formulae for the two minerals in this setting conform to the general formula A1A2M12M22M3(PO4)4X2(H2O)10·4H2O, with K and H2O ordered at separate A sites, whereas K and H2O were disordered over a single A site in the orthorhombic models (space group Pbca). Crystal-chemical aspects of the paulkerrite-group minerals, pleysteinite, hochleitnerite, paulkerrite, rewitzerite, and macraeite, are compared and discussed.

Application of laboratory micro X-ray fluorescence devices for X-ray topography

It is demonstrated that high-resolution energy-dispersive X-ray fluorescence mapping devices based on a micro-focused beam are not restricted to high-speed analyses of element distributions or to the detection of different grains, twins and subgrains in crystalline materials but can also be used for the detection of dislocations in high-quality single crystals. Si single crystals with low dislocation densities were selected as model materials to visualize the position of dislocations by the spatially resolved measurement of Bragg-peak intensity fluctuations. These originate from the most distorted planes caused by the stress fields of dislocations. The results obtained by this approach are compared with laboratory-based Lang X-ray topographs. The presented methodology yields comparable results and it is of particular interest in the field of crystal growth, where fast chemical and microstructural characterization feedback loops are indispensable for short and efficient development times. The beam divergence was reduced via an aperture management system to facilitate the visualization of dislocations for virtually as-grown, non-polished and non-planar samples with a very pronounced surface profile.

Fermiology of a topological line-nodal compound CaSb2 and its implication to superconductivity: Angle-resolved photoemission study

We performed angle-resolved photoemission spectroscopy with micro-focused beam on a topological line-nodal compound CaSb2 which undergoes a superconducting transition at the onset Tc~1.8 K, to clarify the Fermi-surface topology relevant to the occurrence of superconductivity. We found that a three-dimensional hole pocket at the G point is commonly seen for two types of single-crystalline samples fabricated by different growth conditions. On the other hand, the carrier-doping level estimated from the position of the chemical potential was found to be sensitive to the sample fabrication condition. The cylindrical electron pocket at the Y(C) point predicted by the calculations is absent in one of the two samples, despite the fact that both samples commonly show superconductivity with similar Ts's. This suggests a key role of the three-dimensional hole pocket to the occurrence of superconductivity, and further points to an intriguing possibility to control the topological nature of superconductivity by carrier tuning in CaSb2.

AMX - the highly automated macromolecular crystallography (17-ID-1) beamline at the NSLS-II.

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 1012 photons s-1), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5-18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.

Development of a versatile micro-focused angle-resolved photoemission spectroscopy system with Kirkpatrick–Baez mirror optics

Angle-resolved photoemission spectroscopy using a micro-focused beam spot [micro-angle-resolved photoemission spectroscopy (ARPES)] is becoming a powerful tool to elucidate key electronic states of exotic quantum materials. We have developed a versatile micro-ARPES system based on the synchrotron radiation beam focused with a Kirkpatrick-Baez mirror optics. The mirrors are monolithically installed on a stage, which is driven with five-axis motion, and are vibrationally separated from the ARPES measurement system. Spatial mapping of the Au photolithography pattern on Si signifies the beam spot size of 10 µm (horizontal) × 12 µm (vertical) at the sample position, which is well suited to resolve the fine structure in local electronic states. Utilization of the micro-beam and the high precision sample motion system enables the accurate spatially resolved band-structure mapping, as demonstrated by the observation of a small band anomaly associated with tiny sample bending near the edge of a cleaved topological insulator single crystal.

Coaxial μSAXS/POM simultaneous measurement for microstructural characterization of one-dimensional and two-dimensional crystalline polymer

The microfocus beam small-angle X-ray scattering (μSAXS) provides a high spatial resolution ability, and the μSAXS/POM simultaneous measurement facilitates the acquisition of the micro-structural variations in the heterogeneous samples. Herein, at the SSRF BL19U2 beamline, a coaxial μSAXS/POM simultaneous measurement system has been established, comprising of the compound refractive lenses and an in-situ polarizing microscope. The SAXS beam size of 5.43 μm × 6.52 μm with a flux of 2.52 × 1011 photons/s has been employed. In order to obtain realistic microstructural information, the visible light path of the polarizing microscope has been set coaxially with the X-ray to eliminate the field of view deviation. The microstructure of the ringed spherulites of the polyoxymethylene/polybutylenesuccinate blends and high-density polyethene (HDPE) fibers has been simultaneously characterized. The differences in the structural information at different positions inside the banded spherulites have been evaluated. The crystallinity of the HDPE fibers increases from the skin to core, whereas the average crystalline lamellae thickness of the HDPE fibers decreases from skin to core, and the long spacing remains almost unchanged in the fibers.

Optical properties of a liquid-crystal microlens with an arrayed planar non-uniform spiral micro-coil electrode

A new type of liquid-crystal (LC) microlens with an arrayed planar non-uniform spiral micro-coil electrode is proposed. Arrayed cylindrical microbeam focusing and spherical microbeam focusing corresponding to a circular and an elliptical micro-coil are realized, respectively. By applying driving voltage signals over only one electrode plate of the proposed LC microlens, an orderly inclining of LC directors can be achieved in response to the generated electric field, and this is the first time such a method has been proposed to the best of our knowledge. Through adjusting driving voltage signals, the electrically tunable focusing properties are evaluated experimentally. Typical focusing performances such as an arrayed focal line with ${\sim} 1.75\,\,{\rm mm}$∼1.75mm focal length corresponding to a signal voltage of ${\sim}{45.6\,\,{\rm V}_{\rm rms}}$∼45.6Vrms and a focal point with ${\sim} 2.35\,\,{\rm mm}$∼2.35mm focal length corresponding to ${\sim}{55.0\,\,{\rm V}_{\rm rms}}$∼55.0Vrms are given, as well as several typical intermediate states. This research lays a solid basis for continuously developing LC microlens technology.

Micro-focused MHz pink beam for time-resolved X-ray emission spectroscopy.

The full radiation from the first harmonic of a synchrotron undulator (between 5 and 12 keV) at the Advanced Photon Source is microfocused using a stack of beryllium compound refractive lenses onto a fast-moving liquid jet and overlapped with a high-repetition-rate optical laser. This micro-focused geometry is used to perform efficient nonresonant X-ray emission spectroscopy on transient species using a dispersive spectrometer geometry. The overall usable flux achieved on target is above 1015 photons s-1 at 8 keV, enabling photoexcited systems in the liquid phase to be tracked with time resolutions from tens of picoseconds to microseconds, and using the full emission spectrum, including the weak valence-to-core signal that is sensitive to chemically relevant electronic properties.

Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II.

Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II—AMX and FMX—deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins—Akt1, PI3Kα, and CDP-Chase—to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or “raster-collect”, a more automated approach for a larger number of crystals (using CDP-Chase as an example).

The Influence of Photoelectron Escape in Radiation Damage Simulations of Protein Micro-Crystallography

Radiation damage represents a fundamental limit in the determination of protein structures via macromolecular crystallography (MX) at third-generation synchrotron sources. Over the past decade, improvements in both source and detector technology have led to MX experiments being performed with smaller and smaller crystals (on the order of a few microns), often using microfocus beams. Under these conditions, photoelectrons (PEs), the primary agents of radiation-damage in MX, may escape the diffraction volume prior to depositing all of their energy. The impact of PE escape is more significant at higher beam energies (>20 keV) as the electron inelastic mean free path (IMFP) is longer, allowing the electrons to deposit their energy over a larger area, extending further from their point of origin. Software such as RADDOSE-3D has been used extensively to predict the dose (energy absorbed per unit mass) that a crystal will absorb under a given set of experimental parameters and is an important component in planning a successful MX experiment. At the time this study was undertaken, dose predictions made using RADDOSE-3D were spatially-resolved, but did not yet account for the propagation of PEs through the diffraction volume. Hence, in the case of microfocus crystallography, it is anticipated that deviations may occur between the predicted and actual dose absorbed due to the influence of PEs. To explore this effect, we conducted a series of simulations of the dose absorbed by micron-sized crystals during microfocus MX experiments. Our simulations spanned beam and crystal sizes ranging from 1μm to 5μm for beam energies between 9 keV and 30 keV. Our simulations were spatially and temporarily resolved and accounted for the escape of PEs from the diffraction volume. The spatially-resolved dose maps produced by these simulations were used to predict the rate of intensity loss in a Bragg spot, a key metric for tracking global radiation damage. Our results were compared to predictions obtained using a recent version of RADDOSE-3D that did not account for PE escape; the predicted crystal lifetimes are shown to differ significantly for the smallest crystals and for high-energy beams, when PE escape is included in the simulations.

Performance evaluation of an SOI pixel sensor with in-pixel binary counters

Pixel detectors fabricated with the silicon-on-insulator (SOI) technology suffered from the digital pickup, due to the capacitive coupling between the sensing electrode and the in-pixel circuit. In order to tackle this issue, an advanced process called double SOI has been developed. A prototype chip CPIXTEG3b adopting this new process was designed and characterized. While optimization concerning the double-SOI design and testing of the single pixel were already presented in a separate publication, this paper focuses on its noise performance of the full matrix and X-ray detection utilizing a synchrotron photon beam. Equivalent noise charge (ENC) of the full pixel matrix was measured with electrical pulse tests. The threshold dispersion was minimized by the DAC tuning in each individual pixel. As a photon-counting X-ray imager, noise count accumulated up to 1 h was measured. Detection efficiency was measured with a micro-focused beam as well as a flat field generated by the X-ray scattering on a glassy carbon at the KEK PF beam line 14A. The typical ENC is $$52~ \hbox {e}^{-}$$ and the sigma of threshold dispersion is $$10 \,\hbox {e}^{-}$$ over the full matrix. A merit of “zero” noise count is also demonstrated, which is consistent with the low ENC. The prototype chip has been tested with microbeam and used to measure the beam profile to be with a full width of $$50~\upmu \hbox {m}$$ at 2.4% of the maximum height. Both sensor depletion and charge sharing between neighboring pixels have been carefully characterized, providing insights for further development. The homogeneity of response to X-ray photons has been demonstrated in the flat field test. This work has drawn a final conclusion to the solution of digital pickup issue and opened a promising prospect in low-noise and high-resolution X-ray imaging.

X-ray metrology of an array of active edge pixel sensors for use at synchrotron light sources

We report on the production and testing of an array of active edge silicon sensors as a prototype of a large array. Four Medipix3RX.1 chips were bump bonded to four single chip sized Advacam active edge n-on-n sensors. These detectors were then mounted into a 2 by 2 array and tested on B16 at Diamond Light Source with an x-ray beam spot of 2um. The results from these tests, compared with optical metrology demonstrate that this type of sensor is sensitive to the physical edge of the silicon, with only a modest loss of efficiency in the final two rows of pixels. We present the efficiency maps recorded with the microfocus beam and a sample powder diffraction measurement. These results give confidence that this sensor technology can be used effectively in larger arrays of detectors at synchrotron light sources.

From lapis lazuli to ultramarine blue: investigating Cennino Cennini’s recipe using sulfur K-edge XANES

Abstract As one of the most desired and expensive artists’ materials throughout history, there has long been interest in studying natural lapis lazuli. The traditional method of extracting the blue component, lazurite, from lapis lazuli, as outlined in Cennini’s Il Libro dell’Arte, involves a lengthy purification process: (1) finely grind the rock; (2) mix with pine rosin, gum mastic, and beeswax; (3) massage in water to collect the lazurite. Repeating the process produces several grades of the pigment, typically referred to as ultramarine blue. Here, we investigate the sulfur environment within the aluminosilicate framework of lazurite during its extraction from lapis lazuli. The sulfur XANES fingerprint from samples taken at the different stages in Cennini’s extraction method were examined. All spectra contain a strong absorption peak at 2483 eV, attributable to sulfate present in the lazurite structure. However, intensity variations appear in the broad envelope of peaks between 2470 and 2475 eV and the pre-peak at 2469.1 eV, indicating a variation in the content of trisulfur (S3 −˙) radicals. By studying the effect of each step of Cennini’s process, this study elucidates the changes occurring during the extraction and the variability within different grades of the precious coloring material. The increasing application of XANES to the study of artist’s materials and works of art motivated extending the research to assess the possibility of X-ray induced damage. Direct comparison of micro-focused and unfocused beam experiments suggests an increase of the S3 −˙ radicals with prolonged exposure. Analysis indicates that induced damage follows first-order kinetics, providing a first assessment on the acceptable amount of radiation exposure to define the optimal acquisition parameters to allow safe analyses of lapis lazuli and ultramarine pigments.

Novel micro-reactor flow cell for investigation of model catalysts using in situ grazing-incidence X-ray scattering.

The design, fabrication and performance of a novel and highly sensitive micro-reactor device for performing in situ grazing-incidence X-ray scattering experiments of model catalyst systems is presented. The design of the reaction chamber, etched in silicon on insulator (SIO), permits grazing-incidence small-angle X-ray scattering (GISAXS) in transmission through 10 µm-thick entrance and exit windows by using micro-focused beams. An additional thinning of the Pyrex glass reactor lid allows simultaneous acquisition of the grazing-incidence wide-angle X-ray scattering (GIWAXS). In situ experiments at synchrotron facilities are performed utilizing the micro-reactor and a designed transportable gas feed and analysis system. The feasibility of simultaneous in situ GISAXS/GIWAXS experiments in the novel micro-reactor flow cell was confirmed with CO oxidation over mass-selected Ru nanoparticles.

Pressure, stress, and strain distribution in the double-stage diamond anvil cell

Double stage diamond anvil cells (DACs) of two designs have been assembled and tested. We used a standard symmetric DAC with flat or beveled culets as a primary stage and CVD microanvils machined by a focused ion beam as a second. We evaluated pressure, stress, and strain distributions in gold and a mixture of gold and iron as well as in secondary anvils using synchrotron x-ray diffraction with a micro-focused beam. A maximum pressure of 240 GPa was reached independent of the first stage anvil culet size. We found that the stress field generated by the second stage anvils is typical of conventional DAC experiments. The maximum pressures reached are limited by strains developing in the secondary anvil and by cupping of the first stage diamond anvil in the presented experimental designs. Also, our experiments show that pressures of several megabars may be reached without sacrificing the first stage diamond anvils.

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Versatile atomic force microscopy setup combined with micro-focused X-ray beam

Micro-focused X-ray beams produced by third generation synchrotron sources offer new perspective of studying strains and processes at nanoscale. Atomic force microscope setup combined with a micro-focused synchrotron beam allows precise positioning and nanomanipulation of nanostructures under illumination. In this paper, we report on integration of a portable commercial atomic force microscope setup into a hard X-ray synchrotron beamline. Details of design, sample alignment procedure, and performance of the setup are presented.

Soft X-ray angle-resolved photoemission with micro-positioning techniques for metallic V₂O₃.

Soft X-ray angle-resolved photoemission has been performed for metallic V2O3. By combining a microfocus beam (40 µm × 65 µm) and micro-positioning techniques with a long-working-distance microscope, it has been possible to observe band dispersions from tiny cleavage surfaces with a typical size of several tens of µm. The photoemission spectra show a clear position dependence, reflecting the morphology of the cleaved sample surface. By selecting high-quality flat regions on the sample surface, it has been possible to perform band mapping using both photon-energy and polar-angle dependences, opening the door to three-dimensional angle-resolved photoemission spectroscopy for typical three-dimensional correlated materials where large cleavage planes are rarely obtained.