Generation Synchrotron Sources Research Articles

Laminography as a tool for imaging large-size samples with high resolution.

Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.

Growth of ultimate high-density scintillating films for high-resolution X-ray imaging at synchrotrons

Scintillators are X-ray to visible light converters applied in X-ray imaging detectors used at synchrotrons. Drastically improved performances of the 4th generation synchrotron sources enable us to perform X-ray imaging experiments at higher energies. For high spatial resolution X-ray imaging (micrometer to submicrometer), thin scintillating films are required. Consequently, especially for high X-ray energies (30keV to 100keV), the detection efficiency is limited due to the low X-ray absorption efficiency of the thin films. We have used Liquid Phase Epitaxy (LPE) to grow thin films of one of the ultimate high-density materials, Lu2Hf2O7:Eu3+, which demonstrate scintillating properties and thus combine high spatial resolution and maximized absorption efficiency. X-ray imaging experiments demonstrate that the Modulation Transfer Function (MTF) reaches 10% at 900 lp/mm, and radiographs visually confirm the promising imaging properties. We present structural, luminescent, and scintillation characterization of Lu2Hf2O7:Eu thin films grown on ZrO2:Y substrates, showing that the films crystallize in the disordered fluorite structure and the europium ions incorporate into the structure and enhance the luminescence intensity. This contribution is a first step toward developing promising ultra-dense, hafnate-based scintillating screens for high spatial resolution X-ray imaging.

X-ray excited optical luminescence at Carnaúba, the Sirius X-ray nanoprobe beamline

This work presents the developments and initial results obtained using X-ray excited optical luminescence (XEOL) at the Carnaúba, the nanoprobe beamline from Sirius, the Brazilian 4th generation synchrotron source. XEOL is a highly important tool to study luminescence mechanisms and identify optical channels in various types of materials under X-ray irradiation. Using this capability combined with a nanoprobe, one can probe optical channels, for example, in heterogenous materials, and directly correlate them with chemical composition, oxidizing state of absorbers, structure and/or morphology in simultaneous studies. Carnaúba is composed by two experimental station and at the Tarumã station, the first entering in operation, it has been possible to investigate XEOL in the integrated and emission modes, and 2D images in hyperspectral mapping with submicrometric resolution. Herein, it is showed some examples of studies combining excitation energy, emission wavelength and emission intensity in 3D spectra, 2D imaging, and XEOL emission on the study of very sensitive samples that can be easily damaged by the probe. This work also highlights some of the upcoming developments that include the time-resolved and in situ experiments, this last one using microfluidic cells, and the improvement of the covered emission wavelength up to 1700 nm, which will open new opportunities for studying optical materials.

ALBA Synchrotron and its future

The ALBA Synchrotron light source is the Spanish national facility, providing extended research capabilities and a wide range of state-of-the-art instrumentation to academic and industrial users of the Spanish and European Research Area since 2012. It includes ten operating beamlines, two beamlines in commissioning and two more in construction. JEMCA (Joint Electron Microscopy Center at ALBA), a center including advanced electron microscopes, developed in collaboration with partner institutions, has recently been inaugurated. The next years will be dedicated to exploit the existing instrumentation, and in parallel prepare the upgrade toward a fourth generation synchrotron source, by combining the partial substitution of the accelerators with the upgrade of the existing instrumentation, the addition of new cutting-edge beamlines, the development of further capabilities for automatization, simulation, prototyping, nanotechnology and advanced optics, and the extension of the infrastructure in the nearby plots, which will host the new long beamline end-stations and aim at being the seed of a science, technology and innovation park. The 2-year dark period is foreseen for the end of this decade. The status of the facility, few scientific highlights, and the plans for the future are described.

The Promise and Challenge of High Pressure Macromolecular Crystallography

Since its introduction in the early 1970s, high pressure crystallography (HPX) has shown great potential for the investigation of different types of matter. Using diamond anvil cells, HPX is an emerging technique that has been rapidly implemented, making it available to biologists, and there is immense potential for utilizing this technique in biological systems in the future. At the molecular level, high-pressure crystallographic investigation provides information on structural characteristics that not only determine the native conformation of a protein but also the conformations with higher free-energy, thus revealing function-related structural changes and properties that can be modified as a result of pressurization. The increase in the number of crystal structures of different macromolecules determined under high pressure over the last five decades can be ascribed mainly to two factors: the emergence of high-pressure cells with very large, open angles, and the advent of third generation synchrotron sources. The use of high pressure crystallography as a research tool has been shown to contribute to the advancements in the basic fields of biochemistry (protein misfolding and aggregation), biophysics (protein stability), and biotechnology (food processing). Presently, with a growing interest in biomedicine and nanotechnology, this nonstandard method appears to be a valid instrument for probing more challenging and complex systems. In this review, we present the method, highlight a selection of recent applications, and describe challenges for high pressure macromolecular crystallography (HPMX).

4th generation synchrotron source boosts crystalline imaging at the nanoscale

New 4th-generation synchrotron sources, with their increased brilliance, promise to greatly improve the performances of coherent X-ray microscopy. This perspective is of major interest for crystal microscopy, which aims at revealing the 3D crystalline structure of matter at the nanoscale, an approach strongly limited by the available coherent flux. Our results, based on Bragg ptychography experiments performed at the first 4th-generation synchrotron source, demonstrate the possibility of retrieving a high-quality image of the crystalline sample, with unprecedented quality. Importantly, the larger available coherent flux produces datasets with enough information to overcome experimental limitations, such as strongly deteriorated scanning conditions. We show this achievement would not be possible with 3rd-generation sources, a limit that has inhibited the development of this otherwise powerful microscopy method, so far. Hence, the advent of next-generation synchrotron sources not only makes Bragg ptychography suitable for high throughput studies but also strongly relaxes the associated experimental constraints, making it compatible with a wider range of experimental set-ups at the new synchrotrons.

New frontiers in extreme conditions science at synchrotrons and free electron lasers

Synchrotrons and free electron lasers are unique facilities to probe the atomic structure and electronic properties of matter at extreme thermodynamical conditions. In this context, ‘matter at extreme pressures and temperatures’ was one of the science drivers for the construction of low emittance 4th generation synchrotron sources such as the Extremely Brilliant Source of the European Synchrotron Radiation Facility and hard x-ray free electron lasers, such as the European x-ray free electron laser. These new user facilities combine static high pressure and dynamic shock compression experiments to outstanding high brilliance and submicron beams. This combination not only increases the data-quality but also enlarges tremendously the accessible pressure, temperature and density space. At the same time, the large spectrum of available complementary x-ray diagnostics for static and shock compression studies opens unprecedented insights into the state of matter at extremes. The article aims at highlighting a new horizon of scientific opportunities based on the synergy between extremely brilliant synchrotrons and hard x-ray free electron lasers.

Operando 3D imaging of defects dynamics of twinned-nanocrystal during catalysis

Using operando Bragg coherent x-ray diffraction imaging, we visualised three-dimensionally a single twinned-gold nanocrystal during the CO oxidation reaction. We describe the defect dynamics process occurring under operating conditions and indicate the correlation between the nucleation of highly strained regions at the surface of the nanocrystal and its catalytic activity. Understanding the twinning deformation mechanism sheds light on the creation of active sites, and could well contribute to the understanding of the catalytic behaviour of other catalysts. With the start-up of 4th generation synchrotron sources, we anticipate that coherent hard x-ray diffraction imaging techniques will play a major role in imaging in situ chemical processes.

Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future

The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.

The structure of oxide glasses studied by high-energy x-ray diffraction

The use of high‑energy x‑ray diffraction techniques with the latest generation synchrotron sources has created new approaches to study quantitatively the structure of noncrystalline materials. Recently, this technique has been combined with neutron diffraction at pulsed source to provide more detailed and reliable structural information not previously available. This article reviews and summarises recent results obtained from the high energy x‑ray diffraction on several oxide glasses, SiO2, B2O3 and PbSiO3, using bending magnet beamlines at SPring‑8. In particular, it addresses the structural models of the oxide glasses obtained by the reverse Monte Carlo (RMC) modelling technique using both the high energy x‑ray and neutron diffraction data.

Three-Dimensional Coherent Bragg Imaging of Rotating Nanoparticles.

Bragg coherent diffraction imaging is a powerful strain imaging tool, often limited by beam-induced sample instability for small particles and high power densities. Here, we devise and validate an adapted diffraction volume assembly algorithm, capable of recovering three-dimensional datasets from particles undergoing uncontrolled and unknown rotations. We apply the method to gold nanoparticles which rotate under the influence of a focused coherent x-ray beam, retrieving their three-dimensional shapes and strain fields. The results show that the sample instability problem can be overcome, enabling the use of fourth generation synchrotron sources for Bragg coherent diffraction imaging to their full potential.

Algorithm for characterizing the subcellular structures of nanometer-sized biological specimens in a solution using x-ray free-electron lasers

Coherent diffraction imaging using third generation synchrotron sources and x-ray free-electron lasers has been demonstrated to be an excellent tool for revealing the inner structures of a single particle. The primary challenge in imaging pure, tiny, and isolated biological specimens is obtaining a reliable reconstruction from diffraction data that have a poor signal-to-noise ratio. Thus, we developed a robust method that yields the internal density distribution of liposome vesicles immersed in a solution. By combining the guided hybrid input-output method and a new order parameter defined by the consistency of the reconstruction, we, without prior knowledge, retrieved both pure and drug-containing liposome vesicles from individual diffraction patterns. This result is currently the smallest noncrystalline biological specimen resolved by single-shot coherent diffraction microscopy.

Evaluating Biogenicity on the Geological Record With Synchrotron-Based Techniques.

The biogenicity problem of geological materials is one of the most challenging ones in the field of paleo and astrobiology. As one goes deeper in time, the traces of life become feeble and ambiguous, blending with the surrounding geology. Well-preserved metasedimentary rocks from the Archaean are relatively rare, and in very few cases contain structures resembling biological traces or fossils. These putative biosignatures have been studied for decades and many biogenicity criteria have been developed, but there is still no consensus for many of the proposed structures. Synchrotron-based techniques, especially on new generation sources, have the potential for contributing to this field of research, providing high sensitivity and resolution that can be advantageous for different scientific problems. Exploring the X-ray and matter interactions on a range of geological materials can provide insights on morphology, elemental composition, oxidation states, crystalline structure, magnetic properties, and others, which can measurably contribute to the investigation of biogenicity of putative biosignatures. Here, we provide an overview of selected synchrotron-based techniques that have the potential to be applied in different types of questions on the study of biosignatures preserved in the geological record. The development of 3rd and recently 4th generation synchrotron sources will favor a deeper understanding of the earliest records of life on Earth and also bring up potential analytical approaches to be applied for the search of biosignatures in meteorites and samples returned from Mars in the near future.

A chemical perspective on high pressure crystal structures and properties.

The general availability of third generation synchrotron sources has ushered in a new era of high pressure research. The crystal structure of materials under compression can now be determined by X-ray diffraction using powder samples and, more recently, from multi-nano single crystal diffraction. Concurrently, these experimental advancements are accompanied by a rapid increase in computational capacity and capability, enabling the application of sophisticated quantum calculations to explore a variety of material properties. One of the early surprises is the finding that simple metallic elements do not conform to the general expectation of adopting 3D close-pack structures at high pressure. Instead, many novel open structures have been identified with no known analogues at ambient pressure. The occurrence of these structural types appears to be random with no rules governing their formation. The adoption of an open structure at high pressure suggested the presence of directional bonds. Therefore, a localized atomic hybrid orbital description of the chemical bonding may be appropriate. Here, the theoretical foundation and experimental evidence supporting this approach to the elucidation of the high pressure crystal structures of group I and II elements and polyhydrides are reviewed. It is desirable and advantageous to extend and apply established chemical principles to the study of the chemistry and chemical bonding of materials at high pressure.

X-ray photon correlation spectroscopy of protein dynamics at nearly diffraction-limited storage rings.

This study explores the possibility of measuring the dynamics of proteins in solution using X-ray photon correlation spectroscopy (XPCS) at nearly diffraction-limited storage rings (DLSRs). We calculate the signal-to-noise ratio (SNR) of XPCS experiments from a concentrated lysozyme solution at the length scale of the hydrodynamic radius of the protein molecule. We take into account limitations given by the critical X-ray dose and find expressions for the SNR as a function of beam size, sample-to-detector distance and photon energy. Specifically, we show that the combined increase in coherent flux and coherence lengths at the DLSR PETRA IV yields an increase in SNR of more than one order of magnitude. The resulting SNR values indicate that XPCS experiments of biological macromolecules on nanometre length scales will become feasible with the advent of a new generation of synchrotron sources. Our findings provide valuable input for the design and construction of future XPCS beamlines at DLSRs.

New Opportunities for in Situ and Operando Characterization of Electrochemical Systems at I07

The range of material systems and architectures used in electrochemical research is vast, spanning from solid-solid electrolyte interfaces for solid state batteries to nano-sized particles systems for electrocatalytic materials in fuel cells. Despite the physical differences among these systems the possibility of establishing relationships between structure and activity is a common key aspect for understanding interfacial electrochemical processes. I07 is the surface and interface x-ray diffraction beamline at the Diamond synchrotron (Didcot,UK). The beamline exploits a high brilliance 3rd generation synchrotron source to allow the characterization of a wide array of possible sample types, opening up experimental possibilities which are not feasible using standard lab based x-ray sources. The use of grazing incidence angle techniques available on I07 not only allows reduction of background signal from the bulk enabling measurements of signals from the top layers of a sample, but it also enables investigation of the relationship between nano-scale structural changes and reactivity during time-resolved experiments. The current capabilities of beamline I07 will be outlined regarding in-situ and operando measurements of material systems for applications in energy storage. Also opportunities for investigating novel solid-state electrolyte material interfaces will be detailed. Experimental techniques discussed will include surface x-ray diffraction, x-ray reflectivity, grazing incidence small angle x-ray scattering, grazing incidence wide angle x-ray scattering, and liquid surface x-ray scattering.

Ab initio nonrigid X-ray nanotomography

Reaching the full potential of X-ray nanotomography, in particular for biological samples, is limited by many factors, of which one of the most serious is radiation damage. Although sample deformation caused by radiation damage can be partly mitigated by cryogenic protection, it is still present in these conditions and, as we exemplify here using a specimen extracted from scales of the Cyphochilus beetle, it will pose a limit to the achievable imaging resolution. We demonstrate a generalized tomographic model, which optimally follows the sample morphological changes and attempts to recover the original sample structure close to the ideal, damage-free reconstruction. Whereas our demonstration was performed using ptychographic X-ray tomography, the method can be adopted for any tomographic imaging modality. Our application demonstrates improved reconstruction quality of radiation-sensitive samples, which will be of increasing relevance with the higher brightness of 4th generation synchrotron sources.

High Resolution Mapping of Orientation and Strain Gradients in Metals by Synchrotron 3D X-ray Laue Microdiffraction

Synchrotron 3D X-ray Laue microdiffraction, available at beamline 34-ID-E at Advanced Photon Source in Argonne National Laboratory, is a powerful tool for 3D non-destructive mapping of local orientations and strains at sub-micron scale in the bulk. With this technique, it is possible to study local residual stresses developed during manufacturing or while in service due to interactions between, for example, different phases and/or grains with different orientations in materials containing multiple or single phase(s). Such information is essential for understanding mechanical properties and designing advanced materials, but is largely non-existent in the current generation of materials models. In the present paper, the principle and experimental set-up of the 3D microdiffraction are introduced, followed by a description of a method for quantification of the local plastic deformation based on high-angular-resolution orientation maps. The quantification of local residual stresses in two model materials, ductile cast iron (two phases) and partially recrystallized pure nickel (single phase), using 3D microdiffraction will then be presented. The results show that 3D microdiffraction is important for understanding the origin of local residual stresses and to relate them to the microstructural evolution. Finally, the limitations of the 3D microdiffraction on the current generation synchrotron source and new possibilities after the synchrotron upgrade are discussed.

DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system.

The application of X-ray emission spectroscopy (XES) has grown substantially with the development of X-ray free electron lasers, third and fourth generation synchrotron sources and high-power benchtop sources. By providing the high X-ray flux required for XES, these sources broaden the availability and application of this method of probing electronic structure. As the number of sources increase, so does the demand for X-ray emission detection and sample delivery systems that are cost effective and customizable. Here, we present a detailed fabrication protocol for von Hamos X-ray optics and give details for a 3D-printed spectrometer design. Additionally, we outline an automated, externally triggered liquid sample delivery system that can be used to repeatedly deliver nanoliter droplets onto a plastic substrate for measurement. These systems are both low cost, efficient and easy to recreate or modify depending on the application. A low cost multiple X-ray analyzer system enables measurement of dilute samples, whereas the sample delivery limits sample loss and replaces spent sample with fresh sample in the same position. While both systems can be used in a wide range of applications, the design addresses several challenges associated specifically with time-resolved XES (TRXES). As an example application, we show results from TRXES measurements of photosystem II, a dilute, photoactive protein.

Development and Characterisation of New Biocompatible Sn-Mg Lead-Free Solder

This work is focused on a development and research of a new lead-free Sn-Mg solder, alloy compatible with the human body. Tin and magnesium are biocompatible elements which do not cause an inflammation or allergic reactions with living tissues. We have prepared the Sn97Mg3 solder (wt. %) by a rapid solidification of its melt on a copper wheel (melt-spinning technique). This solder may find applications in electronic devices for intracorporeal utilisation. The microstructure of the prepared solder exhibits a heterogeneous distribution of the SnMg2 intermetallic particles within the β-Sn matrix. Structure of the solder was studied by an in-situ high energy X-ray diffraction experiment (energy of an X-ray photon: 60 keV) where 2D XRD patterns were collected from the sample in the temperature range from 298 K to 566 K. The experiment was performed at a high brilliance 3rd generation synchrotron source of radiation (PETRA III storage ring, DESY, Hamburg, Germany) at the P02 undulator beamline. From the measured X-ray diffraction data by applying the Rietveld refinement technique we have obtained thermal volume expansion data, mean positions of atoms as well as isotropic atomic displacement parameters of the constituent SnMg2 and the β-Sn crystalline phases. Thermal behaviour was studied by differential scanning calorimetry at heating rates of 5, 15, 30 and 60 K.min-1 and compared with the measured X-ray data. Our main goal lies in a preparation of a lead-free solder with fine grain structure made exclusively of biocompatible elements. We demonstrated that the rapid melt solidification technique leads to in an improvement and better thermal stability of this alloy.