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Physical review / B 97(10), 104101 (2018). doi:10.1103/PhysRevB.97.104101, Solving the phase problem in x-ray crystallography has occupied a considerable scientific effort in the 20th century and led to great advances in structural science. Here we use x-ray ptychography to demonstrate an interference method which measures the phase of the beam transmitted through a crystal, relative to the incoming beam, when diffraction takes place. The observed phase change of the direct beam through a small gold crystal is found to agree with both a quasikinematical model and full dynamical theories of diffraction. Our discovery of a diffraction contrast mechanism will enhance the interpretation of data obtained from crystalline samples using the ptychography method, which provides some of the most accurate x-ray phase-contrast images., Published by APS, Woodbury, NY

The paper presents the results of application of machine learning methods: principle component analysis and support vector machine for classification of diffraction images produced in experiments at free-electron lasers. High efficiency of this approach presented by application to simulated data of adenovirus capsid and bluetongue virus core. This dataset were simulated with taking into account the real conditions of the experiment on lasers free electrons such as noise and features of used detectors.

Scientific data 4, 170079 (2017). doi:10.1038/sdata.2017.79, Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single- particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency., Published by Macmillan, London

Coherent X-ray diffractive imaging (CXDI) is a new imaging technique that offers the potential to image non-crystalline materials to sub-nanometer resolutions. Here we review the progress in CXDI of biological samples at both synchrotron and free electron laser (FEL) sources. We outline the experimental design of a CXDI experiment and summarize the iterative phase retrieval techniques that are used to produce images from the measured diffraction patterns. We describe a selection of key experiments performed in bio-imaging with CXDI from synchrotron sources, and we discuss the proof-of-principle experiments performed at FLASH at DESY in Hamburg. Finally, we show through simulation that for realistic parameters of hard X-ray FELs a resolution of a few nanometers may be achieved for individual biological objects imaged with single pulses of FEL radiation. Furthermore, we revise how this resolution may be improved to the sub-nanometer range if we image multiple copies of samples with a reproducible structure.

The combination of grazing-incidence small-angle x-ray scattering (GISAXS) with tomographic methods and phase retrieval is proposed for the reconstruction of the three-dimensional (3D) electron density of nanometer sized objects. In this approach GISAXS data from a small object are collected successively at different azimuthal angular positions. This 3D intensity distribution in reciprocal space is used for the phase retrieval and reconstruction of the 3D electron density. The power of our approach is demonstrated in a series of calculations performed in the frame of kinematical and distorted-wave Born approximation (DWBA) theories for the case of GISAXS scattering on a 200 nm island in the form of truncated pyramid.

Variation of the phase of the beam transmitted through a crystalline material as a function of the rocking angle is a well known dynamical effect in x-ray scattering. Unfortunately, it is not so easy to measure directly these phase variations in a conventional scattering experiment. It was recently suggested that the transmitted phase can be directly measured in ptychography experiments performed on nanocrystal samples. Results of such experiment for different crystal thickness, reflections and incoming photon energies, in principle, can be fully described in the frame of dynamical theory. However, dynamical theory does not provide a simple analytical expression for the further analysis. We develop here quasi-kinematical theory approach that allows to describe correctly the phase of the transmitted beam for the crystal thickness less than extinction length that is beyond applicability of the conventional kinematical theory., Comment: 22 pages, 7 figures, 3 tables

The analysis of X-ray standing wave (XSW) data for the determination of structural parameters of adsorbates (coherent position, P C h , and coherent fraction, F C h ) is usually done in the dipole approximation. Using carbon and oxygen containing molecular adsorbates on Ag(1 1 1), we show how the non-dipolar contributions can be quantified and that they can have a strong impact on the resulting P C h and F C h . The results are particularly important for XPS detection of XSW intensities from light elements, for which fluorescence detection does not work. Moreover, we discuss how the XSW technique allows determining both the amplitude and the phase from quadrupole contributions in photoelectric scattering.

Any available form of the statistical dynamical theory contains an approximation based on the assumption that the correlation length of the random imperfection of the crystal is much smaller than the Pendellosung length . A new formulation is developed for the coherent part of the rocking curve, without this short correlation approximation. Numerical calculations are carried out in order to discuss the validity of this approximation when the ratio / is varied.

The influence of higher-order multipole terms in the photoelectron yield on the result of an X-ray Standing Wave (XSW) measurement is discussed. The contributions of dipole, quadrupole and octupole term are analyzed for the simple model of a single atom within the XSW field. It is shown that each multiple term shows a different dependence on the polarization vectors and wavevectors of the direct and diffracted beam. The model is generalized for the case of a monolayer of atoms adsorbed on the surface of a crystal. We outline how multipole contributions can be determined by an XSW measurement.

Angular X-ray cross-correlation analysis (XCCA) is an approach to study the structure of disordered systems using the results of X-ray scattering experiments. In this paper we summarize recent theoretical developments related to the Fourier analysis of the cross-correlation functions. Results of our simulations demonstrate the application of XCCA to two- and three-dimensional (2D and 3D) disordered ensembles of particles. We show that the structure of a single particle can be recovered using X-ray data collected from a 2D disordered system of identical particles. We also demonstrate that valuable structural information about the local structure of 3D systems, inaccessible from a standard small-angle X-ray scattering experiment, can be resolved using XCCA.

We present a time-resolved infrared (IR) pump and extreme-ultraviolet (XUV) probe diffraction experiment to investigate ultrafast structural dynamics in colloidal crystals with picosecond resolution. The experiment was performed at the FLASH facility at DESY with a fundamental wavelength of 8 nm. In our experiment, the temporal changes of Bragg peaks were analyzed and their frequency components were calculated using Fourier analysis. Periodic modulations in the colloidal crystal were localized at a frequency of about 4-5 GHz. Based on the Lamb theory, theoretical calculations of vibrations of the isotropic elastic polystyrene spheres of 400 nm in size reveal a 5.07 GHz eigenfrequency of the ground (breathing) mode., 12 pages, 3 figures

Angular x-ray cross-correlation analysis (XCCA) is an approach to study the structure of disordered systems using the results of coherent x-ray scattering experiments. Here, we present the results of simulations that validate our theoretical findings for XCCA obtained in a previous paper [M. Altarelli et al., Phys. Rev. B 82, 104207 (2010)]. We consider as a model two-dimensional (2D) disordered systems composed of non-interacting colloidal clusters with fivefold symmetry and with orientational and positional disorder. We simulate a coherent x-ray scattering in the far field from such disordered systems and perform the angular cross-correlation analysis of calculated diffraction data. The results of our simulations show the relation between the Fourier series representation of the cross-correlation functions (CCFs) and different types of correlations in disordered systems. The dependence of structural information extracted by XCCA on the density of disordered systems and the degree of orientational disorder of clusters is investigated. The statistical nature of the fluctuations of the CCFs in the model `single-shot' experiments is demonstrated and the potential of extracting structural information from the analysis of CCFs averaged over a set of diffraction patterns is discussed. We also demonstrate the effect of partial coherence of x-rays on the results of XCCA., Comment: 45 pages, 11 figures

The imaging of hydrated biological samples - especially in the energy window of 284-540 eV, where water does not obscure the signal of soft organic matter and biologically relevant elements - is of tremendous interest for life sciences. Free-electron lasers can provide highly intense and coherent pulses, which allow single pulse imaging to overcome resolution limits set by radiation damage. One current challenge is to match both the desired energy and the intensity of the light source. We present the first images of dehydrated biological material acquired with 3rd harmonic radiation from FLASH by digital in-line zone plate holography as one step towards the vision of imaging hydrated biological material with photons in the water window. We also demonstrate the first application of ultrathin molecular sheets as suitable substrates for future free-electron laser experiments with biological samples in the form of a rat fibroblast cell and marine biofouling bacteria Cobetia marina.

First results of the theory of the standing wave behaviour in curved crystals are presented. The proposed theory is based on the Taupin theory of dynamical X-ray diffraction in curved crystals and the theory of the secondary radiation yield in deformed crystals. This theory is applied for a calculation of the angular dependence of the secondary emission yield in a cylindrically bent Si(400) monocrystal, CuKa radiation. Processes with different depths of the secondary emission yield, i.e. photoemission (Lyi = 0.1 μm) and fluorescence (Lyi = 70 μm), are considered.

A general theoretical approach based on the results of statistical optics is used for the analysis of the transverse coherence properties of thirdgeneration hard x-ray synchrotron sources and x-ray free-electron lasers (XFEL). Correlation properties of the wavefields are calculated at different distances from an equivalent Gaussian Schell-model source. This model is used to describe coherence properties of the 5m undulator source at the synchrotron storage ring PETRA III. In the case of XFEL sources the decomposition of the statistical fields into a sum of independently propagating transverse modes is used for the analysis of the coherence properties of these new sources. A detailed calculationis performed for the parameters of the SASE1 undulator at the European XFEL. It is demonstrated that only a few modes contribute significantly to the total radiation field of that source.

We report on a resonant magnetic scattering experiment using soft x-ray pulses generated from a free-electron laser (FEL). The free-electron laser was operated at a fundamental wavelength of 7.97 nm and radiation at the fifth harmonic originating from self-amplified stimulated emission at 1.59 nm with an average energy of 4 nJ per pulse was detected. We demonstrate the feasibility of resonant magnetic scattering at FEL sources by using a Co/Pd multilayer as prototype sample that was illuminated with 20-fs-long soft x-ray pulses tuned to the Co L{sub 3} absorption edge at 778.1 eV (1.59 nm)

Coherent diffractive imaging for the reconstruction of a two-dimensional (2D) finite crystal structure with a single pulse train of free-electron laser radiation at 7.97 nm wavelength is demonstrated. This measurement shows an advance on traditional coherent imaging techniques by applying it to a periodic structure. It is also significant that this approach paves the way for the imaging of the class of specimens which readily form 2D, but not three-dimensional crystals. We show that the structure is reconstructed to the detected resolution, given an adequate signal-to-noise ratio.

The adsorption geometry of perfluorinated copper-phthalocyanine molecules $({\mathrm{F}}_{16}\mathrm{CuPc})$ on Cu(111) and Ag(111) is studied using x-ray standing waves. A detailed, element-specific analysis taking into account nondipolar corrections to the photoelectron yield shows that on both surfaces the molecules adsorb in a lying down, but significantly distorted configuration. While on copper (silver) the central carbon rings reside 2.61 \AA{} (3.25 \AA{}) above the substrate, the outer fluorine atoms are located 0.27 \AA{} (0.20 \AA{}) further away from the surface. This nonplanar adsorption structure is discussed in terms of the outer carbon atoms in ${\mathrm{F}}_{16}\mathrm{CuPc}$ undergoing a partial rehybridization $(s{p}^{2}\ensuremath{\rightarrow}s{p}^{3}).$

The spatial coherence of free-electron laser radiation in the water window spectral range was studied, using the third harmonic (λ

The Green's function formalism is applied to the analysis of the surface contribution to the inelastic scattering of x-rays by acoustic modes of thermal excitations in a crystal. It is shown that the surface contribution to thermal diffuse scattering (TDS) near the surface can become comparable to and can even exceed the volume contribution. The same formalism is applied to the investigation of TDS in the case of dynamical diffraction, when an x-ray standing wave is generated in a crystal. TDS yield curves calculated according to this model show good agreement with the experimental results.