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The Keck-PAD (pixel array detector) was developed at Cornell as a burst-rate imager capable of recording images from successive electron bunches (153â ns period) from the Advanced Photon Source (APS). Both Si and hole-collecting Schottky CdTe have been successfully bonded to this ASIC (application-specific integrated circuit) and used with this frame rate. The facility upgrades at the APS will lower the bunch period to 77â ns, which will require modifications to the Keck-PAD electronics to image properly at this reduced period. In addition, operation at high X-ray energies will require a different sensor material having a shorter charge collection time. For the target energy of 40â keV for this project, simulations have shown that electron-collecting CdTe should allow >90% charge collection within 35â ns. This collection time will be sufficient to sample the signal from one frame and prepare for the next. 750â µm-thick electron-collecting Schottky CdTe has been obtained from Acrorad and bonded to two different charge-integrating ASICs developed at Cornell, the Keck-PAD and the CU-APS-PAD. Carrier mobility has been investigated using the detector response to single X-ray bunches at the Cornell High Energy Synchrotron Source and to a pulsed optical laser. The tests indicate that the collection time will meet the requirements for 77â ns imaging.
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Precision and accuracy of quantitative scanning transmission electron microscopy (STEM) methods such as ptychography, and the mapping of electric, magnetic, and strain fields depend on the dose. Reasonable acquisition time requires high beam current and the ability to quantitatively detect both large and minute changes in signal. A new hybrid pixel array detector (PAD), the second-generation Electron Microscope Pixel Array Detector (EMPAD-G2), addresses this challenge by advancing the technology of a previous generation PAD, the EMPAD. The EMPAD-G2 images continuously at a frame-rates up to 10 kHz with a dynamic range that spans from low-noise detection of single electrons to electron beam currents exceeding 180 pA per pixel, even at electron energies of 300 keV. The EMPAD-G2 enables rapid collection of high-quality STEM data that simultaneously contain full diffraction information from unsaturated bright-field disks to usable Kikuchi bands and higher-order Laue zones. Test results from 80 to 300 keV are presented, as are first experimental results demonstrating ptychographic reconstructions, strain and polarization maps. We introduce a new information metric, the maximum usable imaging speed (MUIS), to identify when a detector becomes electron-starved, saturated or its pixel count is mismatched with the beam current.
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Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14â keV is described, providing a q range of 0.01 < q < 0.7â Å-1, pressures of 0-400â MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
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In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand-maximize-compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1â Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
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Aberration-corrected optics have made electron microscopy at atomic resolution a widespread and often essential tool for characterizing nanoscale structures. Image resolution has traditionally been improved by increasing the numerical aperture of the lens (α) and the beam energy, with the state-of-the-art at 300 kiloelectronvolts just entering the deep sub-ångström (that is, less than 0.5 ångström) regime. Two-dimensional (2D) materials are imaged at lower beam energies to avoid displacement damage from large momenta transfers, limiting spatial resolution to about 1 ångström. Here, by combining an electron microscope pixel-array detector with the dynamic range necessary to record the complete distribution of transmitted electrons and full-field ptychography to recover phase information from the full phase space, we increase the spatial resolution well beyond the traditional numerical-aperture-limited resolution. At a beam energy of 80 kiloelectronvolts, our ptychographic reconstruction improves the image contrast of single-atom defects in MoS2 substantially, reaching an information limit close to 5α, which corresponds to an Abbe diffraction-limited resolution of 0.39 ångström, at the electron dose and imaging conditions for which conventional imaging methods reach only 0.98 ångström.
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Next-generation, atomically thin devices require in-plane, one-dimensional heterojunctions to electrically connect different two-dimensional (2D) materials. However, the lattice mismatch between most 2D materials leads to unavoidable strain, dislocations, or ripples, which can strongly affect their mechanical, optical, and electronic properties. We have developed an approach to map 2D heterojunction lattice and strain profiles with subpicometer precision and the ability to identify dislocations and out-of-plane ripples. We collected diffraction patterns from a focused electron beam for each real-space scan position with a high-speed, high dynamic range, momentum-resolved detector-the electron microscope pixel array detector (EMPAD). The resulting four-dimensional (4D) phase space data sets contain the full spatially resolved lattice information on the sample. By using this technique on tungsten disulfide (WS2) and tungsten diselenide (WSe2) lateral heterostructures, we have mapped lattice distortions with 0.3 pm precision across multimicron fields of view and simultaneously observed the dislocations and ripples responsible for strain relaxation in 2D laterally epitaxial structures.
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[This corrects the article DOI: 10.1107/S1600576717006537.].
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Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such 'sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand-maximize-compress; Loh & Elser (2009). Phys. Rev. E, 80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.
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X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so 'sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only â¼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are sparse.
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A wide-dynamic-range imaging X-ray detector designed for recording successive frames at rates up to 10â MHz is described. X-ray imaging with frame rates of up to 6.5â MHz have been experimentally verified. The pixel design allows for up to 8-12 frames to be stored internally at high speed before readout, which occurs at a 1â kHz frame rate. An additional mode of operation allows the integration capacitors to be re-addressed repeatedly before readout which can enhance the signal-to-noise ratio of cyclical processes. This detector, along with modern storage ring sources which provide short (10-100â ps) and intense X-ray pulses at megahertz rates, opens new avenues for the study of rapid structural changes in materials. The detector consists of hybridized modules, each of which is comprised of a 500â µm-thick silicon X-ray sensor solder bump-bonded, pixel by pixel, to an application-specific integrated circuit. The format of each module is 128 × 128â pixels with a pixel pitch of 150â µm. In the prototype detector described here, the three-side buttable modules are tiled in a 3 × 2 array with a full format of 256 × 384â pixels. The characteristics, operation, testing and application of the detector are detailed.
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SincrotronesRESUMEN
We describe a hybrid pixel array detector (electron microscope pixel array detector, or EMPAD) adapted for use in electron microscope applications, especially as a universal detector for scanning transmission electron microscopy. The 128×128 pixel detector consists of a 500 µm thick silicon diode array bump-bonded pixel-by-pixel to an application-specific integrated circuit. The in-pixel circuitry provides a 1,000,000:1 dynamic range within a single frame, allowing the direct electron beam to be imaged while still maintaining single electron sensitivity. A 1.1 kHz framing rate enables rapid data collection and minimizes sample drift distortions while scanning. By capturing the entire unsaturated diffraction pattern in scanning mode, one can simultaneously capture bright field, dark field, and phase contrast information, as well as being able to analyze the full scattering distribution, allowing true center of mass imaging. The scattering is recorded on an absolute scale, so that information such as local sample thickness can be directly determined. This paper describes the detector architecture, data acquisition system, and preliminary results from experiments with 80-200 keV electron beams.
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Procesamiento de Imagen Asistido por Computador/métodos , Microscopía Electrónica de Transmisión de Rastreo/instrumentación , Microscopía Electrónica de Transmisión de Rastreo/métodos , Imagen Óptica/instrumentación , Imagen Óptica/métodosRESUMEN
Observation of theorized glass-to-liquid transitions between low-density amorphous (LDA) and high-density amorphous (HDA) water states had been stymied by rapid crystallization below the homogeneous water nucleation temperature (â¼235 K at 0.1 MPa). We report optical and X-ray observations suggestive of glass-to-liquid transitions in these states. Crack healing, indicative of liquid, occurs when LDA ice transforms to cubic ice at 160 K, and when HDA ice transforms to the LDA state at temperatures as low as 120 K. X-ray diffraction study of the HDA to LDA transition clearly shows the characteristics of a first-order transition. Study of the glass-to-liquid transitions in nanoconfined aqueous solutions shows them to be independent of the solute concentrations, suggesting that they represent an intrinsic property of water. These findings support theories that LDA and HDA ice are thermodynamically distinct and that they are continuously connected to two different liquid states of water.
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Vidrio , Soluciones/química , Agua/química , Cristalización , Hielo/análisis , Cinética , Modelos Teóricos , Óptica y Fotónica , Transición de Fase , Presión , Temperatura , Termodinámica , Difracción de Rayos XRESUMEN
X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. The EMC algorithm [Loh & Elser (2009 â¶), Phys. Rev. E, 80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philipp et al. (2012 â¶), Opt. Express, 20, 13129-13137; Ayyer et al. (2014 â¶), Opt. Express, 22, 2403-2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35â kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.
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Coherent (X-ray) diffractive imaging (CDI) is an increasingly popular form of X-ray microscopy, mainly due to its potential to produce high-resolution images and the lack of an objective lens between the sample and its corresponding imaging detector. One challenge, however, is that very high dynamic range diffraction data must be collected to produce both quantitative and high-resolution images. In this work, hard X-ray ptychographic coherent diffractive imaging has been performed at the P10 beamline of the PETRAâ III synchrotron to demonstrate the potential of a very wide dynamic range imaging X-ray detector (the Mixed-Mode Pixel Array Detector, or MM-PAD). The detector is capable of single photon detection, detecting fluxes exceeding 1 × 10(8) 8-keV photons pixel(-1) s(-1), and framing at 1â kHz. A ptychographic reconstruction was performed using a peak focal intensity on the order of 1 × 10(10)â photons µm(-2) s(-1) within an area of approximately 325â nm × 603â nm. This was done without need of a beam stop and with a very modest attenuation, while `still' images of the empty beam far-field intensity were recorded without any attenuation. The treatment of the detector frames and CDI methodology for reconstruction of non-sensitive detector regions, partially also extending the active detector area, are described.
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Aumento de la Imagen/métodos , Imagen Óptica/métodos , Difracción de Rayos X/métodos , Aumento de la Imagen/instrumentación , Imagen Óptica/instrumentación , Sincrotrones , Difracción de Rayos X/instrumentaciónRESUMEN
Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each with a random and unknown orientation. Due to the small size of the molecules and short exposure times, average signal levels of much less than 1 photon/pixel/frame are expected, much too low to be processed using standard methods. One approach to process the data is to use statistical methods developed in the EMC algorithm (Loh & Elser, Phys. Rev. E, 2009) which processes the data set as a whole. In this paper we apply this method to a real-space tomographic reconstruction using sparse frames of data (below 10(-2) photons/pixel/frame) obtained by performing x-ray transmission measurements of a low-contrast, randomly-oriented object. This extends the work by Philipp et al. (Optics Express, 2012) to three dimensions and is one step closer to the single molecule reconstruction problem.
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Algoritmos , Imagenología Tridimensional/métodos , Proteínas/química , Proteínas/ultraestructura , Interpretación de Imagen Radiográfica Asistida por Computador/métodos , Tomografía Computarizada por Rayos X/métodos , Difracción de Rayos X/métodos , Interpretación Estadística de Datos , Conformación ProteicaRESUMEN
The fabrication and testing of a prototype deep-depletion direct-conversion X-ray CCD detector are described. The device is fabricated on 600â µm-thick high-resistivity silicon, with 24â ×â 24â µm pixels in a 4kâ ×â 4k pixel format. Calibration measurements and the results of initial protein crystallography experiments at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline are described, as well as suggested improvements for future versions of the detector.
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Single-particle imaging experiments of biomolecules at x-ray free-electron lasers (XFELs) require processing hundreds of thousands of images that contain very few x-rays. Each low-fluence image of the diffraction pattern is produced by a single, randomly oriented particle, such as a protein. We demonstrate the feasibility of recovering structural information at these extremes using low-fluence images of a randomly oriented 2D x-ray mask. Successful reconstruction is obtained with images averaging only 2.5 photons per frame, where it seems doubtful there could be information about the state of rotation, let alone the image contrast. This is accomplished with an expectation maximization algorithm that processes the low-fluence data in aggregate, and without any prior knowledge of the object or its orientation. The versatility of the method promises, more generally, to redefine what measurement scenarios can provide useful signal.
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Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
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Cristalografía por Rayos X/métodos , Conformación Proteica , Animales , Rayos Láser , Muramidasa/química , Muramidasa/efectos de la radiaciónRESUMEN
The production of high-performance carbon nanotube (CNT) materials demands understanding of the growth behavior of individual CNTs as well as collective effects among CNTs. We demonstrate the first use of grazing incidence small-angle X-ray scattering to monitor in real time the synthesis of CNT films by chemical vapor deposition. We use a custom-built cold-wall reactor along with a high-speed pixel array detector resulting in a time resolution of 10 msec. Quantitative models applied to time-resolved X-ray scattering patterns reveal that the Fe catalyst film first rapidly dewets into well-defined hemispherical particles during heating in a reducing atmosphere, and then the particles coarsen slowly upon continued annealing. After introduction of the carbon source, the initial CNT diameter distribution closely matches that of the catalyst particles. However, significant changes in CNT diameter can occur quickly during the subsequent CNT self-organization process. Correlation of time-resolved orientation data to X-ray scattering intensity and height kinetics suggests that the rate of self-organization is driven by both the CNT growth rate and density, and vertical CNT growth begins abruptly when CNT alignment reaches a critical threshold. The dynamics of CNT size evolution and self-organization vary according to the catalyst annealing conditions and substrate temperature. Knowledge of these intrinsically rapid processes is vital to improve control of CNT structure and to enable efficient manufacturing of high-density arrays of long, straight CNTs.
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Membranas Artificiales , Nanopartículas/química , Nanopartículas/ultraestructura , Cristalización/métodos , Sustancias Macromoleculares/química , Sustancias Macromoleculares/efectos de la radiación , Ensayo de Materiales , Conformación Molecular/efectos de la radiación , Nanopartículas/efectos de la radiación , Tamaño de la Partícula , Propiedades de Superficie/efectos de la radiación , Rayos XRESUMEN
BACKGROUND: In the cellular environment, macromolecules occupy about 30% of a cell's volume. In this crowded environment, proteins behave very differently than in dilute solution where scientists typically study the properties of proteins. For this reason, recent studies have investigated proteins in cell-like crowded conditions so as to understand if this changes their properties. The present study was performed to examine if molecular crowding impedes the protein unfolding process that is known to occur upon the application of high pressure. METHODS: Crowding of staphylococcal nuclease (SNase) was induced by dissolving low concentrations of SNase in high concentrations of crowding agents (16 wt.% or 25 wt.% PEG 3000 or 16 wt.% Dextran T10). SNase unfolding was then monitored via tryptophan fluorescence as pressure was applied. RESULTS: Fluorescence spectra can be decomposed into the sum of two components indicative, respectively, of native and unfolded states, and the center of spectral mass was then used as a measure of the degree of protein unfolding. It was found that SNase unfolding as a function of pressure was impeded in crowded solutions. These results suggest that crowded environments, such as those found in the cellular cytoplasm, may also impede high-pressure protein unfolding in cells. GENERAL SIGNIFICANCE: This is the first report on the effect of crowding on the pressure-induced unfolding of a protein (staphylococcal nuclease) monitored via tryptophan fluorescence.