Start-to-End XFEL experiment simulation:A framework and coherent imaging example

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. We present a framework for Start-to-End (S2E) simulations of a coherent X-ray experiment, including source parameters, propagation of the coherent X-rays though optical elements, interaction of the photons with matter, and their subsequent detection and analysis. To demonstrate this framework, we show a single-particle structure determination example using parameters of the Single Particles, Clusters and Biomolecules (SPB) instrument [1] at the under-construction European XFEL [2, 3]. We use cross platform wave optics software [4] for the propagation of the coherent beams, a molecular dynamics treatment of real space dynamics of atoms, ions and free electrons to account for radiation damage [5], and the Expansion-Maximization-Compression (EMC) algorithm [6] for assembling the simulated data before subsequent phasing and structure determination. It is hoped such simulations can provide an insight into the critical regions of parameter space for the single-particle imaging problem, and hence direct efforts to best utilize these next generation light sources.

Retrieval of 3D deformations of single crystal defects by X-ray topo-tomography

A challenge in X-ray topo-tomography is the issue of quantitatively determining the 3D-deformation-distribution field associated with single defects of crystal lattices. In the present report an endeavor is made to retrieve a 3D-deformation-distribution field around single line defects (dislocations) in crystals by using the X-ray topo-tomography method. The general layout of the X-ray topo-tomography experiment is depicted in Fig. 1[1]. For our purposes we have used plane-parallel samples of crystal Si with surface orientation (111), the sample thickness being 1 mm, in which the linear dislocations have been inserted according to [2]. The experiments were carried out at the X-ray wavelength of MoKα1 (λ=0.071 nm). Experimental series of the X-ray (2 20)-reflection topography images with the rotation angle step 2⁰ around the diffraction vector, the total angular range 360⁰, have been got out. Furthermore, such the 2D- topographic images are used for getting 3D-images by means of the modified algebraic method SART developed in [3]. In parallel, for 3D reconstruction the corresponding 2D-topographic dislocation images are simulated by use of the Born-approximation analytical and numerical solutions based on Takagi-Taupin equations describing the two-beam X-ray diffraction by the deformed crystals. Certainly, all the above approaches are applied to the comparative analysis of opportunities of determining 3D-deformation-distribution field around the dislocations under consideration.