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The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods. [ABSTRACT FROM AUTHOR]

The use of X-ray synchrotron radiation makes it possible to observe the polarization, spectral, and angular dependences for diffraction reflections. Their theoretical study calls for application of a tensor approach to describe the interaction of X-rays with atoms of matter. Various representations of the tensor atomic scattering amplitude, results of experimental observations of the anisotropy of resonant X-ray scattering, and the relationship of the electric and magnetic multipole moments on atoms with the properties of forbidden resonant reflections are considered. [ABSTRACT FROM AUTHOR]

The polarization dependence of the cross sections of two-photon transitions including X-ray scattering was analyzed. We developed the regular approach to the derivation of the polarization parameters of photoprocesses. Our approach is based on the tensor representation of the photon density matrix, which is written in terms of the unit vectors directed along the major axis of the polarization ellipse ( ϵ ˆ ) and the photon propagation ( k ˆ ). Explicit expressions for the product of two photon density matrices were derived. As an example, the parametrization of the polarization dependence of the X-ray scattering by closed-shell atoms is given both in terms of (i) scalar products of photon vectors ϵ ˆ 1 , 2 , k ˆ 1 , 2 and (ii) X-ray Stokes parameters. We discuss the applicability of the atomic scattering for the measurement of the polarization of X-rays. [ABSTRACT FROM AUTHOR]

We study through simulations a layout mixing RF and THz technologies for a compact ultrafast X-ray pulse source based on Inverse Compton Scattering (ICS), aiming to deliver few femtoseconds to sub-femtosecond pulses. The layout consists of an S-band gun as the electron source and a dielectric-loaded circular waveguide driven by a multicycle THz pulse to accelerate and longitudinally compress the bunch, before X-ray generation via ICS with a laser pulse. We detail several schemes allowing the optimization of the electron bunch properties. This optimization leads to a preliminary layout and various working points able to deliver 0.1–5 pC bunches, ranging from 15 to 18 MeV average kinetic energy, 0.4 to 5 fs rms length, 0.1% to 2.6% rms energy spread, and 5 to 13 μm rms transverse size. Simultaneously, the beamline is kept compact (≈1.3 m up to the ICS point), which has not yet been achieved using only conventional RF technologies. The properties of the X-ray pulse are investigated with simulations, showing the possibility to tune its energy between 2.9 and 11.5 keV. For 400 mJ of laser energy, 1.5 × 104–7.7 × 104 photons/pulse in 1.5% rms bandwidth or 6.2 × 103–3.5 × 104 photons/pulse with lower bandwidths (0.56%–1.5% rms along the energy range) can be expected. The properties of the DLW and of the THz pulse driving it, the state-of-the-art of the THz pulse generation schemes, and the influence of various jitters and the limits that they should not exceed for a reasonably stable operation are finally given. [ABSTRACT FROM AUTHOR]

The crystal structure of zinc metal deviates from the ideal hexagonal close packing structure by a significantly increased axial ratio (c/a). The local atomic structure of zinc metal is investigated using the total scattering atomic pair distribution function (PDF) analysis based on X-ray powder diffraction data collected at ambient conditions. The X-ray total scattering PDF analysis confirms that the crystal structure of zinc can be described in terms of wurtzite structure, but with an anomalously atomic displacement parameters U 3 3 , indicating a significant displacement disorder along the c -axis. For the long r -range PDF refinements, the thermal motion of zinc shows a notable anisotropy as expressed by the ratio U 3 3 / U 1 1 of 2.5 at ambient conditions. This average distortion level along the c -axis, was not reflected locally for the features below 5.0 Å as it fits the high r region. Based on PDF refinements over different r -ranges, we measure an interesting increase of the U 3 3 value with decreasing the r -range of the refinement. This suggests that the local structure features in zinc metal differ from the average structure ones. [ABSTRACT FROM AUTHOR]

• Maps derived by X-ray crystallography display electron density, whereas maps derived by electron microscopy display Coulomb potential. • Negatively charged oxygen can result in attenuated positive potentials and even regions of negative density or 'holes' in Coulomb potential maps. • Biological molecules are exquisitely sensitive to damage from electron irradiation, especially the carboxylates of acidic amino acids. • A challenge in the interpretation of Coulomb potential maps is distinguishing the relative contributions from the charged states of oxygen atoms versus radiation damage. • High-resolution Coulomb potential maps can reveal information lacking in electron density maps, including protein and ion charged states, bond visualization and the presence of hydrogen atoms. Electron microscopy is based on elastic scattering due to Coulomb forces between the incident electrons and the sample; thus, electron scattering is dependent on the charge distribution in the sample. Unlike atomic scattering factors for X-rays, electron scattering factors for some atoms are strongly dependent on scattering angle, and the scattering factor for ionic oxygen is negative at low scattering angle. This phenomenon can result in a significant negative contribution to Coulomb potential maps by oxygen and can result in deviations in the positions of positive map features from atomic centers. An important factor that can also complicate the interpretation of cryoEM maps is the exquisite sensitivity of macromolecules to damage from electron irradiation, especially the carboxylates of acidic amino acids. Ideally, when compared with electron density maps derived by X-ray crystallography, Coulomb potential maps can provide additional details about the electrostatic environment and charge state of atoms. Enhancements in model building, refinement and computational simulation will be required to realize the full potential of EM-derived maps to reveal deeper insight into the electronic structure and functional properties of macromolecular complexes and their interactions with binding partners, ligands, cofactors, and drugs. [ABSTRACT FROM AUTHOR]

A "cutoff probe" uses microwaves to measure the electron density in a plasma. It is particularly attractive because it is easy to fabricate and use, its measurement is immune to surface contamination by dielectric materials, and it has a straightforward analysis to measure electron density in real time. In this work, we experimentally investigate the accuracy of the cutoff probe through a detailed comparison with Thomson scattering in a low temperature, high density processing plasma. The result shows that the electron density measured by the cutoff probe is lower than that by Thomson scattering and that the discrepancy of the two results becomes smaller as the gap between the two tips increases and/or the neutral gas pressure decreases. The underestimated electron density found by the cutoff probe can be explained by the influence of the probe holder, which becomes important as the pressure increases and the gap gets closer. [ABSTRACT FROM AUTHOR]

The application of a space-resolving spectrometer to X-ray Thomson Scattering (XRTS) experiments has the potential to advance the study of warm dense matter. This has motivated the design of a spherical crystal spectrometer, which is a doubly focusing geometry with an overall high sensitivity and the capability of providing high-resolution, space-resolved spectra. A detailed analysis of the image fluence and crystal throughput in this geometry is carried out and analytical estimates of these quantities are presented. This analysis informed the design of a new spectrometer intended for future XRTS experiments on the Z-machine. The new spectrometer collects 6 keV x-rays with a spherically bent Ge (422) crystal and focuses the collected x-rays onto the Rowland circle. The spectrometer was built and then tested with a foam target. The resulting high-quality spectra prove that a spherical spectrometer is a viable diagnostic for XRTS experiments. [ABSTRACT FROM AUTHOR]

Kramers-Kronig analysis is commonly used to estimate the optical properties of new materials. The analysis typically uses data from far infrared through near ultraviolet (say 40-40000 cm-1 or 5 meV-5 eV) and uses extrapolations outside the measured range. Most high-frequency extrapolations use a power law, 1 /con, transitioning to 1/tu4 at a considerably higher frequency and continuing this free-carrier extension to infinity. The midrange power law is adjusted to match the slope of the data and to give pleasing curves, but the choice of power (usually between 0.5 and 3) is arbitrary. Instead of an arbitrary power law, it is better to use x-ray atomic scattering functions such as those presented by Henke and co-workers. These basically treat the solid as a linear combination of its atomic constituents and, knowing the chemical formula and the density, allow the computation of dielectric function, reflectivity, and other optical functions. The 'Henke reflectivity' can be used over photon energies of 10 eV to 34 keV, after which a 1/w4 continuation is perfectly fine. The bridge between experimental data and the Henke reflectivity as well as two corrections made to the latter are discussed. [ABSTRACT FROM AUTHOR]

We present the first spectrally resolved measurements of x-rays scattered from cryogenic hydrogen jets in the single photon counting limit. The 120 Hz capabilities of the LCLS, together with a novel hydrogen jet design [J. B. Kim et al., Rev. Sci. Instrum. (these proceedings)], allow for the ability to record a near background free spectrum. Such high-dynamic-range x-ray scattering measurements enable a platform to study ultra-fast, laser-driven, heating dynamics of hydrogen plasmas. This measurement has been achieved using two highly annealed pyrolytic graphite crystal spectrometers to spectrally resolve 5.5 keV x-rays elastically and inelastically scattered from cryogenic hydrogen and focused on Cornell-SLAC pixel array detectors [S. Herrmann et al., Nucl. Instrum. Methods Phys. Res., Sect. A 718, 550 (2013)]. [ABSTRACT FROM AUTHOR]

We study resonant inelastic x-ray scattering (RIXS) peaks corresponding to low-energy particle-hole excited states of metallic FeTe and semimetallic TiSe2 for photon incident energy tuned near the L3 absorption edge of Fe and Ti, respectively. We show that the cross-section amplitudes are well described within a renormalization-group theory where the effect of the core electrons is captured by effective dielectric functions expressed in terms of the the atomic scattering parameters f1 of Fe and Ti. This method can be used to extract the dynamical structure factor from experimental RIXS spectra in metallic systems. [ABSTRACT FROM AUTHOR]

A practical and accurate method to obtain the index of refraction, especially the decrement δ, across the carbon 1s absorption edge is demonstrated. The combination of absorption spectra scaled to the Henke atomic scattering factor database, the use of the doubly subtractive Kramers-Kronig relations, and high precision specular reflectivity measurements from thin films allow the notoriously difficult-to-measure δ to be determined with high accuracy. No independent knowledge of the film thickness or density is required. High confidence interpolation between relatively sparse measurements of δ across an absorption edge is achieved. Accurate optical constants determined by this method are expected to greatly improve the simulation and interpretation of resonant soft x-ray scattering and reflectivity data. The method is demonstrated using poly(methyl methacrylate) and should be extendable to all organic materials. [ABSTRACT FROM AUTHOR]

We report on formation of a bicontinuous double gyroid phase by a wedge-shaped amphiphilic mesogen, pyridinium 4′-[3″,4″,5″-tris-(octyloxy)benzoyloxy]azobenzene-4-sulfonate. It is found that this compound can self-organize in zeolite-like structures adaptive to environmental conditions (e.g., temperature, humidity, solvent vapors). Depending on the type of the phase, the structure contains 1D, 2D, or 3D networks of nanometer-sized ion channels. Of particular interest are bicontinuous phases, such as the double gyroid phase, as they hold promise for applications in separation and energy. Specially designed environmental cells compatible with grazing-incidence X-ray scattering and atomic force microscopy enable simultaneous measurements of structural parameters/morphology during vapor-annealing treatment at different temperatures. Such in-situ approach allows finding the environmental conditions at which the double gyroid phase can be formed and provide insights on the supramolecular structure of thin films at different spatial levels. [ABSTRACT FROM AUTHOR]