Alexey V. Buzmakov

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

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. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

The optimal XFEL pulse duration for single-particle imaging of small proteins is narrowed down to the 3–9 fs range, using start-to-end simulations of a single-particle imaging experiment at the European XFEL.

Laboratory X-ray microtomographs with the use of monochromatic radiation

The possibility and expediency of designing X-ray microtomographs based on X-ray diffractometers have been analyzed. Some biomedical objects have been investigated. It has been demonstrated that it is possible to achieve a resolution of the order 10 μm with a field of view of the order of 20 mm without recourse to magnifying X-ray optical elements.

Growth of nano-dots on the grazing-incidence mirror surface under FEL irradiation.

A new phenomenon on X-ray optics surfaces has been observed: the growth of nano-dots (40-55 nm diameter, 8-13 nm height, 9.4 dots µm(-2) surface density) on the grazing-incidence mirror surface under irradiation by the free-electron laser (FEL) FLASH (5-45 nm wavelength, 3° grazing-incidence angle). With a model calculation it is shown that these nano-dots may occur during the growth of a contamination layer due to polymerization of incoming hydrocarbon molecules. The crucial factors responsible for the growth of nano-dots in the model are the incident peak intensity and the reflection angle of the beam. A reduction of the peak intensity (e.g. replacement of the FEL beam by synchrotron radiation) as well as a decrease of the incident angle by just 1° (from 3° to 2°) may result in the total disappearance of the nano-dots. The model calculations are compared with surface analysis of two FLASH mirrors.

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations

The WavePropaGator (WPG) package is a new interactive cross-platform open-source software framework for modeling of coherent and partially coherent X-ray wavefront propagation. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The paper presents a general description of the package and gives some recent application examples.

Upgraded X-ray topography and microtomography beamline at the Kurchatov synchrotron radiation source

An upgraded X-ray Topography and Microtomography (XRT-MT) station is described, the parameters of the optical schemes and detectors are given, and the experimental possibilities of the station are analyzed. Examples of tomographic reconstructions are reported which demonstrate spatial resolutions of 2.5 and 10 μm at fields of view of 2.5 and 10 mm, respectively.

Effective regularized algebraic reconstruction technique for computed tomography

A new fast version of the reconstruction algorithm for computed tomography based on the simultaneous algebraic reconstruction technique (SART) is proposed. The algorithm iteration is asymptotically accelerated using the fast Hough transform from O(n3) to O(n2logn). Similarly to the algebraic reconstruction technique (RegART), which was proposed by us previously, the regularization operator is applied after each iteration. A bilateral filter plays the role of this operator. The algorithm behavior is investigated using the model experiment.

Cross-platform wave optics software for XFEL applications

We present a new software project aimed at development of a novel and unique software environment, suited and capable of solving a wide set of X-ray FEL optics problems. The complex of programs is based upon libraries of the Synchrotron Radiation Workshop (SRW) package. The software can be used by XFEL experimental groups for developing scientific instruments, planning experiments and processing experimental data. Specific examples of applications of FEL wavefront propagation simulations are presented: modeling of edge radiation at the soft X-ray FEL facility FLASH and of the wavefront propagation through grazing incidence optics of the hard X-ray beamlines of the European XFEL. Possible ways for parallelization of calculations are also discussed.

Study of the internal structure of lithium fluoride single crystal by laboratory X-ray topo-tomography

Defects in a synthetic LiF crystal have been studied by X-ray topo-tomography on laboratory X-ray sources with a spatial resolution of ∼10 μm. An algebraic reconstruction method was applied to reconstruct the defect 3D structure of the crystal based on the diffraction data. The results presented in this study are in good agreement with the topographic data obtained by the Lang method.

CT metal artifact reduction by soft inequality constraints

The artifacts (known as metal-like artifacts) arising from incorrect reconstruction may obscure or simulate pathology in medical applications, hide or mimic cracks and cavities in the scanned objects in industrial tomographic scans. One of the main reasons caused such artifacts is photon starvation on the rays which go through highly absorbing regions. We indroduce a way to suppress such artifacts in the reconstructions using soft penalty mimicing linear inequalities on the photon starved rays. An efficient algorithm to use such information is provided and the effect of those inequalities on the reconstruction quality is studied.