Publications by authors named "Richard J Bean"

10 Publications

  • Page 1 of 1

The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation.

J Synchrotron Radiat 2019 May 12;26(Pt 3):660-676. Epub 2019 Apr 12.

European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany.

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.
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http://dx.doi.org/10.1107/S1600577519003308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510195PMC
May 2019

Analysis of XFEL serial diffraction data from individual crystalline fibrils.

IUCrJ 2017 Nov 20;4(Pt 6):795-811. Epub 2017 Oct 20.

Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.

Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.
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http://dx.doi.org/10.1107/S2052252517014324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668865PMC
November 2017

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source.

Sci Data 2016 08 1;3:160064. Epub 2016 Aug 1.

Arizona State University, School of Molecular Sciences (SMS), Tempe, Arizona 85287-1604, USA.

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.
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http://dx.doi.org/10.1038/sdata.2016.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968191PMC
August 2016

High numerical aperture multilayer Laue lenses.

Sci Rep 2015 Jun 1;5:9892. Epub 2015 Jun 1.

Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.

The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilise their capability for imaging and probing biological cells, nanodevices, and functional matter on the nanometer scale with chemical sensitivity. Here we demonstrate focusing a hard X-ray beam to an 8 nm focus using a volume zone plate (also referred to as a wedged multilayer Laue lens). This lens was constructed using a new deposition technique that enabled the independent control of the angle and thickness of diffracting layers to microradian and nanometer precision, respectively. This ensured that the Bragg condition is satisfied at each point along the lens, leading to a high numerical aperture that is limited only by its extent. We developed a phase-shifting interferometric method based on ptychography to characterise the lens focus. The precision of the fabrication and characterisation demonstrated here provides the path to efficient X-ray optics for imaging at 1 nm resolution.
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http://dx.doi.org/10.1038/srep09892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450759PMC
June 2015

Phasing coherently illuminated nanocrystals bounded by partial unit cells.

Philos Trans R Soc Lond B Biol Sci 2014 Jul;369(1647):20130331

Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany.

With the use of highly coherent femtosecond X-ray pulses from a free-electron laser, it is possible to record protein nanocrystal diffraction patterns with far more information than is present in conventional crystallographic diffraction data. It has been suggested that diffraction phases may be retrieved from such data via iterative algorithms, without the use of a priori information and without restrictions on resolution. Here, we investigate the extension of this approach to nanocrystals with edge terminations that produce partial unit cells, and hence cannot be described by a common repeating unit cell. In this situation, the phase problem described in previous work must be reformulated. We demonstrate an approximate solution to this phase problem for crystals with random edge terminations.
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http://dx.doi.org/10.1098/rstb.2013.0331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052867PMC
July 2014

Conformation sequence recovery of a non-periodic object from a diffraction-before-destruction experiment.

Opt Express 2014 Apr;22(7):8085-93

Knowledge of the sequence of different conformational states of a protein molecule is key to better understanding its biological function. A diffraction pattern from a single conformational state can be captured with an ultrafast X-ray Free-Electron Laser (XFEL) before the target is completely annihilated by the radiation. In this paper, we report the first experimental demonstration of conformation sequence recovery using diffraction patterns from randomly ordered conformations of a non-periodic object using the dimensional reduction technique Isomap and coherent diffraction imaging.
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http://dx.doi.org/10.1364/OE.22.008085DOI Listing
April 2014

Coherent x-ray imaging of collagen fibril distributions within intact tendons.

Biophys J 2014 Jan;106(2):459-66

London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell, Harwell Oxford Campus, Didcot, United Kingdom.

The characterization of the structure of highly hierarchical biosamples such as collagen-based tissues at the scale of tens of nanometers is essential to correlate the tissue structure with its growth processes. Coherent x-ray Bragg ptychography is an innovative imaging technique that gives high resolution images of the ordered parts of such samples. Herein, we report how we used this method to image the collagen fibrillar ultrastructure of intact rat tail tendons. The images show ordered fibrils extending over 10-20 μm in length, with a quantifiable D-banding spacing variation of 0.2%. Occasional defects in the fibrils distribution have also been observed, likely indicating fibrillar fusion events.
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http://dx.doi.org/10.1016/j.bpj.2013.12.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907247PMC
January 2014

Size-dependent shape and tilt transitions in In2O3 nanoislands grown on cubic Y-stabilized ZrO2(001) by molecular beam epitaxy.

ACS Nano 2012 Aug 9;6(8):6717-29. Epub 2012 Jul 9.

Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.

The growth of In(2)O(3) on cubic Y-stabilized ZrO(2)(001) by molecular beam epitaxy leads to formation of nanoscale islands which may tilt relative to the substrate in order to help accommodate the 1.7% tensile mismatch between the epilayer and the substrate. High-resolution synchrotron-based X-ray diffraction has been used in combination with atomic force microscopy to probe the evolution in island morphology, orientation, and tilt with island size. Very small islands formed at low substrate coverage are highly strained but exhibit no tilt, while intermediate islands are tilted randomly in all directions, giving rise to distinctive doughnut-shaped structure in three-dimensional reciprocal space isosurfaces. The largest islands with lateral sizes on the order of 1 μm tilt away from the four equivalent in-plane <110> directions, giving three-dimensional scattering isosurfaces dominated by structure at the four corners of a square. Spatially resolved reciprocal space mapping using an X-ray beam with dimensions on the order of 1 μm suggests that the four-fold symmetry observed using a larger beam arises from averaging over an ensemble of islands, each with an individual tilt down one direction, rather than from the coexistence of differently tilted domains within a given island.
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http://dx.doi.org/10.1021/nn301382jDOI Listing
August 2012

Coherent X-ray diffraction investigation of twinned microcrystals.

J Synchrotron Radiat 2010 Nov 8;17(6):751-60. Epub 2010 Oct 8.

Departamento de Química Inorgánica, Cristalografía y Mineralogía, Universidad de Málaga, 29071 Málaga, Spain.

Coherent X-ray diffraction has been used to study pseudo-merohedrally twinned manganite microcrystals. The analyzed compositions were Pr(5/8)Ca(3/8)MnO(3) and La(0.275)Pr(0.35)Ca(3/8)MnO(3). The prepared loose powder was thermally attached to glass (and quartz) capillary walls by gentle heating to ensure positional stability during data collection. Many diffraction data sets were recorded and some of them were split as expected from the main observed twin law: 180° rotation around [101]. The peak splitting was measured with very high precision owing to the high-resolution nature of the diffraction data, with a resolution (Δd/d) better than 2.0 × 10(-4). Furthermore, when these microcrystals are illuminated coherently, the different crystallographic phases of the structure factors induce interference in the form of a speckle pattern. The three-dimensional speckled Bragg peak intensity distribution has been measured providing information about the twin domains within the microcrystals. Research is ongoing to invert the measured patterns. Successful phase retrieval will allow mapping out the twin domains and twin boundaries which play a key role in the physical properties.
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http://dx.doi.org/10.1107/S0909049510039774DOI Listing
November 2010

Coherent X-ray diffraction from collagenous soft tissues.

Proc Natl Acad Sci U S A 2009 Sep 24;106(36):15297-301. Epub 2009 Aug 24.

London Centre for Nanotechnology (LCN), University College London (UCL), London WC1H 0AH, United Kingdom.

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60-70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the 'speckled' nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques.
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http://dx.doi.org/10.1073/pnas.0905151106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730963PMC
September 2009