Orientation Determination in Single Particle X-ray Coherent Diffraction Imaging Experiments

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 100\times 100 nm^2.Comment: 23 pages, 10 figures, 40 reference

Perspectives of Imaging of Single Protein Molecules with the Present Design of the European XFEL. - Part I - X-ray Source, Beamlime Optics and Instrument Simulations

The Single Particles, Clusters and Biomolecules (SPB) instrument at the European XFEL is located behind the SASE1 undulator, and aims to support imaging and structure determination of biological specimen between about 0.1 micrometer and 1 micrometer size. The instrument is designed to work at photon energies from 3 keV up to 16 keV. This wide operation range is a cause for challenges to the focusing optics. In particular, a long propagation distance of about 900 m between x-ray source and sample leads to a large lateral photon beam size at the optics. The beam divergence is the most important parameter for the optical system, and is largest for the lowest photon energies and for the shortest pulse duration (corresponding to the lowest charge). Due to the large divergence of nominal X-ray pulses with duration shorter than 10 fs, one suffers diffraction from mirror aperture, leading to a 100-fold decrease in fluence at photon energies around 4 keV, which are ideal for imaging of single biomolecules. The nominal SASE1 output power is about 50 GW. This is very far from the level required for single biomolecule imaging, even assuming perfect beamline and focusing efficiency. Here we demonstrate that the parameters of the accelerator complex and of the SASE1 undulator offer an opportunity to optimize the SPB beamline for single biomolecule imaging with minimal additional costs and time. Start to end simulations from the electron injector at the beginning of the accelerator complex up to the generation of diffraction data indicate that one can achieve diffraction without diffraction with about 0.5 photons per Shannon pixel at near-atomic resolution with 1e13 photons in a 4 fs pulse at 4 keV photon energy and in a 100 nm focus, corresponding to a fluence of 1e23 ph/cm^2. This result is exemplified using the RNA Pol II molecule as a case study

Extension of SASE bandwidth up to 2% as a way to increase the efficiency of protein structure determination by x-ray nanocrystallography at the European XFEL

Femtosecond x-ray nanocrystallography exploiting XFEL radiation is an emerging method for protein structure determination using crystals with sizes ranging from a few tens to a few hundreds nanometers. Crystals are randomly hit by XFEL pulses, producing diffraction patterns at unknown orientations. One can determine these orientations by studying the diffraction patterns themselves, i.e. by indexing the Bragg peaks. The number of indexed individual images and the SASE bandwidth are inherently linked, because increasing the number of Bragg peaks per individual image requires increasing the bandwidth of the spectrum. This calls for a few percent SASE bandwidth, resulting in an increase in the number of indexed images at the same number of hits. Based on start-to-end simulations for the baseline of the European XFEL, we demonstrate here that it is possible to achieve up to a tenfold increase in SASE bandwidth, compared with the nominal mode of operation. This provides a route for further increasing the efficiency of protein structure determination at the European XFEL. We illustrate this concept with simulations of lysozyme nanocrystals

«Phenomenon of D. Shurygina», or About the Media-Preferences of the Consumer Society

The article discusses the features of media-preferences of a modern audience, for example, the representation of the story about D. Shurygina. The discourse analysis of mediacontroller’s strategies in the fields of television (Pervyj kanal) and Internet (social networks VKontakte, Instagram, Facebook) was conducted. For substantiation of the “Phenomenon of D. Shurygina” the author refers to the concepts of the consumer society by J. Baudrillard and the mediavirus by D. Rashkoff. The conclusion is that the media-preferences of the consumer society are characterized by a polyphonic nature, combining the archetypes of low and high culture.Рассматриваются особенности медиапредпочтений современной аудитории на примере репрезентации истории о Д. Шурыгиной. Проводится дискурсанализ стратегий медиаконтролеров в полях телевидения (Первый канал) и интернета (социальные сети ВКонтакте, Instagram, Facebook). Для обоснования «Феномена Д. Шурыгиной» автор обращается к концепциям общества риска Ж. Бодрийяра и медиавируса Д. Рашкоффа. Делается вывод, что медиапредпочтения общества потребления характеризуются полифоничностью, сочетая в себе архетипы как низкой, так и высокой культуры

Continuous Diffraction of Molecules and Disordered Molecular Crystals

The diffraction pattern of a single non-periodic compact object, such as a molecule, is continuous and is proportional to the square modulus of the Fourier transform of that object. When arrayed in a crystal, the coherent sum of the continuous diffracted wave-fields from all objects gives rise to strong Bragg peaks that modulate the single-object transform. Wilson statistics describe the distribution of continuous diffraction intensities to the same extent that they apply to Bragg diffraction. The continuous diffraction obtained from translationally-disordered molecular crystals consists of the incoherent sum of the wave-fields from the individual rigid units (such as molecules) in the crystal, which is proportional to the incoherent sum of the diffraction from the rigid units in each of their crystallographic orientations. This sum over orientations modifies the statistics in a similar way that crystal twinning modifies the distribution of Bragg intensities. These statistics are applied to determine parameters of continuous diffraction such as its scaling, the beam coherence, and the number of independent wave-fields or object orientations contributing. Continuous diffraction is generally much weaker than Bragg diffraction and may be accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities to guide the subtraction of the background it is shown how all measured values can be utilised to estimate the background, noise, and signal, by employing a modified "noisy Wilson" distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously-published continuous diffraction data measured from imperfect crystals of photosystem II.Comment: 34 pages, 11 figures, 2 appendice

Use of computers to exclude the influence of radiometer instability upon measurement results

A radiometer, practically insensitive to great fluctuations in the equipment amplification coefficient, was developed by dividing the useful signal by a reference signal and modulating the two signals at different frequencies. The signals are simultaneously separated by corresponding synchronous detectors and recorded over two channels. The operation is simplified by replacing the continuous signals by a sampling of discrete values, and using a digital computer. The four steps involved in the process are described and a block diagram is included. This technique not only directly connects the radiometer with the computer, but also records all data provided by the control and signal channels

Hanbury Brown and Twiss interferometry at a free-electron laser

We present measurements of second- and higher-order intensity correlation functions (so-called Hanbury Brown and Twiss experiment) performed at the free-electron laser (FEL) FLASH in the non-linear regime of its operation. We demonstrate the high transverse coherence properties of the FEL beam with a degree of transverse coherence of about 80% and degeneracy parameter of the order 10^9 that makes it similar to laser sources. Intensity correlation measurements in spatial and frequency domain gave an estimate of the FEL average pulse duration of 50 fs. Our measurements of the higher-order correlation functions indicate that FEL radiation obeys Gaussian statistics, which is characteristic to chaotic sources.Comment: 19 pages, 6 figures, 1 table, 40 reference

Characterization of Spatial Coherence of Synchrotron Radiation with Non-Redundant Arrays of Apertures

We present a method to characterize the spatial coherence of soft X-ray radiation from a single diffraction pattern. The technique is based on scattering from non-redundant arrays (NRA) of slits and records the degree of spatial coherence at several relative separations from one to 15 microns, simultaneously. Using NRAs we measured the transverse coherence of the X-ray beam at the XUV X-ray beamline P04 of the PETRA III synchrotron storage ring as a function of different beam parameters. To verify the results obtained with the NRAs additional Young's double pinhole experiments were conducted and show good agreement.Comment: 15 pages, 6 figures, 2 tables, 42 reference