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abstracts
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.
abstracts
In many XFEL experiments small objects with unknown orientations are introduced into the x-ray beam. However, understanding the measured quantities it would be desirable to know their orientations. This is the situation in the case of single-molecule imaging one of the main target areas of X-ray free-electron lasers. Here, the solution to the orientation problem is based on the possibility of orienting the large number of low-counting-statistics 2D diffraction patterns taken at random orientations of identical replicas of the sample. This is a difficult process and the low statistics limits the usability of these methods and ultimately it could prevent single-molecule imaging. We suggest a new approach, which avoids the use of the diffraction patterns. We propose to determine the sample orientation through identifying the direction of ejection fragments. The orientation of the sample is measured together with the diffraction pattern by detecting some fragments of the Coulomb explosion. We show by molecular-dynamics simulations that from the angular distribution of the fragments one can obtain the orientation of the samples [1].The figure shows the distribution of heavy atoms coming from different depth of the sample ( upper panel homogeneous, lower panel inhomogeneous model samples, and left to right is heavy atom at the outer boundary, halfway to center and at the center).
