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Phase Aberrations in Diffraction Microscopy

Description: In coherent X-ray diffraction microscopy the diffraction pattern generated by a sample illuminated with coherent x-rays is recorded, and a computer algorithm recovers the unmeasured phases to synthesize an image. By avoiding the use of a lens the resolution is limited, in principle, only by the largest scattering angles recorded. However, the imaging task is shifted from the experiment to the computer, and the algorithm's ability to recover meaningful images in the presence of noise and limited prior knowledge may produce aberrations in the reconstructed image. We analyze the low order aberrations produced by our phase retrieval algorithms. We present two methods to improve the accuracy and stability of reconstructions.
Date: September 29, 2005
Creator: Marchesini, S; Chapman, H N; Barty, A; Howells, M R; Spence, J H; Cui, C et al.
Partner: UNT Libraries Government Documents Department

Damped and thermal motion of large, laser-aligned molecules in droplet beams

Description: We consider a monodispersed Rayleigh droplet beam of water droplets doped with proteins. An intense infrared laser is used to align these droplets. The arrangement has been proposed for electron and X-ray diffraction studies of proteins which are difficult to crystallize. This paper considers the effect of thermal fluctuations on the angular spread of alignment in thermal equilibrium, and relaxation phenomena, particularly the damping of oscillations excited as the molecules enter the field. The possibility of adiabatic alignment is also considered. We find that damping times in high pressure gas cell as used in X-ray diffraction experiments are short compared to the time taken for molecules to traverse the beam, and that a suitably shaped field might be used for electron diffraction experiments in vacuum to provide adiabatic alignment, thus obviating the need for a damping gas cell.
Date: September 29, 2005
Creator: Starodub, D; Doak, B; Schmidt, K; Weierstall, U; Wu, J; Spence, J et al.
Partner: UNT Libraries Government Documents Department

High-resolution ab initio Three-dimensional X-ray Diffraction Microscopy

Description: Coherent X-ray diffraction microscopy is a method of imaging non-periodic isolated objects at resolutions only limited, in principle, by the largest scattering angles recorded. We demonstrate X-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the 3D diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a non-periodic object. We also construct 2D images of thick objects with infinite depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution using X-ray undulator radiation, and establishes the techniques to be used in atomic-resolution ultrafast imaging at X-ray free-electron laser sources.
Date: August 19, 2005
Creator: Chapman, H N; Barty, A; Marchesini, S; Noy, A; Cui, C; Howells, M R et al.
Partner: UNT Libraries Government Documents Department

Progress in Three-Dimensional Coherent X-Ray Diffraction Imaging

Description: The Fourier inversion of phased coherent diffraction patterns offers images without the resolution and depth-of-focus limitations of lens-based tomographic systems. We report on our recent experimental images inverted using recent developments in phase retrieval algorithms, and summarize efforts that led to these accomplishments. These include ab-initio reconstruction of a two-dimensional test pattern, infinite depth of focus image of a thick object, and its high-resolution ({approx}10 nm resolution) three-dimensional image. Developments on the structural imaging of low density aerogel samples are discussed.
Date: September 30, 2005
Creator: Marchesini, S; Chapman, H N; Barty, A; Howells, M R; Cui, C; Spence, J H et al.
Partner: UNT Libraries Government Documents Department

Dose, exposure time, and resolution in Serial X-ray Crystallography

Description: Using detailed simulation and analytical models, the exposure time is estimated for serial crystallography, where hydrated laser-aligned proteins are sprayed across a continuous synchrotron beam. The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available fluxes of molecules and X-rays. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of a density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 7 {angstrom} should be possible with short (below 100 s) exposures.
Date: March 22, 2007
Creator: Starodub, D; Rez, P; Hembree, G; Howells, M; Shapiro, D; Chapman, H N et al.
Partner: UNT Libraries Government Documents Department