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

Spectrometer for Hard X-Ray Free Electron Laser Based on Diffraction Focusing

X-ray free electron lasers (XFELs) generate sequences of ultra-short, spatially coherent pulses of x-ray radiation. We propose the diffraction focusing spectrometer (DFS), which is able to measure the whole energy spectrum of the radiation of a single XFEL pulse with an energy resolution of $\Delta E/E\approx 2\times 10^{-6}$. This is much better than for most modern x-ray spectrometers. Such resolution allows one to resolve the fine spectral structure of the XFEL pulse. The effect of diffraction focusing occurs in a single crystal plate due to dynamical scattering, and is similar to focusing in a Pendry lens made from the metamaterial with a negative refraction index. Such a spectrometer is easier to operate than those based on bent crystals. We show that the DFS can be used in a wide energy range from 5 keV to 20 keV.Comment: 9 pages, 8 figures, 2 table

Direct reconstruction of the two-dimensional pair distribution function in systems with angular correlations

An x-ray scattering approach to determine the two-dimensional (2D) pair distribution function (PDF) in partially ordered 2D systems is proposed. We derive relations between the structure factor and PDF that enable quantitative studies of positional and bond-orientational (BO) order in real space. We apply this approach in the x-ray study of a liquid crystal (LC) film undergoing the smectic-hexatic phase transition, to analyze the interplay between the positional and BO order during the temperature evolution of the LC film. We analyze the positional correlation length in different directions in real space.Comment: 23 pages, 8 figure

Enhancement of Coherent X ray Diffraction from Nanocrystals by Introduction of X ray Optics

Coherent X-ray Diffraction is applied to investigate the structure of individual nanocrystalline silver particles in the 100nm size range. In order to enhance the available signal, Kirkpatrick-Baez focusing optics have been introduced in the 34-ID-C beamline at APS. Concerns about the preservation of coherence under these circumstances are addressed through experiment and by calculations

Theoretical study of electronic damage in single particle imaging experiments at XFELs for pulse durations 0.1 - 10 fs

X-ray free-electron lasers (XFELs) may allow to employ the single particle imaging (SPI) method to determine the structure of macromolecules that do not form stable crystals. Ultrashort pulses of 10 fs and less allow to outrun complete disintegration by Coulomb explosion and minimize radiation damage due to nuclear motion, but electronic damage is still present. The major contribution to the electronic damage comes from the plasma generated in the sample that is strongly dependent on the amount of Auger ionization. Since the Auger process has a characteristic time scale on the order of femtoseconds, one may expect that its contribution will be significantly reduced for attosecond pulses. Here, we study the effect of electronic damage on the SPI at pulse durations from 0.1 fs to 10 fs and in a large range of XFEL fluences to determine optimal conditions for imaging of biological samples. We analyzed the contribution of different electronic excitation processes and found that at fluences higher than $10^{13}$-$10^{15}$ photons/$\mu$m$^2$ (depending on the photon energy and pulse duration) the diffracted signal saturates and does not increase further. A significant gain in the signal is obtained by reducing the pulse duration from 10 fs to 1 fs. Pulses below 1 fs duration do not give a significant gain in the scattering signal in comparison with 1 fs pulses. We also study the limits imposed on SPI by Compton scattering.Comment: 35 pages, 9 figures, 1 table, 2 appendixes, 45 reference

Spatial properties of π−π\pi-\pi conjugated network in semicrystalline polymer thin films studied by intensity x-ray cross-correlation functions

We present results of x-ray study of spatial properties of $\pi-\pi$ conjugated networks in polymer thin films. We applied the x-ray cross-correlation analysis to x-ray scattering data from blends of poly(3-hexylthiophene) (P3HT) and gold nanoparticles. The Fourier spectra of the intensity cross-correlation functions for different films contain non-zero components of orders $n=2,4$ and $6$ measuring the degree of structural order in the system.Comment: 6 pages, 2 figures, Proceedings ICXOM22 Conference, 2-6 September 2013, Hamburg, German

Shearing Interferometer for Quantifying the Coherence of Hard X-Ray Beams

We report a quantitative measurement of the full transverse coherence function of the 14.4 keV x-ray radiation produced by an undulator at the Swiss Light Source. An x-ray grating interferometer consisting of a beam splitter phase grating and an analyzer amplitude grating has been used to measure the degree of coherence as a function of the beam separation out to 30 m. Importantly, the technique provides a model-free and spatially resolved measurement of the complex coherence function and is not restricted to high resolution detectors and small fields of view. The spatial characterization of the wave front has important applications in discovering localized defects in beam line optics