X-ray Absorption Spectroscopy and Coherent X-ray Diffraction Imaging for Time-Resolved Investigation of the Biological Complexes: Computer Modelling towards the XFEL Experiment

The development of the next generation synchrotron radiation sources – free electron lasers – is approaching to become an effective tool for the time-resolved experiments aimed to solve actual problems in various fields such as chemistry, biology, medicine, etc. In order to demonstrate, how these experiments may be performed for the real systems to obtain information at the atomic and macromolecular levels, we have performed a molecular dynamics computer simulation combined with quantum chemistry calculations for the human phosphoglycerate kinase enzyme with Mg containing substrate. The simulated structures were used to calculate coherent X-ray diffraction patterns, reflecting the conformational state of the enzyme, and Mg K-edge X-ray absorption spectra, which depend on the local structure of the substrate. These two techniques give complementary information making such an approach highly effective for time-resolved investigation of various biological complexes, such as metalloproteins or enzymes with metal-containing substrate, to obtain information about both metal-containing active site or substrate and the atomic structure of each conformation

Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers

Modern X-ray free-electron lasers (XFELs) operating at high repetition ratesproduce a tremendous amount of data. It is a great challenge to classify thisinformation and reduce the initial data set to a manageable size for furtheranalysis. Here an approach for classification of diffraction patterns measured inprototypical diffract-and-destroy single-particle imaging experiments at XFELsis presented. It is proposed that the data are classified on the basis of a set ofparameters that take into account the underlying diffraction physics and specificrelations between the real-space structure of a particle and its reciprocal-spaceintensity distribution. The approach is demonstrated by applying principalcomponent analysis and support vector machine algorithms to the simulated andmeasured X-ray data sets

Software Platform for European XFEL: Towards Online Experimental Data Analysis

Large amount of data being generated at large scale facilities like European X-ray Free-Electron Laser (XFEL) requires new approaches for data processing and analysis. One of the mostcomputationally challenging experiments at an XFEL is single-particle structure determination.In this paper we propose a new design for an integrated software platform which combines well establishedtechniques for XFEL data analysis with High Performance Data Analysis (HPDA)methods. In our software platform we use streaming data analysis algorithms with high performancecomputing solutions. This approach should allow analysis of the experimental dataflow in quasionlineregime

Ptychographic X-Ray Imaging of Colloidal Crystals

Ptychographic coherent X-ray imaging is applied to obtain a projection of the electron density of colloidal crystals, which are promising nanoscale materials for optoelectronic applications and important model systems. Using the incident X-ray wavefield reconstructed by mixed states approach, a high resolution and high contrast image of the colloidal crystal structure is obtained by ptychography. The reconstructed colloidal crystal reveals domain structure with an average domain size of about 2 µm. Comparison of the domains formed by the basic close-packed structures, allows us to conclude on the absence of pure hexagonal close-packed domains and confirms the presence of random hexagonal close-packed layers with predominantly face-centered cubic structure within the analyzed part of the colloidal crystal film. The ptychography reconstruction shows that the final structure is complicated and may contain partial dislocations leading to a variation of the stacking sequence in the lateral direction. As such in this work, X-ray ptychography is extended to high resolution imaging of crystalline samples

Diffraction based Hanbury Brown and Twiss interferometry at a hard x-ray free-electron laser

X-ray free-electron lasers (XFELs) provide extremely bright and highly spatially coherent x-rayradiation with femtosecond pulse duration. Currently, they are widely used in biology and materialscience. Knowledge of the XFEL statistical properties during an experiment may be vitally importantfor the accurate interpretation of the results. Here, for the first time, we demonstrate Hanbury Brownand Twiss (HBT) interferometry performed in diffraction mode at an XFEL source. It allowed us todetermine the XFEL statistical properties directly from the Bragg peaks originating from colloidalcrystals. This approach is different from the traditional one when HBT interferometry is performedin the direct beam without a sample. Our analysis has demonstrated nearly full (80%) global spatialcoherence of the XFEL pulses and an average pulse duration on the order of ten femtoseconds forthe monochromatized beam, which is significantly shorter than expected from the electron bunchmeasurements

Coherent-Pulse 2D Crystallography Using a Free-Electron Laser X-Ray Source.

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