120 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
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
Revealing three-dimensional structure of individual colloidal crystal grain by coherent x-ray diffractive imaging
We present results of a coherent x-ray diffractive imaging experiment
performed on a single colloidal crystal grain. The full three-dimensional (3D)
reciprocal space map measured by an azimuthal rotational scan contained several
orders of Bragg reflections together with the coherent interference signal
between them. Applying the iterative phase retrieval approach, the 3D structure
of the crystal grain was reconstructed and positions of individual colloidal
particles were resolved. As a result, an exact stacking sequence of hexagonal
close-packed layers including planar and linear defects were identified.Comment: 8 pages, 5 figure
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
Revealing misfit dislocations InAs<sub>x</sub>P<sub>1-x</sub>-InP core-shell nanowires by x-ray diffraction
Bragg coherent x-ray diffractive imaging of a single indium phosphide nanowire
Three-dimensional (3D) Bragg coherent x-ray diffractive imaging (CXDI) with a nanofocused beam was applied to quantitatively map the internal strain field of a single indium phosphide nanowire. The quantitative values of the strain were obtained by pre-characterization of the beam profile with transmission ptychography on a test sample. Our measurements revealed the 3D strain distribution in a region of 150 nm below the catalyst Au particle. We observed a slight gradient of the strain in the range of ±0.6% along the [111] growth direction of the nanowire. We also determined the spatial resolution in our measurements to be about 10 nm in the direction perpendicular to the facets of the nanowire. The CXDI measurements were compared with the finite element method simulations and show a good agreement with our experimental results. The proposed approach can become an effective tool for in operando studies of the nanowires
New aerodynamic lens injector for single particle diffractive imaging
An aerodynamic lens injector was developed specifically for the needs of single-particle diffractive imaging experiments at free-electron lasers. Its design allows for quick changes of injector geometries and focusing properties in order to optimize injection for specific individual samples. Here, we present results of its first use at the FLASH free-electron-laser facility. Recorded diffraction patterns of polystyrene spheres are modeled using Mie scattering, which allowed for the characterization of the particle beam under diffractive-imaging conditions and yield good agreement with particle-trajectory simulations
NCBI GEO: archive for functional genomics data sets—10 years on
A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/
Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse
Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed
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