187 research outputs found
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
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
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 . 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
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 - photons/m (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 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
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 and 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
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