Good agreement between the high-resolution experimental results for (222, 113) three-beam diffraction in Ge and computer simulations based on the dynamical multiple diffraction theory are presented.
The results of high-resolution analysis of the (222, >113) three-beam diffraction in Ge are presented. For monochromatization and angular collimation of the incident synchrotron beam a multi-crystal arrangement in a dispersive setup in both vertical and horizontal planes was used in an attempt to experimentally approach plane-wave incident conditions. Using this setup, for various azimuthal angles the polar angular curves which are very close to theoretical computer simulations for the plane monochromatic wave were measured. The effect of the strong two-beam 222 diffraction was observed for the first time with the maximum reflectivity close to 60% even though the total reflection of the incident beam into a forbidden reflection was not achieved owing to absorption. The structure factor of the 222 reflection in Ge was experimentally determined.
dynamical diffraction; multiple diffraction; synchrotron radiation; plane waves; X-ray optics
The spatial structure of an X-ray beam focused by a planar refractive lens and Bragg diffracted from perfect silicon crystals has been studied experimentally and theoretically.
The spatial structure of a beam focused by a planar refractive lens and Bragg diffracted from perfect silicon crystals was experimentally studied at the focal plane using a knife-edge scan and a high-resolution CCD camera. The use of refractive lenses allowed for a detailed comparison with theory. It was shown that diffraction leads to broadening of the focused beam owing to the extinction effect and, for a sufficiently thin crystal, to the appearance of a second peak owing to reflection from the back surface. It was found that the spatial structure of the diffracted beam depends on whether the crystal diffracts strongly (dynamically) or weakly (kinematically). The results help to understand the physical origin of the diffracted intensity recorded in a typical microbeam diffraction experiment.
X-rays; focusing; refractive lenses; X-ray diffraction; extinction effect
To test the efficacy of phase-sensitive x-ray imaging for intact synovial joints, whereby refraction effects, along with the attenuation of conventional radiography, can be exploited.
Intact cadaveric human knee joints were imaged, in the computed tomographic mode, using an analyzer based x-ray system at the National Synchrotron Light Source, Brookhaven National Laboratory. A collimated fan beam of 51 keV X-rays was prepared by a silicon [1,1,1 reflection] double-crystal monochromator. The x-ray beam transmitted through the specimen was imaged after diffraction in the vertical plane by means of the analyzer crystal with the analyzer crystal tuned to its half-reflectivity point (6.5 microradians). A two-dimensional filtered backprojection (FBP) algorithm was used for reconstructing transverse slices of images.
The resulting images demonstrate simultaneous soft-tissue and bone contrast at a level that has not been achieved previously. Identifiable structures include articular cartilage, cruciate ligaments, loose connective tissue, menisci, and chondrocalcinosis.
Phase-sensitive x-ray imaging using an analyzer-based system renders exceptionally high quality images of soft and hard tissues within synovial joints, with high contrast and resolution, and thus holds promise for the eventual clinical utility.
Recently developed microscopy techniques, such as 4Pi, break the Abbe diffraction limit and allow for imaging at unprecedented resolution. The effective focal volume is also reduced, leading to more sensitive measurements in fluorescence microphotolysis or correlation spectroscopy. In 4Pi microscopy, the improvement is due to the utilization of two interfering laser beams for illumination, rather than a single one as in conventional microscopy. We study theoretically the possibility of further reduction of the focal volume with employment of three or more interfering beams, including the limiting case of an inifinite number of beams. The volume is indeed reduced, but reaches a limit quickly as beams are added. The volume obtained in the setups with three or four beams is about half of that in the 4Pi case and is close to the volume computed for the limit of an infinite number of beams. The setups suggested employ purely optical principles, and, thus, the considered limiting case arguably represents the maximal reduction in focal volume possible for a purely optical far-field setup.
The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Å wavelength) with fluxes up to 8–18 × 1012 photons s−1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a κ-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented.
X-ray beamline; protein crystallography; MAD/SAD; X-ray optics
Crystallization of human membrane proteins in lipidic cubic phase often results in very small but highly ordered crystals. Advent of the sub-10 µm minibeam at the APS GM/CA CAT has enabled the collection of high quality diffraction data from such microcrystals. Herein we describe the challenges and solutions related to growing, manipulating and collecting data from optically invisible microcrystals embedded in an opaque frozen in meso material. Of critical importance is the use of the intense and small synchrotron beam to raster through and locate the crystal sample in an efficient and reliable manner. The resulting diffraction patterns have a significant reduction in background, with strong intensity and improvement in diffraction resolution compared with larger beam sizes. Three high-resolution structures of human G protein-coupled receptors serve as evidence of the utility of these techniques that will likely be useful for future structural determination efforts. We anticipate that further innovations of the technologies applied to microcrystallography will enable the solving of structures of ever more challenging targets.
lipidic cubic phase; G protein-coupled receptor; minibeam; microcrystallography
The currently largest perfect-crystal neutron interferometer with six beam splitters and two interference loops offers novel applications in neutron interferometry. The two additional lamellas can be used for quantitative measurements of a phase shift due to crystal diffraction in the vicinity of a Bragg condition. The arising phase, referred to as “Laue phase,” reveals an extreme angular sensitivity, which allows the detection of beam deflections of the order of 10−6 s of arc. Furthermore, a precise measurement of the Laue phase at different reflections might constitute an interesting opportunity for the extraction of fundamental quantities like the neutron–electron scattering length, gravitational short-range interactions in the sub-micron range and the Debye Waller factor. For that purpose several harmonics can be utilized at the interferometer instrument ILL-S18.
Perfect crystal interferometer; Dynamical diffraction; Beam deflection; High angular resolution; Short-range interaction; Coriolis force
Characterization of PILATUS single-photon-counting X-ray detector modules regarding charge sharing, energy resolution and rate capability is presented. The performance of the detector was tested with surface diffraction experiments at the synchrotron.
PILATUS is a silicon hybrid pixel detector system, operating in single-photon-counting mode, that has been developed at the Paul Scherrer Institut for the needs of macromolecular crystallography at the Swiss Light Source (SLS). A calibrated PILATUS module has been characterized with monochromatic synchrotron radiation. The influence of charge sharing on the count rate and the overall energy resolution of the detector were investigated. The dead-time of the system was determined using the attenuated direct synchrotron beam. A single module detector was also tested in surface diffraction experiments at the SLS, whereby its performance regarding fluorescence suppression and saturation tolerance were evaluated, and have shown to greatly improve the sensitivity, reliability and speed of surface diffraction data acquisition.
hybrid pixel detector; single photon counting; energy resolution; charge sharing; dead-time; surface X-ray diffraction
The sonar beam of an echolocating bat forms a spatial window restricting the echo information returned from the environment. Investigating the shape and orientation of the sonar beam produced by a bat as it flies and performs various behavioral tasks may yield insight into the operation of its sonar system. This paper presents recordings of vertical and horizontal cross-sections of the sonar beam produced by Eptesicus fuscus (big brown bats) as they fly and pursue prey in a laboratory flight-room. In the horizontal plane the sonar beam consists of one large lobe and in the vertical plane the beam consists of two lobes of comparable size oriented frontally and ventrally. In level flight, the bat directs its beam such that the ventral lobe is pointed forward and down toward the ground ahead of its flight path. The bat may utilize the downward directed lobe to measure altitude without the need for vertical head movements.
echolocation; sonar; side-lobe; altimeter
Beam-induced damage on diffractive hard X-ray optics is studied by means of X-ray diffraction and scanning electron microscopy.
The issue of beam-induced damage on diffractive hard X-ray optics is addressed. For this purpose a systematic study on the radiation damage induced by a high-power X-ray beam is carried out in both ambient and inert atmospheres. Diffraction gratings fabricated by three different techniques are considered: electroplated Au gratings both with and without the polymer mold, and Ir-coated Si gratings. The beam-induced damage is monitored by X-ray diffraction and evaluated using scanning electron microscopy.
diffractive X-ray optics; radiation damage
Using a convergent X-ray beam having continuously varying energy and glancing angle as a function of direction, the whole profile of a specular X-ray reflectivity curve is measured with no need for any mechanical motion during the measurement.
An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed.
X-ray reflectivity curve; time-resolved measurement; bent-twisted polychromator crystal; simultaneous measurement
Beamline ID23-2, the first dedicated and highly automated high-throughput monochromatic macromolecular crystallography microfocus beamline, is described.
The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick–Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.
macromolecular crystallography; automation; microfocus
A novel design is described for an aperture that blocks a half-plane of the electron diffraction pattern out to a desired scattering angle, and then – except for a narrow support beam – transmits all of the scattered electrons beyond that angle. Our proposed tulip-shaped design is thus a hybrid between the single-sideband (ssb) aperture, which blocks a full half-plane of the diffraction pattern, and the conventional (i.e. fully open) double-sideband (dsb) aperture. The benefits of this hybrid design include the fact that such an aperture allows one to obtain high-contrast images of weak-phase objects with the objective lens set to Scherzer defocus. We further demonstrate that such apertures can be fabricated from thin-foil materials by milling with a focused ion beam (FIB), and that such apertures are fully compatible with the requirements of imaging out to a resolution of at least 0.34 nm. As is known from earlier work with single-sideband apertures, however, the edge of such an aperture can introduce unwanted, electrostatic phase shifts due to charging. The principal requirement for using such an aperture in a routine data-collection mode is thus to discover appropriate materials, protocols for fabrication and processing, and conditions of use such that the hybrid aperture remains free of charging over long periods of time.
Phase contrast; single-sideband aperture; charging
Laguerre-Gaussian (LG) beams have been extensively studied due to their unique structure, characterized by a phase singularity at the center of the beam. Common methods for generating such beams include the use of diffractive optical elements and spatial light modulators, which although offering excellent versatility, suffers from several drawbacks, including in many cases a low power damage threshold as well as complexity and expense. This paper presents a simple, low cost method for the generation of high-fidelity LG beams using rapid prototyping techniques. Our approach is based on a fluidic-hologram concept, whereby the properties of the LG beam can be finely controlled by varying the refractive-index of the fluid that flows through the hologram. This simple approach, while optimized here for LG beam generation, is also expected to find applications in the production of tunable fluidic optical trains.
Anomalous extra spots visible in electron diffraction patterns of silicon nanowires and silicon thin films are explained by the presence of micro- and nanotwins.
Odd electron diffraction patterns (EDPs) have been obtained by transmission electron microscopy (TEM) on silicon nanowires grown via the vapour–liquid–solid method and on silicon thin films deposited by electron beam evaporation. Many explanations have been given in the past, without consensus among the scientific community: size artifacts, twinning artifacts or, more widely accepted, the existence of new hexagonal Si phases. In order to resolve this issue, the microstructures of Si nanowires and Si thin films have been characterized by TEM, high-resolution transmission electron microscopy (HRTEM) and high-resolution scanning transmission electron microscopy. Despite the differences in the geometries and elaboration processes, the EDPs of the materials show great similarities. The different hypotheses reported in the literature have been investigated. It was found that the positions of the diffraction spots in the EDPs could be reproduced by simulating a hexagonal structure with c/a = 12(2/3)1/2, but the intensities in many EDPs remained unexplained. Finally, it was established that all the experimental data, i.e. EDPs and HRTEM images, agree with a classical cubic silicon structure containing two microstructural defects: (i) overlapping Σ3 microtwins which induce extra spots by double diffraction, and (ii) nanotwins which induce extra spots as a result of streaking effects. It is concluded that there is no hexagonal phase in the Si nanowires and the Si thin films presented in this work.
silicon nanowires; silicon thin films; artifacts; twinning
The parasitoid fly Ormia ochracea shows an astonishing localization ability with its tiny hearing organ. A novel MEMS biomimetic acoustic pressure gradient sensitive structure was designed and fabricated by mimicking the mechanically coupled tympana of the fly. Firstly, the analytic representation formulas of the resultant force and resultant moment of the incoming plane wave acting on the structure were derived. After that, structure modal analysis was performed and the results show that the structure has out-of-phase and in-phase vibration modes, and the corresponding eigenfrequency is decided by the stiffness of vertical torsional beam and horizontal beam respectively. Acoustic-structural coupled analysis was performed and the results show that phase difference and amplitude difference between the responses of the two square diaphragms of the sensitive structure are effectively enlarged through mechanical coupling beam. The phase difference and amplitude difference increase with increasing incident angle and can be used to distinguish the direction of sound arrival. At last, the fabrication process and results of the device is also presented.
MEMS; biomimetic; parasitoid fly; pressure gradient; sound source localization
A tunable X-ray focusing and/or monochromating device, called a transfocator, is described. Examples of its implementation on ID11 at the ESRF are given.
This paper describes a tunable X-ray focusing apparatus, referred to as a transfocator, based on compound refractive lenses. By varying the number of lenses in the beam, the X-ray energy focused and the focal length can be varied continuously throughout a large range of energies and distances. The instrument can be used in both white and monochromatic beams to focus, pre-focus or collimate the beam. The transfocator can be used with other monochromators and/or other focusing elements, leading to significant increases in flux. Furthermore, the chromatic nature of the focusing means the transfocator suppresses harmonics and can also be used as an extremely high flux broad-band-pass monochromator. These devices have been installed in the first optics and second experimental hutches at the ID11 beamline at the ESRF.
compound refractive lens; X-ray optics; monochromator; microfocus
Rigorous calculations are performed to study the effective reduction of the nonlinear excitation volumes when using phase-only masks to condition the pump and Stokes driving fields. Focal volume reduction was achieved using both a multiplicative operation of the excitation fields as well as a subtractive operation. Using a tunable optical bottle beam for the Stokes field, an effective reduction of the width of the excitation volume by a factor of 1.5 can be achieved in the focal plane. Further reduction of the focal volume introduces a rapid growth of sidelobes, which renders such volumes unsuitable for imaging applications. In addition, phase sensitive detection was found to provide information from selective sub-divisions of the engineered coherent anti-Stokes Raman scattering excitation volume. In the case of isolated nanoparticles, an apparent resolution improvement by a factor of 3 is demonstrated, and it is shown that the size of sub-diffraction-limited particles can be accurately determined using phase sensitive detection.
X-ray computed tomography (XCT) has become a very important method for non-destructive 3D-characterization and evaluation of materials. Due to measurement speed and quality, XCT systems with cone beam geometry and matrix detectors have gained general acceptance. Continuous improvements in the quality and performance of X-ray tubes and XCT devices have led to cone beam CT systems that can now achieve spatial resolutions down to 1 μm and even below. However, the polychromatic nature of the source, limited photon flux and cone beam artefacts mean that there are limits to the quality of the CT-data achievable; these limits are particularly pronounced with materials of higher density like metals. Synchrotron radiation offers significant advantages by its monochromatic and parallel beam of high brilliance. These advantages usually cause fewer artefacts, improved contrast and resolution.
Tomography data of a steel sample and of two multi-phase Al-samples (AlSi12Ni1, AlMg5Si7) are recorded by advanced cone beam XCT-systems with a μ-focus (μXCT) and a sub-μm (nano-focus, sub-μXCT) X-ray source with voxel dimensions between 0.4 and 3.5 μm and are compared with synchrotron computed tomography (sXCT) with 0.3 μm/voxel. CT data features like beam hardening and ring artefacts, detection of details, sharpness, contrast, signal-to-noise ratio and the grey value histogram are systematically compared. In all cases μXCT displayed the lowest performance. Sub-μXCT gives excellent results in the detection of details, spatial and contrast resolution, which are comparable to synchrotron-XCT recordings. The signal-to-noise ratio is usually significantly lower for sub-μXCT compared with the two other methods. With regard to measurement costs “for industrial users”, scanning volume, accessibility and user-friendliness sub-μXCT has significant advantages in comparison to synchrotron-XCT.
X-ray computed tomography; Synchrotron tomography; High resolution tomography; 3D-characterization
Small-angle X-ray scattering (SAXS) is an X-ray diffraction-based technique where a narrow collimated beam of X-rays is focused onto a sample and the scattered X-rays recorded by a detector. The pattern of the scattered X-rays carries information on the molecular structure of the material. As breast cancer is the most widespread cancer in women and differentiation among its tumors is important, this project compared the results of coherent X-ray scattering measurements obtained from benign and malignant breast tissues. The energy-dispersive method with a setup including X-ray tube, primary collimator, sample holder, secondary collimator and high-purity germanium (HpGe) detector was used. One hundred thirty-one breast-tissue samples, including normal, fibrocystic changes and carcinoma, were studied at the 6° scattering angle. Diffraction profiles (corrected scattered intensity versus momentum transfer) of normal, fibrocystic changes and carcinoma were obtained. These profiles showed a few peak positions for adipose (1.15 ± 0.06 nm−1), mixed normal (1.15 ± 0.06 nm−1 and 1.4 ± 0.04 nm−1), fibrocystic changes (1.46 ± 0.05 nm−1 and 1.74 ± 0.04 nm−1) and carcinoma (1.55 ± 0.04 nm−1, 1.73 ± 0.06 nm−1, 1.85 ± 0.05 nm−1). We were able to differentiate between normal, fibrocystic changes (benign) and carcinoma (malignant) breast tissues by SAXS. However, we were unable to differentiate between different types of carcinoma.
Breast tumor; coherent scattering; small-angle X-ray scattering
A novel fabrication method of Si photonic slabs based on the selective formation of porous silicon is reported. Free-standing square lattices of cylindrical air holes embedded in a Si matrix can be achieved by proton beam irradiation followed by electrochemical etching of Si wafers. The photonic band structures of these slabs show several gaps for the two symmetry directions for reflection through the z-plane. The flexibility of the fabrication method for tuning the frequency range of the gaps over the near- and mid-infrared ranges is demonstrated. This tunability can be achieved by simply adjusting the main parameters in the fabrication process such as the proton beam line spacing, proton fluence, or anodization current density. Thus, the reported method opens a promising route towards the fabrication of Si-based photonic slabs, with high flexibility and compatible with the current microelectronics industry.
Photonic slabs; NanoPSi; Photonic band structure; Proton beam writing
In this work, we investigate the use of a three-stage Compton camera to measure secondary prompt gamma rays emitted from patients treated with proton beam radiotherapy. The purpose of this study was (1) to develop an optimal three-stage Compton camera specifically designed to measure prompt gamma rays emitted from tissue and (2) to determine the feasibility of using this optimized Compton camera design to measure and image prompt gamma rays emitted during proton beam irradiation. The three-stage Compton camera was modeled in Geant4 as three high-purity germanium detector stages arranged in parallel-plane geometry. Initially, an isotropic gamma source ranging from 0 to 15 MeV was used to determine lateral width and thickness of the detector stages that provided the optimal detection efficiency. Then, the gamma source was replaced by a proton beam irradiating a tissue phantom to calculate the overall efficiency of the optimized camera for detecting emitted prompt gammas. The overall calculated efficiencies varied from ~10−6 to 10−3 prompt gammas detected per proton incident on the tissue phantom for several variations of the optimal camera design studied. Based on the overall efficiency results, we believe it feasible that a three-stage Compton camera could detect a sufficient number of prompt gammas to allow measurement and imaging of prompt gamma emission during proton radiotherapy.
The modal characterization of various families of beams is a topic of current interest. We recently reported a new method for the simultaneous determination of both the azimuthal and radial mode indices for light fields possessing orbital angular momentum. The method is based upon probing the far-field diffraction pattern from a random aperture and using the recorded data as a ‘training set'. We then transform the observed data into uncorrelated variables using the principal component analysis (PCA) algorithm. Here, we show the generic nature of this approach for the simultaneous determination of the modal parameters of Hermite-Gaussian and Bessel beams. This reinforces the widespread applicability of this method for applications including information processing, spectroscopy and manipulation. Additionally, preliminary results demonstrate reliable decomposition of superpositions of Laguerre-Gaussians, yielding the intensities and relative phases of each constituent mode. Thus, this approach represents a powerful method for characterizing the optical multi-dimensional Hilbert space.
Synthesis and characterization of nano-crystalline silicon grown by atom beam sputtering technique are reported. Rapid thermal annealing of the deposited films is carried out in Ar + 5% H2 atmosphere for 5 min at different temperatures for precipitation of silicon nano-crystals. The samples are characterized for their optical and structural properties using various techniques. Structural studies are carried out by micro-Raman spectroscopy, Fourier transform infrared spectroscopy, transmission electron microscopy (TEM), high resolution transmission electron microscopy, and selected area electron diffraction. The optical properties are studied by photoluminescence and UV-vis absorption spectroscopy, and bandgaps are evaluated. The bandgaps are found to decrease after rapid thermal treatment. The micro-Raman studies show the formation of nano-crystalline silicon in as-deposited as well as annealed films. The shifting and broadening in Raman peak suggest formation of nano-phase in the samples. Results of micro-Raman, photoluminescence, and TEM studies suggest the presence of a bimodal crystallite size distribution for the films annealed at higher temperatures. The results show that atom beam sputtering is a suitable technique to synthesize nearly mono-dispersed silicon nano-crystals. The size of the nano-crystals may be controlled by varying annealing parameters.
Silicon nano-crystals; Atom beam sputtering; Rapid thermal annealing; TEM; Raman; Photoluminescence; 81.07; Bc68.37; Lp78.67; Bf
An X-ray stereo imaging system with synchrotron radiation was developed to perform real-time stereo imaging and stereo angiography.
An X-ray stereo imaging system with synchrotron radiation was developed at BL20B2, SPring-8. A portion of a wide X-ray beam was Bragg-reflected by a silicon crystal to produce an X-ray beam which intersects with the direct X-ray beam. Samples were placed at the intersection point of the two beam paths. X-ray stereo images were recorded simultaneously by a detector with a large field of view placed close to the sample. A three-dimensional wire-frame model of a sample was created from the depth information that was obtained from the lateral positions in the stereo image. X-ray stereo angiography of a mouse femoral region was performed as a demonstration of real-time stereo imaging. Three-dimensional arrangements of the femur and blood vessels were obtained.
X-ray stereo imaging; real-time imaging; angiography