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The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 1012 photons s−1), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5–18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 - 1012 photons s-1), micro-focus (7 mm - 5 mm), low-divergence (1 mrad - 0.35 mrad) energy-tunable (5-18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented. [ABSTRACT FROM AUTHOR]

The morphology of supermultiperiod Al0.3Ga0.7As/GaAs superlattices grown by molecular-beam epitaxy has been determined using X-ray reflectometry (including the one on a synchrotron source) and photoluminescence. The layer thicknesses of a superlattice with 100 periods determined in laboratory and synchrotron studies correlate with an error of ~1%. Reflection peaks, which are not observed in measurements on a diffractometer and are likely related to the technological growth features of these structures, are revealed on a synchrotron beginning with high (>4–5) Bragg orders. It is analytically shown that these peaks correspond to modulation in the superlattice with a period that is three to five times larger and characterize the thickness dispersion over the structure depth of a few percent. [ABSTRACT FROM AUTHOR]

High-pressure single-crystal X-ray diffraction experiments were conducted on natural grunerite crystals with composition (Fe5.237Mg1.646Ca0.061Mn0.051Na0.015Ti0.002Cr0.001K0.001)(Si7.932Al0.083)O22(OH)2, using a synchrotron X-ray source. Grunerite has C2/m symmetry at ambient conditions. The samples were compressed at 298 K in a diamond-anvil cell to a maximum pressure of 25.6(5) GPa. We observe a previously described phase transition from C2/m (α) to P21/m (β) to take place at 7.4(1) GPa, as well as a further transition from P21/m (β) to C2/m (γ) at 19.2(3) GPa. The second-order Birch–Murnaghan equation of state fit to our compressional data, yielded the values V0 = 914.7(7) Å3 and K0 = 78(1) GPa for α-grunerite, V0 = 926(5) Å3 and K0 = 66(4) GPa for β-grunerite and V0 = 925(27) Å3 and K0 = 66(13) GPa for γ-grunerite. The β–γ phase transition produces a greater degree of kinking in the double silicate chains of tetrahedra accompanied by a discontinuous change in the a and c unit cell parameters and the monoclinic β angle. At 22.8(4) GPa the O5–O6–O5 kinking angle of the new high-pressure C2/m phase is 137.5(4)°, which is the lowest reported for any monoclinic amphibole. This study is the first structural report to show the existence of three polymorphs within an amphibole group mineral. The high-pressure γ-phase illustrates the parallel structural relations and phase transformation behavior of both monoclinic single and double chain silicates. [ABSTRACT FROM AUTHOR]

Bubbles, found in a huge variety of food products, are known to afford desirable quality attributes, especially those related to texture, mouthfeel and taste. However, the presence of bubbles and their effects on wheat flour noodles is an aspect that has been, until now, largely overlooked, despite the positive and negative connotations of bubbly inclusions on Asian noodle quality. X-rays from a synchrotron source (Biomedical Imaging and Therapy facility at the Canadian Light Source) were used to rapidly and non-destructively acquire tomographic images of noodle dough. Appropriate image analysis protocols were used to determine the bubble size distribution, the orientation of bubbles, and their position within the dough sheet. The effect of processing (one or multiple lamination steps) on bubble properties in the dough that was subsequently sheeted (gradual elongation and reduction in thickness) was investigated. Bubble size distributions, well captured by lognormal distribution function, showed that the lamination process induced bubble entrapment and reduction in bubble size. Bubbles were found to be flat, elongated and oriented in the sheeting direction, this effect being less for doughs laminated ten times (90° rotations between lamination steps). Interestingly, a gradient in concentration of bubbles within the dough sheet was found from the noodle core to the sheet edges. Aging effects were also apparent. This first non-destructive study of bubbles in wheat-flour noodle dough provides a more complete knowledge of the dough sheet's internal structure, and how it originates via processing, and this has repercussions on the overall quality of Asian noodles. [ABSTRACT FROM AUTHOR]

High-pressure diamond-anvil cell synchrotron X-ray diffraction experiments were conducted on single-crystal samples of natural orthoamphibole; gedrite; with composition; (K0.002Na0.394)(Mg2)(Mg1.637Fe2.245Mn0.004Ca0.022Cr0.003Na0.037Al1.052)(Si6.517Al1.483)O22(OH)2. The samples were compressed at 298 K up to a maximum pressure of 27(1) GPa. In this pressure regime, we observed a displacive phase transition between 15.1(7) and 21(1) GPa from the orthorhombic Pnma phase to a new structure with space group P21/m; which is different from the familiar P21/m structure of cummingtonite and retains the (+, +, −, −) I-beam stacking sequence of the orthorhombic structure. The unit cell parameters for the new phase at 21(1) GPa are a = 17.514(3), b = 17.077(1), c = 4.9907(2) Å and β = 92.882(6)°. The high-pressure P21/m phase is the first amphibole structure to show the existence of four crystallographically distinct silicate double chains. The orthorhombic to monoclinic phase transition is characterized by an increase in the degree of kinking of the double silicate chains and is analogous to displacive phase changes recently reported in orthopyroxenes, highlighting the parallel structural relations and phase transformation behavior of orthorhombic single- and double-chain silicates.

The more than 100.000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic artifacts, including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density map, thus limiting the relevance of structure determinations. Moreover, for most of these structures no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in the inference for protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5’-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.

Determination of the bubble size distribution at the end of mixing and controlling its changes are the basis for improving bread quality before it is fully manufactured. X-rays from a synchrotron source (Biomedical Imaging and Therapy beamline, Canadian Light Source) were used to rapidly characterize the bubble size distribution and its evolution in non-yeasted dough subsamples as a function of time for 3 h following mixing. A complete X-ray microtomography scan was completed within 120 s. The higher number density of bubbles in dough compared to results previously reported in the literature was attributed to the better contrast and higher resolution (smaller pixel size, 8.75 μm) of the reconstructed X-ray images generated from synchrotron X-rays. The bubble size distribution was very well characterized with a lognormal distribution function. This distribution had a median bubble radius of 22.1 ± 0.7 μm at 36 min after the end of mixing which increased to 27.3 ± 0.7 μm over 162 min, a trend indicative of transport of gas in the dough due to disproportionation. This is the first time disproportionation in non-yeasted wheat flour doughs has been monitored directly under bulk conditions relevant to dough in bakery conditions. These results show that the diffusion-driven dynamics of bubbles in non-yeasted bread doughs can be followed by X-rays from a synchrotron source via feature extraction using image analysis software. [ABSTRACT FROM AUTHOR]

Forsterite, Mg2SiO4, the magnesian end-member of the olivine system, is the archetypal example of an orthosilicate structure. We have conducted synchrotron-based single-crystal X-ray diffraction experiments to 90 GPa on synthetic end-member forsterite to study its equation of state and phase transitions. Upon room-temperature compression, the forsterite structure is observed to 48 GPa. By fitting a third-order Birch-Murnaghan equation of state to our compression data, we obtain the zeropressure isothermal bulk modulus, K0T = 130.0(9) GPa and its pressure derivative, K0T' = 4.12(7) for a fixed room-pressure volume, V0 = 290.1(1) Å3, in good agreement with earlier work. At 50 GPa, a phase transition to a new structure (forsterite II) occurs, followed by a second transition to forsterite III at 58 GPa. Forsterite III undergoes no additional phase transitions until at least 90 GPa. There is an ~4.8% volume reduction between forsterite and forsterite II, and a further ~4.2% volume reduction between forsterite II and III. On decompression forsterite III remains until as low as 12 GPa, but becomes amorphous at ambient conditions. Using our X-ray diffraction data together with an evolutionary crystal structure prediction algorithm and metadynamics simulations, we find that forsterite II has triclinic space group P1 and forsterite III has orthorhombic space group Cmc21. Both high-pressure phases are metastable. Metadynamics simulations show a stepwise phase transition sequence from 4-coordinated Si in forsterite to mixed tetrahedral and octahedral Si (as in forsterite II), and then fully sixfold-coordinated Si (as in forsterite III), occurring by displacement in [001](100). The forsterite III structure is a member of the family of post-spinel structures adopted by compositions such as CaFe2O4 and CaTi2O4. [ABSTRACT FROM AUTHOR]

Abstract: The high temperature effective (constrained) γ/γ′ lattice mismatch of a Ni-based single crystal superalloy has been measured in a wide temperature range [930°C–1125°C] using three different techniques: in-situ X-ray diffraction under synchrotron radiation, and post-mortem γ/γ′ interfacial dislocation network mesh size measurements using Transmission Electron Microscopy (TEM) or high resolution Scanning Electron Microscopy (SEM). It is shown that all three techniques are complementary considering precision and spatial distribution of lattice mismatches in the analyzed volume and that they provide a very similar average value of the γ/γ′ lattice mismatch. Since isothermal creep experiments were performed under variable applied stress, it is deduced that the post-mortem lattice misfit measurements using both TEM and SEM are representative of the very last loading step of the experiments, even if dislocation networks are out of an equilibrium configuration. Contrary to the unconstrained γ/γ′ lattice mismatch, it is shown that the effective lattice mismatch is a function of the temperature, applied stress and accumulated plastic strain, i.e. of the thermomechanical histories of the samples. [Copyright &y& Elsevier]

Abstract: The ν9 fundamental band (C–C–C deformation) of propane (C3H8) at 369cm−1 has been studied at high-resolution (0.0011cm−1) with spectra recorded using the synchrotron radiation from the French light source facility at SOLEIL coupled to a Bruker IFS 125HR Fourier transform spectrometer. A 2.526m base multipass cell with optical paths from 10.296 to 151.78m was used. In addition, a spectrum was also recorded using a conventional globar source. Comparison of these experimental spectra shows clearly the gain obtained on the signal-to-noise ratios with the synchrotron radiation. The spectra have been thoroughly analyzed and transitions up to J=65 and K a=33 have been assigned. The upper-state rotational levels were fitted using an A-type Watson Hamiltonian written in the I r representation. An accurate band center ν0 (ν 9)=369.228080(25)cm−1 as well as accurate rotational and centrifugal distortion constants have been obtained and used to simulate a synthetic spectrum. These parameters should be useful to simulate hot bands of propane involving the 91 vibrational level as their lower state. [Copyright &y& Elsevier]

The Paul Scherrer Institute (PSI/Switzerland) is planning an X-ray free electron laser facility (SwissFEL) using novel concepts for electron emission, high gradient acceleration and effective bunch compression. Based on a normal-conducting 5.8 GeV linear accelerator, SwissFEL will cover a spectral range of 0.1-7 nm wavelength. An ultra bright electron source was first developed and commissioned in 2008 followed by the construction of a 250 MeV accelerator facility in order to validate the concepts to generate and transport high brightness beams. This facility will be used in the future as the injector for the SwissFEL linac. An amount of typically 100 magnets of 4 different types (solenoids, quadrupoles, dipoles and correctors) is required in order to preserve the high brightness and the low emittance of the femto-second electron pulses. All the magnets are designed and magnetically measured at PSI in order to ensure that the required tolerances are fulfilled. The field gradient, the multipole contents and the magnetic center position are measured with two independent systems, an automated scanner and a uniaxial Hall Probe. We review the magnet design required for the injection phase and discuss the first results of the magnetic measurements. [ABSTRACT FROM AUTHOR]

Mapping of residual stresses at the mesoscale is increasingly practical thanks to technological developments in electron backscatter diffraction (EBSD) and X-ray microdiffraction using high brilliance synchrotron sources. An analysis is presented of a Cu single crystal deformed in compression to about 10% macroscopic strain. Local orientation measurements were made on sectioned and polished specimens using EBSD and X-ray microdiffraction. In broad strokes, the results are similar to each other with orientations being observed that are on the order of 5° misoriented from that of the original crystallite. At the fine scale it is apparent that the X-ray technique can distinguish features in the structure that are much finer in detail than those observed using EBSD even though the spatial resolution of EBSD is superior to that of X-ray diffraction by approximately two orders of magnitude. The results are explained by the sensitivity of the EBSD technique to the specimen surface condition. Dislocation dynamics simulations show that there is a relaxation of the dislocation structure near the free surface of the specimen that extends approximately 650 Å into the specimen. The high spatial resolution of the EBSD technique is detrimental in this respect as the information volume extends only 200 Å or so into the specimen. The X-rays probe a volume on the order of 2 µm in diameter, thus measuring the structure that is relatively unaffected by the near-surface relaxation. [ABSTRACT FROM AUTHOR]

Phase-contrast imaging provides enhanced image contrast and is important for non-destructive evaluation of structural materials. In this paper, experimental results on in-line phase-contrast imaging using a synchrotron source (ELETTRA, Italy) for objects required in material science applications are discussed. Experiments have been carried out on two types of samples, pyrocarl~on-coated zirconia and pyrocarbon-coated alumina microspheres. These have applications in both reactor and industrial fields. The phase-contrast imaging 1technique is found to be very useful in visualizing and determining the coating thickness of pyrocarbon on zirconia and alumina microspheres. The experiments were carried out at X-ray energies of 16, 18 and 20 keV and different object-to-detector distances. The results describe the contrast values and signal-to-noise ratio for both samples. A comprehensive study was carried out to determine the thickness of the pyrocarbon coating on zirconia and alumina microspheres of diameter 500 ~m. The advantages of phase-contrast images are discussed in terms of contrast and resolution, and a comparison is made with absorption images. The results show considerable improvement in contrast with phase-contrast imaging as compared with absorption radiography. [ABSTRACT FROM AUTHOR]

Abstract: Coronary stents are small scaffolds routinely implanted during angioplasty procedures to re-open coronary arteries which have become narrowed by an atherosclerotic plaque. Despite the advent of drug-eluting stents to reduce restenosis (re-narrowing) after the procedure, complications still arise and mechanical factors may be partly the cause. Stents are being used in increasingly complex cases, so new forms of pre-clinical testing may be helpful in evaluating stent designs and deployment techniques. With this in mind, an in vitro experiment was conducted to evaluate the use of X-ray micro-tomography to image stents at various stages of deployment. A stent was deployed in an artificial artery while using a synchrotron X-ray source to obtain the tomography scans. A volume element (voxel) size of 5.3μm was achieved, with a vertical field of view of 4.5mm. The imaging of the stent and artificial artery materials was better than expected, despite some attenuation artifacts and the high monochromatic beam energy used (25keV). Experimental problems are discussed, together with recommendations for improving the technique. It is intended that this technique will be of interest to engineers and clinicians as a pre-clinical test. [Copyright &y& Elsevier]

Hard X-ray diffraction enhanced imaging (DEI), which is based on a synchrotron source and monochromator-analyzer-crystal system, is an effective method for imaging X-ray phase shift. Utilizing an analyzer crystal with high angular sensitivity of micro-radian, DEI can measure the transmitted, refracted and scattered X-rays when projecting onto a sample. It dramatically improves the contrast and spatial resolution of the resultant images. At the topography station of Beijing Synchrotron Radiation Facilities (BSRF), we implemented DEI method in guinea pig cochleae imaging and acquired a series of DEI images. Based on these images, the apparent absorption and refraction images were calculated. The DEI images revealed the holistic spiral structures and inner details of guinea pig cochleae clearly, even including the structures at the cellular level, such as the static cilia of hairy cells and the limbus of Hansen cell. Due to the advantages of high contrast, high spatial resolution and distinct edge-enhanced effect, DEI method promises extensive applications in biology, medicine and clinic in the near future. [ABSTRACT FROM AUTHOR]

The systematic X-ray absorption near edge structure (XANES) investigation at Au L 3 -edge was made on Au in metallic form and its compounds in various definite oxidation states, viz., Au(OH) 3 , AuCl, AuCl 3 , HAuCl 4 , AuI and AuBr 3. The spectra have been recorded with linearly polarized photon beam from 2.5 GeV INDUS-2 Synchrotron source. All XANES spectra were deconvoluted to configure the energy positions of bound and continuum state transitions. With respect to the reference metallic Au, the absorption edge of the Au-compounds shifts towards higher energies with increasing valency of the absorbing atom. The origin of different shifts is found to be dependent on the charge transfer mechanism between Au and ligands in the measured spectra at Au L 3 -edge. The shifts in the absorption energies have also correlated to an increase in the ligand field strength. The absorption edge energy and area of the white-line peaks for the Au-compounds with Au in +3 oxidation state increase systematically in the spectrochemical series as AuBr< AuCl< HAuCl 4 < Au(OH) 3 , which indicates hybridization of d -orbitals and increasing tendency of ligand atom to attract electrons. Theoretical simulations are in line with this trend and the Au-series demonstrates that energy shifts in XANES spectra of Au(III) compounds can be understood in terms of crystal field theory. • The systematic XANES investigation at Au L 3 edge for various definite oxidation states and ligand field strength. • The shifts found to be dependent on charge transfer mechanism between Au and ligands in the measured spectra at Au L 3 edge. • The absorption edge energy for Au compounds in +3 oxidation state increases systematically in the spectrochemical series. • The areas of the pre-edge peaks for Au in +3 oxidation state increases systematically in the spectroschemical series. • The systematic increase indicates hybridization of d orbitals and increasing tendency of ligand atom to attract electrons. [ABSTRACT FROM AUTHOR]