arXiv subjects

U. Weierstall

Publications and source records attributed to U. Weierstall.

15 recordsLinked to original sources

arXiv2011

A pump-probe XFEL particle injector for hydrated samples

We have developed a liquid jet injector system that can be used for hydrated sample delivery at X-ray Free Electron Laser (XFEL) sources and 3rd generation synchrotron sources. The injector is based on the Gas Dynamic Virtual Nozzle (GDVN), which generates a liquid jet with diameter ranging from 300 nm to 20 μm without the clogging problems associated with conventional Rayleigh jets. An improved nozzle design is presented here. A differential pumping system protects the vacuum chamber and an in-vacuum microscope allows observation of the liquid jet for diagnostics while it is being exposed to the X-ray beam. A fiber optically coupled pump laser illuminating the jet is incorporated for pump-probe experiments. First results with this injector system have been obtained at the LCLS.

physics.ins-det↗

arXiv2009

Tomographic femtosecond X-ray diffractive imaging

A method is proposed for obtaining three simultaneous projections of a target from a single radiation pulse, which also allows the relative orientation of successive targets to be determined. The method has application to femtosecond X-ray diffraction, and does not require solution of the phase problem. We show that the principle axes of a compact charge-density distribution can be obtained from projections of its autocorrelation function, which is directly accessible in diffraction experiments. The results may have more general application to time resolved tomographic pump-probe experiments and time-series imaging.

cond-mat.soft↗

arXiv2008

X-Ray Powder Diffraction from Sub-Micron Crystals of Photosystem-1 Membrane Protein

We demonstrate that powder diffraction data can be collected from sub-micron crystals of a mbrane protein with nearly two orders of magnitude more atoms than the molecules commonly used for powder diffraction. The crystals of photosystem-1 protein were size-selected using a 500 nm pore- size filter and delivered to a soft x-ray beam with a photon energy of 1.5 keV using a dynamically focused micro-jet developed for the serial crystallography experiment at beamline 9.0.1. The 10-micron jet places many such randomly oriented crystals in the x-ray beam simultaneously resulting in a powder diffraction pattern which extends to 28 angstrom resolution with just 200 seconds of x-ray exposure. The use of the jet for particle delivery allows for a thin sample, appropriate for the soft x-rays used, and continuously refreshes the crystals so that radiation damage is not possible. The small size of the crystals requires the use of lower energy photons for increased scattering strength and increased spacing between powder rings. The powder patterns obtained in this way, from abundant nano-crystals, could be used to provide low resolution molecular envelopes if phased using techniques such as compressive sensing which do not require atomic resolution data. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in Free Electron X-ray Laser schemes, and for Serial Crystallography using a single-file beam of aligned hydrated molecules.

physics.bio-ph↗

arXiv2008

Three-dimensional coherent X-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms

Ultra-low density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by X-ray diffractive imaging. Finite element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.

cond-mat.mtrl-sci↗

arXiv2008

Gas Dynamic Virtual Nozzle for Generation of Microscopic Droplet Streams

As shown by Ganan-Calvo and co-workers, a free liquid jet can be compressed in iameter through gas-dynamic forces exerted by a co-flowing gas, obviating the need for a solid nozzle to form a microscopic liquid jet and thereby alleviating the clogging problems that plague conventional droplet sources of small diameter. We describe in this paper a novel form of droplet beam source based on this principle. The source is miniature, robust, dependable, easily fabricated, and eminently suitable for delivery of microscopic liquid droplets, including hydrated biological samples, into vacuum for analysis using vacuum instrumentation. Monodisperse, single file droplet streams are generated by triggering the device with a piezoelectric actuator. The device is essentially immune to clogging.

physics.bio-ph↗

arXiv2007

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

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 molecular and X-ray fluxes and molecular alignment. 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 an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and 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 0.7 nm should be possible with short exposures.

physics.optics↗

arXiv2007

Droplet beams for serial crystallography of proteins

Serial diffraction of proteins requires an injection method to deliver protein molecules - preferably uncharged, fully hydrated, spatially oriented, and with high flux - into the crossed beams of an alignment laser and a focused probe beam of electrons or X-rays of typically only a few tens of microns diameter. The aim of this work has been to examine several potential droplet sources as to their suitability for this task. We compare Rayleigh droplet sources, electrospray sources, nebulizers and aerojet-focused droplet sources using time-resolved optical images of the droplet beams. Shrinkage of droplets by evaporation as a means of removing most of the water surrounding the proteins is discussed. Experimental measurements of droplet size, conformation of proteins after passing through a Rayleigh jet, and triboelectric charging are presented and conclusions are drawn about the source configuration for serial diffraction. First experimental X-ray diffraction patterns from Rayleigh droplet beams doped with 100nm gold balls are shown.

physics.optics↗

arXiv2005

Progress in Three-Dimensional Coherent X-Ray Diffraction Imaging

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 (~10 nm resolution) three-dimensional image. Developments on the structural imaging of low density aerogel samples are discussed.

physics.optics↗

arXiv2005

Phase Aberrations in Diffraction Microscopy

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.

physics.optics↗

arXiv2005

High-resolution ab initio three-dimensional X-ray diffraction microscopy

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.

physics.optics↗

arXiv2004

Use of extended and prepared reference objects in experimental Fourier transform X-ray holography

The use of one or more gold nanoballs as reference objects for Fourier Transform holography (FTH) is analysed using experimental soft X-ray diffraction from objects consisting of separated clusters of these balls. The holograms are deconvoluted against ball reference objects to invert to images, in combination with a Wiener filter to control noise. A resolution of ~30nm, smaller than one ball, is obtained even if a large cluster of balls is used as the reference, giving the best resolution yet obtained by X-ray FTH. Methods of dealing with missing data due to a beamstop are discussed. Practical prepared objects which satisfy the FTH condition are suggested, and methods of forming them described.

physics.optics↗

arXiv2004

Phasing diffuse scattering. Application of the SIR2002 algorithm to the non-crystallographic phase problem

A new phasing algorithm has been used to determine the phases of diffuse elastic X-ray scattering from a non-periodic array of gold balls of 50 nm diameter. Two-dimensional real-space images, showing the charge-density distribution of the balls, have been reconstructed at 50 nm resolution from transmission diffraction patterns recorded at 550 eV energy. The reconstructed image fits well with scanning electron microscope (SEM) image of the same sample. The algorithm, which uses only the density modification portion of the SIR2002 program, is compared with the results obtained via the Gerchberg-Saxton-Fienup HIO algorithm. In this way the relationship between density modification in crystallography and the HiO algorithm used in signal and image processing is elucidated.

physics.optics↗

arXiv2004

SPEDEN: Reconstructing single particles from their diffraction patterns

Speden is a computer program that reconstructs the electron density of single particles from their x-ray diffraction patterns, using a single-particle adaptation of the Holographic Method in crystallography. (Szoke, A., Szoke, H., and Somoza, J.R., 1997. Acta Cryst. A53, 291-313.) The method, like its parent, is unique that it does not rely on ``back'' transformation from the diffraction pattern into real space and on interpolation within measured data. It is designed to deal successfully with sparse, irregular, incomplete and noisy data. It is also designed to use prior information for ensuring sensible results and for reliable convergence. This article describes the theoretical basis for the reconstruction algorithm, its implementation and quantitative results of tests on synthetic and experimentally obtained data. The program could be used for determining the structure of radiation tolerant samples and, eventually, of large biological molecular structures without the need for crystallization.

physics.optics↗

arXiv2003

X-ray image reconstruction from a diffraction pattern alone

A solution to the inversion problem of scattering would offer aberration-free diffraction-limited 3D images without the resolution and depth-of-field limitations of lens-based tomographic systems. Powerful algorithms are increasingly being used to act as lenses to form such images. Current image reconstruction methods, however, require the knowledge of the shape of the object and the low spatial frequencies unavoidably lost in experiments. Diffractive imaging has thus previously been used to increase the resolution of images obtained by other means. We demonstrate experimentally here a new inversion method, which reconstructs the image of the object without the need for any such prior knowledge.

physics.optics↗

arXiv2003

Coherent X-ray Diffractive Imaging; applications and limitations

The inversion of a diffraction pattern offers aberration-free diffraction-limited 3D images without the resolution and depth-of-field limitations of lens-based tomographic systems, the only limitation being radiation damage. We review our experimental results, discuss the fundamental limits of this technique and future plans.

physics.optics↗