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.
An analytical approach describing properties of focused partially coherent X-ray beams is presented. The method is based on the results of statistical optics and gives both the beam size and transverse coherence length at any distance behind an optical element. In particular, here we consider Gaussian Schell-model beams and thin optical elements. Limiting cases of incoherent and fully coherent illumination of the focusing element are discussed. The effect of the beam defining aperture, typically used in combination with focusing elements at synchrotron sources to improve transverse coherence, is also analyzed in detail. As an example the coherence properties in the focal region of compound refractive lenses at the PETRA III synchrotron source are analyzed.
Single particle diffraction imaging experiments at free-electron lasers (FEL) have a great potential for structure determination of reproducible biological specimens that can not be crystallized. One of the challenges in processing the data from such an experiment is to determine correct orientation of each diffraction pattern from samples randomly injected in the FEL beam. We propose an algorithm (see also O. Yefanov et al., Photon Science - HASYLAB Annual Report 2010) that can solve this problem and can be applied to samples from tens of nanometers to microns in size, measured with sub-nanometer resolution in the presence of noise. This is achieved by the simultaneous analysis of a large number of diffraction patterns corresponding to different orientations of the particles. The algorithms efficiency is demonstrated for two biological samples, an artificial protein structure without any symmetry and a virus with icosahedral symmetry. Both structures are few tens of nanometers in size and consist of more than 100 000 non-hydrogen atoms. More than 10 000 diffraction patterns with Poisson noise were simulated and analyzed for each structure. Our simulations indicate the possibility to achieve resolution of about 3.3 {AA} at 3 {AA} wavelength and incoming flux of 10^{12} photons per pulse focused to 100times 100 nm^2.
A general theoretical approach based on the results of statistical optics is used for the analysis of the transverse coherence properties of 3-rd generation 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 five meter 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 calculation is 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.
