Coherent X-ray Diffraction Imaging Experiments Research Articles

Preliminary exploration of hard X-ray coherent diffraction imaging method at SSRF

Coherent X-ray diffraction imaging (CDI) method is a powerful X-ray imaging technique with high resolution up to nanometer scale. Most of the synchrotron radiation facilities and free electron laser facilities are equipped with this state-of-the-art imaging technique and have made many outstanding achievements in multiple scientific areas. Up to now, although scanning CDI (ptychography) method based on a soft X-ray source has been opened to users, the hard X-ray CDI experimental platform has not been built at Shanghai Synchrotron Radiation Facility (SSRF) which can research some relatively thick specimens and easily extend to three-dimensional imaging. As some new beamlines with undulator source were put into operation recently, it is possible and feasible to build up the CDI experimental platform with hard X-ray. In this article, we report the hard X-ray CDI experimental platform development process and preliminary experimental results of coherent diffraction pattern and image reconstruction at SSRF. Based on the operating BL19U2 biological small-angle X-ray scattering (SAXS) beamline at SSRF, the hard X-ray coherent beam is obtained through effective optical path designation at 12 keV and 13.5 keV. The hard X-ray optimization includes tuning several slits, double crystal monochromator (DCM), horizontal deflection mirror, focusing mirror system and pinhole, etc. Furthermore, hard X-ray CDI experiments are conducted. The spatial coherent length of the incident beam is also measured from the pinhole diffraction pattern. This platform can provide both conventional mode and scanning mode (ptychography) for the coherent diffraction imaging method, and the correct image reconstruction from the experimental diffraction patterns proves that the platform has the experimental capability for hard X-ray CDI. In the conventional forward scattering CDI mode, coherent diffraction patterns of pinhole are collected and used to analyse the coherence property of the optimized X-ray beam. The structure of pinhole is also reconstructed from the diffraction pattern. In the scanning CDI mode, a zone plate is used as a sample. The central area of zone plate is reconstructed correctly. About 90 nm/pixel resolution of reconstruction is achieved which is extremely dependent on the X-ray flux density from the undulator source emission. Hard X-ray CDI experimental platform based on the synchrotron radiation facility is first built in China. It will provide effective software and hardware supporting for the development and application of hard X-ray CDI experiments in China in the future.

Coherent X-ray Imaging of CO-Adsorption-Induced Structural Changes in Pt Nanoparticles: Implications for Catalysis

Using coherent X-ray diffraction imaging (CXDI) as an in situ tool, we determined the shape and strain state of a platinum nanoparticle with ≈160 nm diameter supported by a strontium titanate substrate. The experiment was performed at a temperature of 400 K under continuous gas flow conditions of pure Ar and Ar/CO mixtures. The nanoparticle was preselected by scanning electron microscopy (SEM) and postanalyzed by atomic force microscopy (AFM). We obtain a very good agreement between the overall nanoparticle size, shape, and defect structure as determined by CXDI and AFM. In addition, we compare the strain state in the nanoparticle near surface region and its bulk: For pure Ar flow, we find a slight compressive strain in the nanoparticle bulk compared to an expansion in the near surface region. We ascribe the latter to the presence of high index vicinal surfaces. Our analysis suggests that under mixed Ar/CO flow at 400 K reshaping of the nanoparticle occurred. New high index facets developed, leading to a stronger lattice expansion, also propagating into the nanoparticle bulk. Our high-resolution experiments pave the way for future CXDI experiments under operando catalytic reaction conditions.

Классификация дифракционных изображений биологических макромолекул с разными типами симметрии в экспериментах по когерентной рентгеновской дифракционной микроскопии

About 1% of diffraction images produced in coherent X-ray diffraction imaging experiments originate from a single particle of interest and only those images are suitable for structure reconstruction. Other images contain contributions from multiple particles, water or some contaminant. Selection of single particle images is required. A new classification method that is based on cross-correlation analysis were developed. The method was successfully applied to the experimental data, that contain diffraction images of the PBCV-1 virus and T4 bacteriophage. In this article we present classification results for diffraction images of seven biological particles with different symmetry. The results confirm the applicability of the proposed method for correct classification of diffraction images corresponding to different molecules. We also studied influence of particle symmetry type and volume of learning dataset to classification quality.

Atomistic Picture of the Catalytic Activity of Platinum Nanoparticles through Coherent Diffraction Imaging and Reactive Molecular Dynamics Simulations

Platinum nanoparticles are among the most widely used catalysts due to their high chemical stability, surface reactivity and electron transfer rate. They find applications in chemical and bio-sensing, fuel cells, photocatalysis and methanol formation. Elucidating the catalytic mechanism under in-situ conditions is vital to the structural and chemical design of more efficient catalysts that are urgently needed to meet the energy needs of today. Coherent X-ray diffraction imaging (CDI) is a powerful technique for operando characterization with the ability to provide evolving snapshots of defect structure, lattice dynamics and structural evolution at ~10 nm resolution, while reactive molecular dynamics (MD) simulations provide atomistic details of lattice dynamics, bond breakage and formation as well as reaction kinetics at experimentally inaccessible length and time scales. We present results from combined CDI experiments and reactive MD simulations on the atomistic processes underlying methanol formation from methane on Pt nanoparticles. We observe the preferential oxidation of edge and corner sites on the Pt nanoparticle in an O2 rich atmosphere, which when followed by the introduction of methane, leads to the binding of CH4 to disassociated O atoms. Fig. 1 a) shows the partially oxidized Pt particle in a methane atmosphere. O2 on surface sites is not seen to disassociate while oxygen at corner and edge sites disassociates due to the higher site reactivity at edges and corners. Fig 1. b)-c) shows a close-up of the surface during the binding of CH4 to the disassociated oxygen. Finally, the mechanism predicted by the reactive MD simulations is validated through CDI experiments, with the observation of local lattice strains at edge and corner sites, which arise due to the binding of O2 and CH4 molecules. Figure 1

Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA.

Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed.

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA.

Coherent X-ray diffraction imaging (CXDI) is a technique for structure analyses of non-crystalline particles with dimensions ranging from micrometer to sub-micrometer. We have developed a diffraction apparatus named TAKASAGO-6 for use in single-shot CXDI experiments of frozen-hydrated non-crystalline biological particles at cryogenic temperature with X-ray free electron laser pulses provided at a repetition rate of 30 Hz from the SPring-8 Angstrom Compact free-electron LAser. Specimen particles are flash-cooled after being dispersed on thin membranes supported by specially designed disks. The apparatus is equipped with a high-speed translation stage with a cryogenic pot for raster-scanning of the disks at a speed higher than 25 μm/33 ms. In addition, we use devices assisting the easy transfer of cooled specimens from liquid-nitrogen storages to the cryogenic pot. In the current experimental procedure, more than 20 000 diffraction patterns can be collected within 1 h. Here we report the key components and performance of the diffraction apparatus. Based on the efficiency of the diffraction data collection and the structure analyses of metal particles, biological cells, and cellular organelles, we discuss the future application of this diffraction apparatus for structure analyses of biological specimens.

Cryogenic coherent x-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA

We have developed an experimental apparatus named KOTOBUKI-1 for use in the coherent x-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. The apparatus allows us to collect diffraction data for frozen-hydrated specimens at 66 K and provides an experimental environment to easily transfer frozen-hydrated specimens from liquid nitrogen storage to the specimen stage for x-ray exposure. Since 2012, the apparatus has been used in the single-shot diffraction data collection of non-crystalline biological cells and cellular components with dimensions from micrometer to submicrometer using x-ray free electron lasers at SACLA. Here we report on the performance of the KOTOBUKI-1 diffraction apparatus and some structure analyses of biological cells and cellular components. Based on the present results, we also discuss the future developments of diffraction apparatus for more efficient data collection.

Coherent X-Ray Diffraction Imaging of Chloroplasts from Cyanidioschyzon merolae by Using X-Ray Free Electron Laser.

Coherent X-ray diffraction imaging (CXDI) is a lens-less technique for visualizing the structures of non-crystalline particles with the dimensions of submicrometer to micrometer at a resolution of several tens of nanometers. We conducted cryogenic CXDI experiments at 66 K to visualize the internal structures of frozen-hydrated chloroplasts of Cyanidioschyzon merolae using X-ray free electron laser (XFEL) as a coherent X-ray source. Chloroplast dispersed specimen disks at a number density of 7/(10×10 µm(2)) were flash-cooled with liquid ethane without staining, sectioning or chemical labeling. Chloroplasts are destroyed at atomic level immediately after the diffraction by XFEL pulses. Thus, diffraction patterns with a good signal-to-noise ratio from single chloroplasts were selected from many diffraction patterns collected through scanning specimen disks to provide fresh specimens into the irradiation area. The electron density maps of single chloroplasts projected along the direction of the incident X-ray beam were reconstructed by using the iterative phase-retrieval method and multivariate analyses. The electron density map at a resolution of 70 nm appeared as a C-shape. In addition, the fluorescence image of proteins stained with Flamingo™ dye also appeared as a C-shape as did the autofluorescence from Chl. The similar images suggest that the thylakoid membranes with an abundance of proteins distribute along the outer membranes of chloroplasts. To confirm the present results statistically, a number of projection structures must be accumulated through high-throughput data collection in the near future. Based on the results, we discuss the feasibility of XFEL-CXDI experiments in the structural analyses of cellular organelles.

IDATEN and G-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA.

Using our custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors, cryogenic coherent X-ray diffraction imaging experiments have been undertaken at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user-friendly graphical user interfaces have been developed. The first is a program suite named IDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI-1, loading a flash-cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI-1, adjusting the sample position with respect to the X-ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X-ray pulses. Named G-SITENNO, the other suite is an automated version of the original SITENNO suite, which was designed for processing diffraction data. These user-friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

We have developed an experimental apparatus named KOTOBUKI-1 for use in coherent X-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. For cryogenic specimen stage with small positional fluctuation for a long exposure time of more than several minutes, we here use a cryogenic pot cooled by the evaporation cooling effect for liquid nitrogen. In addition, a loading device is developed to bring specimens stored in liquid nitrogen to the specimen stage in vacuum. The apparatus allows diffraction data collection for frozen-hydrated specimens at 66 K with a positional fluctuation of less than 0.4 μm and provides an experimental environment to easily exchange specimens from liquid nitrogen storage to the specimen stage. The apparatus was developed and utilized in diffraction data collection of non-crystalline particles with dimensions of μm from material and biological sciences, such as metal colloid particles and chloroplast, at BL29XU of SPring-8. Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA.

Impact of ultrafast electronic damage in single-particle x-ray imaging experiments

In single-particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces electronic dynamics on the femtosecond time scale in the system, which can reduce the contrast of the obtained diffraction patterns and adds an isotropic background. We quantify the degradation of the diffraction pattern from ultrafast electronic damage by performing simulations on a biological sample exposed to x-ray pulses with different parameters. We find that the contrast is substantially reduced and the background is considerably strong only if almost all electrons are removed from their parent atoms. This happens at fluences of at least one order of magnitude larger than provided at currently available XFEL sources.

Dose requirements for resolving a given feature in an object by coherent x-ray diffraction imaging

We address the question of what dose is required to image an object by coherent x-ray diffraction imaging (CXDI) and to resolve a certain sub-unit or feature of that object. We show that a necessary condition for being able to resolve the detail is that the feature can be imaged by itself. The quality of the reconstruction of the feature is nearly independent of the surrounding, whether it is embedded in a larger object or not. This allows one to easily estimate the dose requirements for identifying atoms and clusters in larger objects. We illustrate the result by a numerical example and give an estimate for the dose required to resolve single atoms of different elemental species in CXDI experiments at free-electron laser and synchrotron radiation sources.

Crystal optics as guard apertures for coherent x-ray diffraction imaging

A crucial issue in coherent x-ray diffraction imaging experiments is how to increase the signal-to-noise ratio when measuring relatively weak diffraction intensities from a nonperiodic object. A novel crystal guard aperture is described that makes use of a pair of multiple-bounce crystal optics to eliminate unwanted parasitic scattering background. This background is often produced by upstream optical elements such as a coherent-beam defining aperture. Recent experimental observation and theoretical analysis confirm the effectiveness of the crystal guard aperture method with coherence-preserved wave propagation through the crystal guard aperture and dramatically reduced scattering background in coherent x-ray diffraction images.