Microcrystallography using single-bounce monocapillary optics.
ABSTRACT: X-ray microbeams have become increasingly valuable in protein crystallography. A number of synchrotron beamlines worldwide have adapted to handling smaller and more challenging samples by providing a combination of high-precision sample-positioning hardware, special visible-light optics for sample visualization, and small-diameter X-ray beams with low background scatter. Most commonly, X-ray microbeams with diameters ranging from 50 microm to 1 microm are produced by Kirkpatrick and Baez mirrors in combination with defining apertures and scatter guards. A simple alternative based on single-bounce glass monocapillary X-ray optics is presented. The basic capillary design considerations are discussed and a practical and robust implementation that capitalizes on existing beamline hardware is presented. A design for mounting the capillary is presented which eliminates parasitic scattering and reduces deformations of the optic to a degree suitable for use on next-generation X-ray sources. Comparison of diffraction data statistics for microcrystals using microbeam and conventional aperture-collimated beam shows that capillary-focused beam can deliver significant improvement. Statistics also confirm that the annular beam profile produced by the capillary optic does not impact data quality in an observable way. Examples are given of new structures recently solved using this technology. Single-bounce monocapillary optics can offer an attractive alternative for retrofitting existing beamlines for microcrystallography.
Project description:Here a direct comparison is made between various X-ray wavefront sensing methods with application to optics alignment and focus characterization at X-ray free-electron lasers (XFELs). Focus optimization at XFEL beamlines presents unique challenges due to high peak powers as well as beam pointing instability, meaning that techniques capable of single-shot measurement and that probe the wavefront at an out-of-focus location are desirable. The techniques chosen for the comparison include single-phase-grating Talbot interferometry (shearing interferometry), dual-grating Talbot interferometry (moiré deflectometry) and speckle tracking. All three methods were implemented during a single beam time at the Linac Coherent Light Source, at the X-ray Pump Probe beamline, in order to make a direct comparison. Each method was used to characterize the wavefront resulting from a stack of beryllium compound refractive lenses followed by a corrective phase plate. In addition, difference wavefront measurements with and without the phase plate agreed with its design to within ?/20, which enabled a direct quantitative comparison between methods. Finally, a path toward automated alignment at XFEL beamlines using a wavefront sensor to close the loop is presented.
Project description:With the rise in popularity of biological small-angle X-ray scattering (BioSAXS) measurements, synchrotron beamlines are confronted with an ever-increasing number of samples from a wide range of solution conditions. To meet these demands, an increasing number of beamlines worldwide have begun to provide automated liquid-handling systems for sample loading. This article presents an automated sample-loading system for BioSAXS beamlines, which combines single-channel disposable-tip pipetting with a vacuum-enclosed temperature-controlled capillary flow cell. The design incorporates an easily changeable capillary to reduce the incidence of X-ray window fouling and cross contamination. Both the robot-control and the data-processing systems are written in Python. The data-processing code, RAW, has been enhanced with several new features to form a user-friendly BioSAXS pipeline for the robot. The flow cell also supports efficient manual loading and sample recovery. An effective rinse protocol for the sample cell is developed and tested. Fluid dynamics within the sample capillary reveals a vortex ring pattern of circulation that redistributes radiation-damaged material. Radiation damage is most severe in the boundary layer near the capillary surface. At typical flow speeds, capillaries below 2?mm in diameter are beginning to enter the Stokes (creeping flow) regime in which mixing due to oscillation is limited. Analysis within this regime shows that single-pass exposure and multiple-pass exposure of a sample plug are functionally the same with regard to exposed volume when plug motion reversal is slow. The robot was tested on three different beamlines at the Cornell High-Energy Synchrotron Source, with a variety of detectors and beam characteristics, and it has been used successfully in several published studies as well as in two introductory short courses on basic BioSAXS methods.
Project description:Megavoltage photon beams are typically used for therapy because of their skin-sparing effect. However, a focused low-energy x-ray beam would also be skin sparing, and would have a higher dose concentration at the focal spot. Such a beam can be produced with polycapillary optics. MCNP5 was used to model dose profiles for a scanned focused beam, using measured beam parameters. The potential of low energy focused x-ray beams for radiation therapy was assessed.A polycapillary optic was used to focus the x-ray beam from a tungsten source. The optic was characterized and measurements were performed at 50 kV. PMMA blocks of varying thicknesses were placed between optic and the focal spot to observe any variation in the focusing of the beam after passing through the tissue-equivalent material. The measured energy spectrum was used to model the focused beam in MCNP5. A source card (SDEF) in MCNP5 was used to simulate the converging x-ray beam. Dose calculations were performed inside a breast tissue phantom.The measured focal spot size for the polycapillary optic was 0.2 mm with a depth of field of 5 mm. The measured focal spot remained unchanged through 40 mm of phantom thickness. The calculated depth dose curve inside the breast tissue showed a dose peak several centimeters below the skin with a sharp dose fall off around the focus. The percent dose falls below 10% within 5 mm of the focus. It was shown that rotating the optic during scanning would preserve the skin-sparing effect of the focused beam.Low energy focused x-ray beams could be used to irradiate tumors inside soft tissue within 5 cm of the surface.
Project description:The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B(4)C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.
Project description:We demonstrate that emission of coherent transition radiation by a ?1?GeV energy-electron beam passing through an Al foil is enhanced in intensity and extended in frequency spectral range, by the energy correlation established along the beam by coherent synchrotron radiation wakefield, in the presence of a proper electron optics in the beam delivery system. Analytical and numerical models, based on experimental electron beam parameters collected at the FERMI free electron laser (FEL), predict transition radiation with two intensity peaks at ?0.3?THz and ?1.5?THz, and extending up to 8.5?THz with intensity above 20?dB w.r.t. the main peak. Up to 80-µJ pulse energy integrated over the full bandwidth is expected at the source, and in agreement with experimental pulse energy measurements. By virtue of its implementation in an FEL beam dump line, this work promises dissemination of user-oriented multi-THz beamlines parasitic and self-synchronized to EUV and x-ray FELs.
Project description:Microbeam radiation therapy is a novel pre-clinical external beam therapy that uses high-brilliance synchrotron X-rays to deliver the necessary high dose rates. The unique conditions of high dose rate and high spatial fractionation demand a new class of detector to experimentally measure important beam quality parameters. Here we demonstrate the highest spatial resolution plastic scintillator fibre-optic dosimeter found in the literature to date and tested it on the Imaging and Medical Beam-Line at the Australian Synchrotron in a X-ray beam where the irradiation dose rate was 4435?Gy/s. With a one-dimensional spatial resolution of 10??m the detector is able to resolve the individual microbeams (53.7?±?0.4??m wide), and measure the peak-to-valley dose ratio to be 55?±?17. We also investigate the role of radioluminescence in the optical fibre used to transport the scintillation photons, and conclude that it creates a significant contribution to the total light detected.
Project description:The emergence of hard X-ray free electron lasers (XFELs) enables new insights into many fields of science. These new sources provide short, highly intense, and coherent X-ray pulses. In a variety of scientific applications these pulses need to be strongly focused. In this article, we demonstrate focusing of hard X-ray FEL pulses to 125 nm using refractive x-ray optics. For a quantitative analysis of most experiments, the wave field or at least the intensity distribution illuminating the sample is needed. We report on the full characterization of a nanofocused XFEL beam by ptychographic imaging, giving access to the complex wave field in the nanofocus. From these data, we obtain the full caustic of the beam, identify the aberrations of the optic, and determine the wave field for individual pulses. This information is for example crucial for high-resolution imaging, creating matter in extreme conditions, and nonlinear x-ray optics.
Project description:The method of X-ray footprinting and mass spectrometry (XFMS) on large protein assemblies and membrane protein samples requires high flux density to overcome the hydroxyl radical scavenging reactions produced by the buffer constituents and the total protein content. Previously, we successfully developed microsecond XFMS using microfluidic capillary flow and a microfocused broadband X-ray source at the Advanced Light Source synchrotron beamlines, but the excessive radiation damage incurred when using capillaries prevented the full usage of a high-flux density beam. Here we present another significant advance for the XFMS method: the instrumentation of a liquid injection jet to deliver container free samples to the X-ray beam. Our preliminary experiments with a liquid jet at a bending magnet X-ray beamline demonstrate the feasibility of the approach and show a significant improvement in the effective dose for both the Alexa fluorescence assay and protein samples compared to conventional capillary flow methods. The combination of precisely controlled high dose delivery, shorter exposure times, and elimination of radiation damage due to capillary effects significantly increases the signal quality of the hydroxyl radical modification products and the dose-response data. This new approach is the first application of container free sample handling for XFMS and opens up the method for even further advances, such as high-quality microsecond time-resolved XFMS studies.
Project description:A double-crystal diamond (111) monochromator recently implemented at the Linac Coherent Light Source (LCLS) enables splitting of the primary X-ray beam into a pink (transmitted) and a monochromatic (reflected) branch. The first monochromator crystal, with a thickness of ?100?µm, provides sufficient X-ray transmittance to enable simultaneous operation of two beamlines. This article reports the design, fabrication and X-ray characterization of the first and second (300?µm-thick) crystals utilized in the monochromator and the optical assemblies holding these crystals. Each crystal plate has a region of about 5 × 2?mm with low defect concentration, sufficient for use in X-ray optics at the LCLS. The optical assemblies holding the crystals were designed to provide mounting on a rigid substrate and to minimize mounting-induced crystal strain. The induced strain was evaluated using double-crystal X-ray topography and was found to be small over the 5 × 2?mm working regions of the crystals.
Project description:The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick-Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.