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Data-processing workflow for single-particle imaging experiments at X-ray free-electron lasers is presented. The analysis developed here revealed nanoscale features of the PR772 virus with a resolution better than 10 nm and without any symmetry constraints.

We show that the combination of X-ray scattering with a nanofocused beam and X-ray cross correlation analysis is an efficient means for the full structural characterization of mesocrystalline nanoparticle assemblies with a single experiment. We analyze several hundred diffraction patterns of individual sample locations, i.e. individual grains, to obtain a meaningful statistical distribution of the superlattice and atomic lattice ordering. Simultaneous small-and wide-angle X-ray scattering of the same sample location allows us to determine the structure and orientation of the superlattice as well as the angular correlation of the first two Bragg peaks of the atomic lattices, their orientation with respect to the superlattice, and the average orientational misfit due to local structural disorder. This experiment is particularly advantageous for synthetic mesocrystals made by the simultaneous self-assembly of colloidal nanocrystals and surfacefunctionalization with conductive ligands. While the structural characterization of such materials has been challenging so far, the present method now allows correlating mesocrystalline structure with optoelectronic properties. Mesocrystals (MC) are three-dimensional arrays of iso-oriented single-crystalline particles with an individual size between 1 -1000 nm. [1][2][3][4][5] Their physical properties are largely determined by structural coherence, for which the angular correlation between their individual atomic lattices and the underlying superlattice of nanocrystals (NC) is a key ingredient. 1,2 Colloidal NCs stabilized by organic surfactants have been shown to pose excellent building blocks for the design of synthetic MCs with tailored structural properties which are conveniently obtained by self-assembly of NCs from solution on a solid or liquid substrate by exploiting ligand-ligand 3 interactions. [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25] Typically, the utilized ligands consist of wide-gap, bulky hydrocarbons which render the MCs insulating. [26][27][28][29][30][31][32][33] MCs obtained in this way exhibit average grain sizes of ~150 µm 2 , which enables a detailed characterization by electron and/or X-ray microscopy. 34 Since the optoelectronic properties of PbS NC ensembles bear many opportunities for applications in solar cells or photodetectors, a number of ligand exchange procedures with small organic or inorganic molecules as well as single atom passivation strategies have been developed, all of which greatly increase the carrier mobilities within the SL of NCs. 28,33,[35][36][37][38][39][40][41][42][43][44] Due to the short interparticle spacing imposed by these ligands, structural coherence is mostly lost in such superlattices, but in rare cases it has been demonstrated that significant long-range order and even mesocrystallinity can be preserved. 25,35,45 However, a persisting problem of these protocols is that they are prone to introduce defects in the superlattice structure with some degree of granularity and signifi...

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

We have used the Berkeley-Illinois-Maryland Association (BIMA) millimeter array outÐtted with sensitive centimeter-wave receivers to search for cosmic microwave background (CMB) anisotropies on arcminute scales. The interferometer was placed in a compact conÐguration that produces high brightness sensitivity, while providing discrimination against point sources. Operating at a frequency of 28.5 GHz, the FWHM primary beam of the instrument isWe have made sensitive images of seven Ðelds, D6@ .6. four of which where chosen speciÐcally to have low IR dust contrast and to be free of bright radio sources. Additional observations with the Owens Valley Radio Observatory (OVRO) millimeter array were used to assist in the location and removal of radio point sources. Applying a Bayesian analysis to the raw visibility data, we place limits on CMB anisotropy Ñat-band power of kK and Q flat \ 5.6~5 .6 3.0 kK at 68% and 95% conÐdence, respectively. The sensitivity of this experiment to Ñat-band Q flat \ 14

An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.

We present a comprehensive experimental analysis of statistical properties of the self-amplified spontaneous emission free-electron laser (FEL) FLASH by means of Hanbury Brown and Twiss interferometry. The experiments were performed at FEL wavelengths of 5.5, 13.4, and 20.8 nm. We determined the second-order intensity correlation function for all wavelengths and different operation conditions of FLASH. In all experiments a high degree of spatial coherence (above 50%) was obtained. Our analysis performed in spatial and spectral domains provided us with the independent measurements of an average pulse duration of the FEL that were below 60 fs. To explain the complicated behavior of the second-order intensity correlation function we developed an advanced theoretical model that includes the presence of multiple beams and external positional jitter of the FEL pulses. By this analysis we determined that in one of the experiments external positional jitter was about 25% of the beam size. We envision that methods developed in our study will be used widely for analysis and diagnostics of FEL radiation.