Reconstruction of high temporal resolution Thomson scattering data during a modulated electron cyclotron resonance heating using conditional averaging

Hydrogen isotope effect on self-organized electron internal transport barrier criticality and role of radial electric field in toroidal plasmas

Self-organized structure formation in magnetically confined plasmas is one of the most attractive subjects in modern experimental physics. Nonequilibrium media are known to often exhibit phenomena that cannot be predicted by superposition of linear theories. One representative example of such phenomena is the hydrogen isotope effect in fusion plasmas, where the larger the mass of the hydrogen isotope fuel is the better the plasma confinement becomes, contrary to what simple scaling models anticipate. In this article, threshold condition of a plasma structure formation is shown to have a strong hydrogen isotope effect. To investigate the underlying mechanism of this isotope effect, the electrostatic potential is directly measured by a heavy ion beam probe. It is elucidated that the core electrostatic potential transition occurs with less input power normalized by plasma density in plasmas with larger isotope mass across the structure formation. This observation is suggestive of the isotope effect in the radial electric field structure formation.

Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser

Visualization of intracellular structures and their spatial organization inside cells without any modification is essential to understand the mechanisms underlying the biological functions of cells. Here, we investigated the intracellular structure of cyanobacteria Prochlorococcus in the interphase by X-ray diffraction imaging using X-ray free-electron laser. A number of diffraction patterns from single cells smaller than 1 µm in size were collected with high signal-to-noise ratio with a resolution of up to 30 nm. From diffraction patterns, a set of electron density maps projected along the direction of the incident X-ray were retrieved with high reliability. The most characteristic structure found to be common among the cells was a C-shaped arrangement of 100-nm sized high-density spots, which surrounded a low-density area of 100 nm. Furthermore, a three-dimensional map reconstructed from the projection maps of individual cells was non-uniform, indicating the presence of common structures among cyanobacteria cells in the interphase. By referring to the fluorescent images for distributions of thylakoid membranes, nucleoids, and carboxysomes, we inferred and represented their spatial arrangements in the three-dimensional map. The arrangement allowed us to discuss the relevance of the intracellular organization to the biological functions of cyanobacteria.

Methods and application of coherent X-ray diffraction imaging of noncrystalline particles

Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. The structure of the particle projected along the direction of the beam is, in principle, retrieved from a finely recorded diffraction pattern alone by using iterative phase-retrieval algorithms. Here, we describe fundamental theory and experimental methods of coherent X-ray diffraction imaging and the recent application in structural studies of noncrystalline specimens by using X-rays available at Super Photon Ring of 8-Gev and SPring-8 Angstrom Compact Free Electron Laser in Japan.

Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation

X-ray diffraction imaging is a technique for visualizing the structure of biological cells. In X-ray diffraction imaging experiments using synchrotron radiation, cryogenic conditions are necessary in order to reduce radiation damage in the biological cells. Frozen-hydrated biological specimens kept at cryogenic temperatures are also free from drying and bubbling, which occurs in wet specimens under vacuum conditions. In a previous study, the diffraction apparatus KOTOBUKI-1 [Nakasako et al. (2013), Rev. Sci. Instrum. 84, 093705] was constructed for X-ray diffraction imaging at cryogenic temperatures by utilizing a cryogenic pot, which is a cooling device developed in low-temperature physics. In this study a new cryogenic pot, suitable for tomography experiments, has been developed. The pot can rotate a biological cell over an angular range of ±170° against the direction of the incident X-ray beam. Herein, the details and the performance of the pot and miscellaneous devices are reported, along with established experimental procedures including specimen preparation. The apparatus has been used in tomography experiments for visualizing the three-dimensional structure of a Cyanidioschyzon merolae cell with an approximate size of 5 µm at a resolution of 136 nm. Based on the experimental results, the necessary improvements for future experiments and the resolution limit achievable under experimental conditions within a maximum tolerable dose are discussed.

Growth of Cuprous Oxide Particles in Liquid-Phase Synthesis Investigated by X-ray Laser Diffraction

Cuprous oxide (Cu₂O) particles obtained by surfactant-assisted liquid-phase synthesis have cuboid shapes but the internal structures are difficult to be visualized by electron microscopy. Herein, we investigated the internal structures of numerous individual Cu₂O particles with submicrometer dimensions by X-ray diffraction imaging (XDI) using X-ray free-electron laser (XFEL) pulses. The reconstructed two-dimensional electron density maps, which displayed inhomogeneous internal structures, were divided into five classes characterized by the positions and shapes of high and low electron density areas. Further analysis of the maps in each class by a manifold learning algorithm revealed that the internal structures of Cu₂O particles varied in correlation with total electron density while retaining the characteristics within each class. On the basis of the analyses, we proposed a growth mechanism to yield the inhomogeneity in the internal structures of Cu₂O particles in surfactant-mediated liquid-phase synthesis.

Atmospheric coherent X-ray diffraction imaging for in situ structural analysis at SPring-8 Hyogo beamline BL24XU

Coherent X-ray diffraction imaging (CXDI) is a promising technique for non-destructive structural analysis of micrometre-sized non-crystalline samples at nanometre resolutions. This article describes an atmospheric CXDI system developed at SPring-8 Hyogo beamline BL24XU for in situ structural analysis and designed for experiments at a photon energy of 8 keV. This relatively high X-ray energy enables experiments to be conducted under ambient atmospheric conditions, which is advantageous for the visualization of samples in native states. The illumination condition with pinhole-slit optics is optimized according to wave propagation calculations based on the Fresnel-Kirchhoff diffraction formula so that the sample is irradiated by X-rays with a plane wavefront and high photon flux of ∼1 × 10¹⁰ photons/16 µmø(FWHM)/s. This work demonstrates the imaging performance of the atmospheric CXDI system by visualizing internal voids of sub-micrometre-sized colloidal gold particles at a resolution of 29.1 nm. A CXDI experiment with a single macroporous silica particle under controlled humidity was also performed by installing a home-made humidity control device in the system. The in situ observation of changes in diffraction patterns according to humidity variation and reconstruction of projected electron-density maps at 5.2% RH (relative humidity) and 82.6% RH at resolutions of 133 and 217 nm, respectively, were accomplished.

Shot-by-shot characterization of focused X-ray free electron laser pulses

X-ray free electron lasers (XFEL) provide intense and almost coherent X-ray pulses. They are used for various experiments investigating physical and chemical properties in materials and biological science because of their complete coherence, high intensity, and very short pulse width. In XFEL experiments, specimens are irradiated by XFEL pulses focused by mirror optics. The focused pulse is too intense to measure its coherence by placing an X-ray detector on the focal spot. Previously, a method was proposed for evaluating the coherence of focused pulses from the visibility of the diffraction intensity of colloidal particles by the speckle visibility spectroscopy (SVS). However, the visibility cannot be determined exactly because the diffraction intensity is integrated into each finite size detector pixel. Here, we propose a method to evaluate the coherence of each XFEL pulse by using SVS in combination with a theory for exact sampling of the diffraction pattern and a technique of multiplying the diffraction data by a Gaussian masks, which reduces the influence of data missing in small-angle regions due to the presence of a direct beamstop. We also introduce a method for characterizing the shot-by-shot size of each XFEL pulse by analysing the X-ray irradiated area.

Magnetically textured powders—an alternative to single-crystal and powder X-ray diffraction methods

Structure determination of materials in their crystalline phase aids in the understanding and design of their functions.

A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation

Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.

Abrupt onset of tongue deformation and phase space response of ions in magnetically-confined plasmas

An abrupt onset of the new tongue-shaped deformation of magnetic surface in magnetized plasmas, which was conjectured in since the 1960s but has not been observed, is experimentally identified just before an abrupt onset of a large-scale collapse event. Two novel properties of the event are identified. First, the transition of symmetry of perturbation (rather than a growth of linearly unstable MHD modes) was found to be a key for the onset of abrupt collapse, i.e., the transition of symmetry gives a new route to the collapse from stable state. Second, as a phase-space response of ions, the distortion from Maxwell-Boltzmann distribution of epithermal ions was observed for the first time.

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.