Intense Synchrotron Radiation Research Articles

Synchrotron radiation X-ray diffraction studies on muscle: past, present, and future.

X-ray diffraction is a technique to study the structure of materials at spatial resolutions up to an atomic scale. In the field of life science, the X-ray diffraction technique is especially suited to study materials having periodical structures, such as protein crystals, nucleic acids, and muscle. Among others, muscle is a dynamic structure and the molecular events occurring during muscle contraction have been the main interest among muscle researchers. In early days, the laboratory X-ray generators were unable to deliver X-ray flux strong enough to resolve the dynamic molecular events in muscle. This situation has dramatically been changed by the advent of intense synchrotron radiation X-rays and advanced detectors, and today X-ray diffraction patterns can be recorded from muscle at sub-millisecond time resolutions. In this review, we shed light mainly on the technical aspects of the history and the current status of the X-ray diffraction studies on muscle and discuss what will be made possible for muscle studies by the advance of new techniques.

Accretion into Black Hole, and Formation of Magnetically Arrested Accretion Disks

The exact time-dependent solution is obtained for a magnetic field growth during a spherically symmetric accretion into a black hole (BH) with a Schwarzschild metric. Magnetic field is increasing with time, changing from the initially uniform into a quasi-radial field. Equipartition between magnetic and kinetic energies in the falling gas is supposed to be established in the developed stages of the flow. Estimates of the synchrotron radiation intensity are presented for the stationary flow. The main part of the radiation is formed in the relativistic region r ≤ 7 r g , where r g is a BH gravitational radius. The two-dimensional stationary self-similar magnetohydrodynamic solution is obtained for the matter accretion into BH, in a presence of a large-scale magnetic field, under assumption, that the magnetic field far from the BH is homogeneous and its influence on the flow is negligible. At the symmetry plane perpendicular to the direction of the distant magnetic field, the dense quasi-stationary disk is formed around BH, which structure is determined by dissipation processes. Solutions of the disk structure have been obtained for a laminar disk with Coulomb resistivity and for a turbulent disk. Parameters of the shock forming due to matter infall onto the disk are obtained. The radiation spectrum of the disk and the shock are obtained for the 10 M ⊙ BH. The luminosity of such object is about the solar one, for a characteristic galactic gas density, with possibility of observation at distances less than 1 kpc. The spectra of a laminar and a turbulent disk structure around BH are very different. The laminar disk radiates mainly in the ultraviolet, the turbulent disk emits a large part of its flux in the infrared. It may occur that some of the galactic infrared star-like sources are a single BH in the turbulent accretion state. The radiative efficiency of the magnetized disk is very high, reaching ∼ 0.5 M ˙ c 2 . This model of accretion was called recently as a magnetically arrested disk (MAD). Numerical simulations of MAD and its appearance during accretion into neutron stars, are considered and discussed.

Studies of the Micro-Bunching Instability in the Presence of a Damping Wiggler

At the KIT storage ring KARA (KArlsruhe Research Accelerator), the momentum compaction factor can be reduced leading to natural bunch lengths in the ps range. Due to the high degree of longitudinal compression, the micro-bunching instability arises. During this longitudinal instability, the bunches emit bursts of intense coherent synchrotron radiation in the THz frequency range caused by the complex longitudinal dynamics. The temporal pattern of the emitted bursts depends on given machine parameters, like momentum compaction factor, acceleration voltage, and damping time. In this paper, the influence of the damping time is studied by utilizing the CLIC damping wiggler prototype installed in KARA as well as by simulations using the Vlasov-Fokker-Planck solver Inovesa.

Synchrotron studies of top-down grown silicon nanowires

Abstract Morphology of the top-down grown silicon nanowires obtained by metal-assisted wet-chemical approach on silicon substrates with different resistance were studied by scanning electron microscopy. Obtained arrays of compact grown Si nanowires were a subject for the high resolution electronic structures studies by X-ray absorption near edge structure technique performed with the usage of high intensity synchrotron radiation of the SRC storage ring of the University of Wisconsin-Madison. The different oxidation rates were found by investigation of silicon atoms local surrounding specificity of the highly developed surface and near surface layer that is not exceeded 70 nm. Flexibility of the wires arrays surface morphology and its composition is demonstrated allowing smoothly form necessary surface oxidation rate and using Si nanowires as a useful matrixes for a wide range of further functionalization.

Synchrotron radiation intensity and energy of runaway electrons in EAST tokamak**Project supported by the National Natural Science Foundation of China (Grant Nos. 11775263 and 11405219), the JSPS-NRF-NSFC A3 Foresight Program in the Field of Plasma Physics, China (Grant No. 11261140328), and the National Magnetic Confnement Fusion Science Program of China (Grant No. 2015GB102004).

A detailed analysis of the synchrotron radiation intensity and energy of runaway electrons is presented for the Experimental Advanced Superconducting Tokamak (EAST). In order to make the energy of the calculated runaway electrons more accurate, we take the Shafranov shift into account. The results of the analysis show that the synchrotron radiation intensity and energy of runaway electrons did not reach the maximum at the same time. The energy of the runaway electrons reached the maximum first, and then the synchrotron radiation intensity of the runaway electrons reached the maximum. We also analyze the runaway electrons density, and find that the density of runaway electrons continuously increased. For this reason, although the energy of the runaway electrons dropped but the synchrotron radiation intensity of the runaway electrons would continue rising for a while.

PTB’s radiometric scales for UV and VUV source calibration based on synchrotron radiation

The radiant intensity of synchrotron radiation can be accurately calculated with classical electrodynamics. This primary realization of the spectral radiant intensity has been used by PTB at several electron storage rings which have been optimized to be operated as primary source standards for the calibration of transfer sources in the spectral range of UV and VUV for almost 30 years. The transfer sources are compared to the primary source standard by means of suitable wavelength-dispersive transfer stations.The spectral range covered by deuterium lamps, which represent transfer sources that are easy to handle, is of particular relevance in practice. Here, we report on developments in the realization and preservation of the radiometric scales for spectral radiant intensity and spectral radiance in the wavelength region from 116 nm to 400 nm, based on a set of deuterium reference lamps, over the last few decades. An inside view and recommendations on the operation of the D2 lamps used for the realization of the radiometric scale are presented. The data has been recently compiled to illustrate the chronological behaviour at various wavelengths. Moreover, an overview of the internal and external validation measurements and intercomparisons is given.

Preliminary study on protection of synchrotron radiation damage in CEPC main ring

The Circular Election–Positron Collider has been proposed by Institute of High Energy Physics (IHEP, CAS). The beam in the main ring with energy up to 120 GeV would produce intense synchrotron radiation (SR) with photon energy up to several MeV. Without shielding, this radiation would be harmful to the accelerator components. To clarify the radiation damage, analyze the source of SR, and design the shielding system to protect the accelerator. The theoretical formula has been used to estimate the spectrum and distribution of SR. Several ways of designing or shielding vacuum chamber with different geometries and various materials are put forward to protect sensitive facility components. The Monte Carlo program FLUKA has been introduced to calculate cumulative dose and heat deposition in all designing cases. The SR in CEPC main ring would be harmful to the coil used in dipole magnets. The design based on LEP with aluminum and lead would need 23 mm lead to make the coil safe. The design based on LEP with copper would need 28 mm of outer copper. And the copper chamber and lead shield design would need 16 mm of Lead. The theoretical formula has been used in source generation of Monte Carlo program to get the distribution of SR in CEPC main ring. The program was also used to simulate SR problems in the vacuum chamber with designs of different geometries and materials. Among these designs, the elliptical pipe with lead shield is preferred in CEPC.

On the In-Situ Grazing Incidence X-ray Diffraction of Electrochemically Formed Thin Films

Existing designs of in-situ X-ray diffraction (XRD) cells for electrochemical experiments are usually cells in which the beam has to penetrate the electrolyte. In order to avoid strong attenuation of primary and diffracted beams, the electrolyte has to be a thin film which is a considerable restriction for electrochemical processes. In this contribution, a novel in-situ cell design is described which avoids the thin electrolyte configuration by backside-illumination of a thin metal film working electrode applied on a polyimide foil. This has the advantage that the X-rays only have to penetrate foil and sputtered electrode, resulting in high signals from the deposited material. Therefore, the cell does not need high intensity synchrotron radiation but works with a laboratory X-ray source. Problems with bulk solution resistance or inhomogeneous current-density distribution during deposition processes are also eliminated. The novel cell design was tested on the cathodic formation of Cu2O on copper.

First look at Jupiter's synchrotron emission from Juno's perspective

AbstractSince August 2016, measurements of Jupiter's microwave emissions at six wavelengths ranging from 1.3 cm to 50 cm have been made with the Juno Microwave Radiometer. In this paper, we introduce the first systematic set of in situ observations of synchrotron radiation in a polar plane while describing the modeling approach we use to analyze this data (collected 27 August 2016). Time series of brightness profiles at all six frequencies present similarities that are explained by the presence of known regions of intense synchrotron radiation. Our model predictions, though limited for now to the total intensity of the radiation, reproduce (qualitatively) the observation of temporal variations and allow to disentangle the synchrotron emission from the atmospheric emission. The discrepancies seen between the data and simulations confirm that physical conditions close to Jupiter affecting synchrotron emission (electron energy spectra, pitch angle distributions, and the magnetic environment) are different than we anticipated.

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

Cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe-C-O angle of ∼142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near CuB, which, in turn, moves closer to the heme a3 iron by ∼0.38 Å. Structural comparison reveals that ligand binding to the heme a3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.

New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences.

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 ‘small molecule’ crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography’s role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

Laboratory based study of dynamical processes by 4D X-ray CT with sub-second temporal resolution

There are numerous applications for which is advantageous to obtain X-ray transmission data necessary for 3D computed tomography (CT) within seconds or faster. The required high frame rates for data acquisition became available during the last decade due to intensive synchrotron radiation sources together with appropriate X-ray imaging detectors. It will be shown in this work that sub-second recording of the full CT data set can be reached even in laboratory conditions employing high power microfocus tubes together with a semiconductor pixelated detector. As an example, bubbles nucleation and evolution during dissolving of a pill in the water, releasing carbon dioxide will be shown in 3D with 2 Hz time resolution.

Advances in threshold photoelectron spectroscopy (TPES) and threshold photoelectron photoion coincidence (TPEPICO).

The history and evolution of molecular threshold photoelectron spectroscopy and threshold photoelectron photoion coincidence spectroscopy (TPEPICO) over the last fifty years are reviewed. Emphasis is placed on instrumentation and the extraction of dynamical information about energy selected ion dissociation, not on the detailed spectroscopy of certain molecules. Three important advances have expanded greatly the power of the technique, and permitted its implementation on modern synchrotron radiation beamlines. The use of velocity focusing of threshold electrons onto an imaging detector in the 1990s simultaneously improved the sensitivity and electron energy resolution, and also facilitated the subtraction of hot electron background in both threshold electron spectroscopy and TPEPICO studies. The development of multi-start multi-stop collection detectors for both electrons and ions in the 2000s permitted the use of the full intensity of modern synchrotron radiation thereby greatly improving the signal-to-noise ratio. Finally, recent developments involving imaging electrons in a range of energies as well as ions onto separate position-sensitive detectors has further improved the collection sensitivity so that low density samples found in a variety of studies can be investigated. As a result, photoelectron photoion coincidence spectroscopy is now well positioned to address a range of challenging problems that include the quantitative determination of compositions of isomer mixtures, and the detection and spectroscopy of free radicals produced in pyrolysis or discharge sources as well as in combustion studies.

The LHC vacuum system: Commissioning up to nominal luminosity

The Large Hadron Collider (LHC), currently under operation at CERN, is colliding intense proton beams at the highest energy frontier up to ∼14 TeV in the centre of mass. This superconducting storage ring is at the origin of the discovery in 2012 of the so-called ‘Higgs’ Boson explaining the origin of the mass of weak bosons W+,W− and Z also discovered at CERN in 1983. The arc vacuum system, which operates at cryogenic temperatures, consists of a 1.9 K cold bore which houses a 5–20 K beam screen. Beam collisions are performed inside a Non-Evaporable-Getter coated vacuum system located in long straight sections held at room temperature. These vacuum systems were designed to be stable under ion bombardment, to cope with intense VUV synchrotron radiation flux and to mitigate beam induced multipacting effects. In this paper, the LHC beam vacuum system design is recalled. Its operation, challenges and achieved performances during the commissioning phase will be discussed in detail.

In vivoXANES measuring technique for studying the arsenic uptake in cucumber plants

New in vivo X-ray absorption near edge structure measuring technique was developed by using liquid nitrogen steam flow for cooling cucumber samples keeping them under cryogenic conditions during the measurement in order to preserve the original chemical states of arsenic species in the hypocotyl. The aim of this study was to determine the As oxidation state in order to identify the possible metabolic processes during the nutrient uptake in cucumber (Cucumis sativus L. cv Joker) as model plant. The plants were grown in Hoagland's modified nutrient solution. The ratio of the quantity of two As species was determined in the hypocotyls of the cucumber samples: arsenite, As(III) and arsenate, As(V). The ultimate biological goal of the in vivo experiments was to investigate the applicability of the X-ray absorption near edge structure technique under cryogenic conditions and to specify the resistance level of the plants to arsenic toxicity when different chemical forms of iron, FeCl3 and Fe-ascorbate were supplied in the nutrient solution. We have examined the influence of the intense synchrotron radiation beam on the transformation of the oxidation number of both As species when the effect of the reactive oxygen forms was eliminated by the presence of ascorbate. Copyright © 2016 John Wiley & Sons, Ltd.

Overview: Experimental studies of crystal nucleation: Metals and colloids.

Crystallization is one of the most important phase transformations of first order. In the case of metals and alloys, the liquid phase is the parent phase of materials production. The conditions of the crystallization process control the as-solidified material in its chemical and physical properties. Nucleation initiates the crystallization of a liquid. It selects the crystallographic phase, stable or meta-stable. Its detailed knowledge is therefore mandatory for the design of materials. We present techniques of containerless processing for nucleation studies of metals and alloys. Experimental results demonstrate the power of these methods not only for crystal nucleation of stable solids but in particular also for investigations of crystal nucleation of metastable solids at extreme undercooling. This concerns the physical nature of heterogeneous versus homogeneous nucleation and nucleation of phases nucleated under non-equilibrium conditions. The results are analyzed within classical nucleation theory that defines the activation energy of homogeneous nucleation in terms of the interfacial energy and the difference of Gibbs free energies of solid and liquid. The interfacial energy acts as barrier for the nucleation process. Its experimental determination is difficult in the case of metals. In the second part of this work we therefore explore the potential of colloidal suspensions as model systems for the crystallization process. The nucleation process of colloids is observed in situ by optical observation and ultra-small angle X-ray diffraction using high intensity synchrotron radiation. It allows an unambiguous discrimination of homogeneous and heterogeneous nucleation as well as the determination of the interfacial free energy of the solid-liquid interface. Our results are used to construct Turnbull plots of colloids, which are discussed in relation to Turnbull plots of metals and support the hypothesis that colloids are useful model systems to investigate crystal nucleation.

Development of intense terahertz coherent synchrotron radiation at KU-FEL

We produced intense coherent synchrotron radiation (CSR) in the terahertz (THz) region using an S-band linac at the Kyoto University Free Electron Laser (KU-FEL), which is a mid-infrared free-electron laser facility. The CSR beam was emitted from short-pulse electron bunches compressed by a 180° arc, and was transferred to air at a large solid angle of 0.10rad. The measured CSR energy was 55μJ per 7μs macropulse, and KU-FEL was one of the most powerful CSR sources in normal conducting linear accelerator facilities. The CSR spectra were measured using an uncooled pyroelectric detector and a Michelson-type interferometer designed specifically for the KU-FEL electron beam, and had a maximum at a frequency of 0.11THz. We found that adjusting the energy slit enhanced the CSR energy and shortened the electron beam bunch length in the CSR spectra measurements. Our results demonstrated that the efficient use of the energy slit can help improve the characteristics of CSR.

Unexpected effects in non crystalline materials exposed to X-ray radiation

The interaction of high intensity synchrotron radiation X-rays in the energy range 5<E<30keV with matter can produce a large number of expected and less expected effects. Whether these be considered radiation damage or are simply ignored, perhaps depends on the context or the eye of the beholder. In many cases however, X-ray induced effects can easily be mistaken for experimental results, and non-crystalline materials and liquids are most affected. We give a brief overview of possible X-ray induced effects, including structural changes and nanoparticle formation in glass, reaction rates in catalysis, the formation of bubbles in aqueous environments due to the presence of salts, and discuss possible mechanisms. The results shown are relevant for time-resolved processes studied by X-ray methods in catalysis, glass devitrification and for liquid samples.

Diffraction imaging forin situcharacterization of double-crystal X-ray monochromators

Imaging of the Bragg-reflected X-ray beam is proposed and validated as anin situmethod for characterization of the performance of double-crystal monochromators under the heat load of intense synchrotron radiation. A sequence of images is collected at different angular positions on the reflectivity curve of the second crystal and analyzed. The method provides rapid evaluation of the wavefront of the exit beam, which relates to local misorientation of the crystal planes along the beam footprint on the thermally distorted first crystal. The measured misorientation can be directly compared with the results of finite element analysis. The imaging method offers an additional insight into the local intrinsic crystal quality over the footprint of the incident X-ray beam.

Spherical quartz crystals investigated with synchrotron radiation.

The quality of x-ray spectra and images obtained from plasmas with spherically bent crystals depends in part on the crystal's x-ray diffraction across the entire crystal surface. We employ the energy selectivity and high intensity of synchrotron radiation to examine typical spherical crystals from alpha-quartz for their diffraction quality, in a perpendicular geometry that is particularly convenient to examine sagittal focusing. The crystal's local diffraction is not ideal: the most noticeable problems come from isolated regions that so far have failed to correlate with visible imperfections. Excluding diffraction from such problem spots has little effect on the focus beyond a decrease in background.