Crystal Mounting Research Articles

Streamlined In Situ X-ray Crystallography of Gas Sorption State as Realized through the De Novo Development of a Novel Crystal Mount

Streamlined In Situ X-ray Crystallography of Gas Sorption State as Realized through the De Novo Development of a Novel Crystal Mount

Rapid Prototyping for Nanoparticle-Based Photonic Crystal Fiber Sensors.

The advent of nanotechnology has motivated a revolution in the development of miniaturized sensors. Such sensors can be used for radiation detection, temperature sensing, radio-frequency sensing, strain sensing, and more. At the nanoscale, integrating the materials of interest into sensing platforms can be a common issue. One promising platform is photonic crystal fibers, which can draw in optically sensitive nanoparticles or have its optical properties changed by specialized nanomaterials. However, testing these sensors at scale is limited by the the need for specialized equipment to integrate these photonic crystal fibers into optical fiber systems. Having a method to enable rapid prototyping of new nanoparticle-based sensors in photonic crystal fibers would open up the field to a wider range of laboratories that could not have initially studied these materials in such a way before. This manuscript discusses the improved processes for cleaving, drawing, and rapidly integrating nanoparticle-based photonic crystal fibers into optical system setups. The method proposed in this manuscript achieved the following innovations: cleaving at a quality needed for nanoparticle integration could be done more reliably (≈100% acceptable cleaving yield versus ≈50% conventionally), nanoparticles could be drawn at scale through photonic crystal fibers in a safe manner (a method to draw multiple photonic crystal fibers at scale versus one fiber at a time), and the new photonic crystal fiber mount was able to be finely adjusted when increasing the optical coupling before inserting it into an optical system (before, expensive fusion splicing was the only other method).

Aluminum channeling in 4H-SiC by high-energy implantation above 10 MeV

This study explores high-energy aluminum (Al) implantation above 10MeV as a fabrication process to facilitate the creation of deep doping regions in silicon carbide (SiC). Experimental investigations were conducted to evaluate the technical feasibility of ultra-high energy implantation and high-energy channeling implantation of aluminum into 4H-SiC. Ultra-high-energy Al implantations at 30 and 48MeV were performed, revealing limitations such as increased charge dispersion and decreased current near accelerator technical limits. In contrast, high-energy channeling implantations at 12, 15, and 20MeV demonstrated successful Al channeling implantations into 4H-SiC, emphasizing the importance of precision in crystal orientation and mounting systems. Results indicate that channeling implantations, with precise instrumentation, are a preferred approach over non-channeled ultra-high-energy methods for fabricating deep doping regions in SiC, holding promise for advancing the next generation of high-voltage SiC devices.

Numerical simulation of flow and mass transfer during growth of the long seed KDP crystals under 2D translation method

A novel motion method, namely, the two-dimensional translation method (2D TM) had been proposed by our team to effectively utilize convection to enhance morphological stability and mass transfer. To evaluate this new method and apply it to the long seed KDP crystals growth, numerical simulations on the hydrodynamics and mass transfer involved in the growth of the long seed KDP crystals through this new method have been performed. Comparisons with the rotating crystal method (RCM) indicates that 2D TM improves the value and distribution homogeneity of the surface supersaturation. As the translational velocity increases, the value of the surface supersaturation on the prismatic faces increases. However, as the translational distance becomes long, there is a decrease in the value of the prismatic surface supersaturation, but the homogeneity of the surface supersaturation is improved. Moreover, the increase of the crystal size not only reduces the value of the surface supersaturation on the prismatic faces, but also degrades the homogeneity of the surface supersaturation. A further improvement in the magnitude and distribution homogeneity of the prismatic face supersaturation can be observed through modifying the crystal mounting method.

Comparative study on pump wavelength dependent efficiency in Nd:YVO4

The influence of the pump wavelength on the heat load and efficiency of Nd:YVO4 crystals is investigated with a specially designed crystal mount. The measurements indicate that the change in heat load in the crystal can be solely ascribed to the difference of quantum defects and no further non-radiative effects.

N2–O2 icing in single-crystal in-house X-ray diffraction experiments using an open-flow helium cryostat

This note reports a study of the coating of a crystal with `ice' at temperatures below 45 K during single-crystal in-house diffraction experiments when using an open-flow helium cryostat. The `ice' consists mainly of crystalline oxygen and nitrogen. This suggests completely different techniques for avoiding this type of icing compared with water icing. With appropriate choices of crystal mount, crystal position with respect to the nozzle and gas flow conditions, it is possible to avoid detectable condensation. However, sometimes this cannot be achieved in practice (poor diffraction from a smaller crystal, necessity of positioning the crystal in certain orientations to achieve desired data completeness, need to reduce helium consumption etc.). The problem of icing seems to be less common for powder experiments where the laminar gas flow is parallel to the capillary containing the sample, and for synchrotron experiments where the sample is comparatively small and almost continuously rotated, which facilitates the ice covering being removed by the gas flow. This last technique can in principle also be applied to single-crystal X-ray diffraction using laboratory diffractometers – periodic rapid rotation of the crystal can help to minimize any icing, but this technique will not work when the condensation rate is comparable to or faster than one frame of data collection. The coating around a sample crystal reduces the quality of the diffraction data, and the temperature at the sample below the coating may differ significantly from that at the cryostat nozzle reported by the instrument.

Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography

The serial crystallography (SX) technique enables the determination of the room-temperature structure of a macromolecule while causing minimal radiation damage, as well as the visualization of the molecular dynamics by time-resolved studies. The fixed-target (FT) scanning approach is one method for SX sample delivery that minimizes sample consumption and minimizes physical damage to crystals during data collection. Settling of the crystals on the sample holder in random orientation is important for complete three dimensional data collection. To increase the random orientation of crystals on the sample holder, we developed a polyimide mesh-based sample holder with irregular crystal mounting holes for FT-SX. The polyimide mesh was fabricated using a picosecond laser. Each hole in the polyimide mesh has irregularly shaped holes because of laser thermal damage, which may cause more crystals to settle at random orientations compared to regular shaped sample holders. A crystal sample was spread onto a polyimide-mesh, and a polyimide film was added to both sides to prevent dehydration. Using this sample holder, FT-SX was performed at synchrotron and determined the room-temperature lysozyme structure at 1.65 Å. The polyimide mesh with irregularly shaped holes will allow for expanded applications in sample delivery for FT-SX experiments.

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble.

EMBL Grenoble operates the High Throughput Crystallization Laboratory (HTX Lab), a large-scale user facility offering high throughput crystallography services to users worldwide. The HTX lab has a strong focus in the development of new methods in macromolecular crystallography. Through the combination of a high throughput crystallization platform, the CrystalDirect technology for fully automated crystal mounting and cryocooling and the CRIMS software we have developed fully automated pipelines for macromolecular crystallography that can be remotely operated over the internet. These include a protein-to-structure pipeline for the determination of new structures, a pipeline for the rapid characterization of protein-ligand complexes in support of medicinal chemistry, and a large-scale, automated fragment screening pipeline enabling evaluation of libraries of over 1000 fragments. Here we describe how to access and use these resources.

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble

EMBL Grenoble operates the High Throughput Crystallization Laboratory (HTX Lab), a large-scale user facility offering high throughput crystallography services to users worldwide. The HTX lab has a strong focus in the development of new methods in macromolecular crystallography. Through the combination of a high throughput crystallization platform, the CrystalDirect technology for fully automated crystal mounting and cryocooling and the CRIMS software we have developed fully automated pipelines for macromolecular crystallography that can be remotely operated over the internet. These include a protein-to-structure pipeline for the determination of new structures, a pipeline for the rapid characterization of protein-ligand complexes in support of medicinal chemistry, and a large-scale, automated fragment screening pipeline enabling evaluation of libraries of over 1000 fragments. Here we describe how to access and use these resources.

The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting.

Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100-240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures.

Neutron crystallography is a structural technique that allows determination of hydrogen atom positions within biological macromolecules, yielding mechanistically important information about protonation and hydration states while not inducing radiation damage. X-ray diffraction, in contrast, provides only limited information on the position of light atoms and the X-ray beamrapidly induces radiation damage of photosensitivecofactors and metal centers. Presented here is the workflow employed for the IMAGINE and MaNDi beamlines at Oak Ridge National Laboratory (ORNL) to obtain a neutron diffraction structure once a protein crystal of suitable size (> 0.1 mm3) has been grown. We demonstrate mounting of hydrogenated proteincrystals in quartz capillaries for neutron diffraction data collection. Also presented is the vapor exchange process of the mounted crystals with D2O-containing buffer to ensure replacement of hydrogen atoms at exchangeable sites with deuterium. The incorporation of deuterium reduces the background arising from the incoherent scattering of hydrogen atoms and prevents density cancellation caused by their negative coherent scattering length. Sample alignment and room temperature data collection strategies are illustrated using quasi-Laue data collection at IMAGINE at the High Flux Isotope Reactor (HFIR). Furthermore, crystal mounting and rapid freezing in liquid nitrogen for cryo-data collection to trap labile reaction intermediates is demonstrated at the MaNDi time-of-flight instrument at the Spallation Neutron Source (SNS). Preparation of the model coordinate and diffraction data files and visualization of the neutron scattering length density (SLD) maps will also be addressed. Structure refinement against neutron data-only or against joint X-ray/neutron data to obtain an all-atom structure of the protein of interest will finally be discussed. The process of determining a neutron structure will be demonstrated using crystals of the lytic polysaccharide monooxygenase Neurospora crassa LPMO9D, a copper-containing metalloprotein involved in the degradation of recalcitrant polysaccharides via oxidative cleavage of the glycosidic bond.

Technologies for tunable gamma-ray lenses

The tunable gamma-ray lens has turned out to be a promising alternative to the classical fixed-energy Laue-lenses discussed in the past. We describe here our development work on a miniature pedestal with one-axis tilt adjustment. We also outline our design for an optical system, capable of monitoring the alignment of the many crystals needed. An added benefit of the tunable crystal pedestal is that it relieves both the demands for high precision in the crystal mounting and the stringent requirements for long-term stability of the support platform on which the crystals are mounted. Moreover, mounting the individual crystals on separate pedestals facilitates the use of double layers of crystals. Keywords: Gamma-ray astronomy, Telescope technology, Laue lenses

A procedure and double-chambered device for macromolecular crystal flash-cooling in different cryogenic liquids.

Flash-cooling of macromolecular crystals for X-ray diffraction analysis is usually performed in liquid nitrogen (LN2). Cryogens different than LN2 are used as well for this procedure but are highly underrepresented, e.g., liquid propane and liquid ethane. These two cryogens have significantly higher cooling rates compared with LN2 and may thus be beneficial for flash-cooling of macromolecular crystals. Flash-cooling in liquid propane or liquid ethane results in sample vitrification but is accompanied by solidification of these cryogens, which is not compatible with the robotic systems nowadays used for crystal mounting at most synchrotrons. Here we provide a detailed description of a new double-chambered device and procedure to flash-cool loop mounted macromolecular crystals in different cryogenic liquids. The usage of this device may result in specimens of better crystal- and optical quality in terms of mosaic spread and ice contamination. Furthermore, applying the described procedure with the new double-chambered device provides the possibility to screen for the best flash-cooling cryogen for macromolecular crystals on a routine basis, and, most importantly, the samples obtained allow the usage of state-of-the-art robotic sample-loading systems at synchrotrons.

3D scanning and 3D printing AlSi10Mg single crystal mounts for neutron scattering

We present methods to quantify sample shapes and generate sample mounts as motivated by the needs of neutron scattering experiments. The 3D sample scanning was performed using photogrammetry and laser scanning, and a comparison is made between the two techniques. The aluminum alloy AlSi10Mg is shown to have favorable properties for many types of mounts used in neutron scattering. Parts were first prototyped with 3D plastic printers, and then, 3D AlSi10Mg prints were made. The final additively manufactured part holds the sample with more points of contact than is possible with traditional manufacturing. The goodness of fit between the mount and sample was measured by x-ray tomography.

Hybrid technology for the production of highly integrated multi-chip microcircuits: problems and solutions

Innovative technologies in the field of microelectronics provide technological transformation of the crystal and multichip microcircuit industry, combining various methods of crystal mounting and packaging processes. An increase in the integration of electronic circuits, an increase in the number of peripheral elements and, as a result, an increase in the energy consumption of the crystal, lead to a significant increase in the complexity of solving the problems of packaging when the case is converted into a complex electronic device.Chip crystals, according to current technological standards, are produced by a small number of specialized companies owned by transnational corporations. At the same time, in a number of countries there are qualified personnel specializing in the design of integrated circuits. One of the trends in the Russian market of multifunctional miniature devices is import substitution. A patent information search was conducted to identify trends and directions in the development of technologies in the field of packaging integrated circuits. A detailed analysis of the problem of the production of multi-chip microcircuits, systems in a package combining various packaging processes is shown; ways to solve it are shown, including applied research aimed at creating a hybrid multi-chip packaging technology combining crystals installed in a single package and on a single substrate using various methods installation - Wire bond and Flip chip.

Study on Carbon Particle Inclusions during 4H-SiC Growth by Using Physical Vapor Transport System

A study on carbon particle inclusions during 4H-SiC bulk growth is presented. Special attentions were paid to design of graphite growth compartment, size of SiC source materials, and process of seed crystal handling. It was found that common carbon inclusions with size of 30μm or less were attributed to carbon particles from graphitized SiC source. Less common carbon inclusions with size of over 100μm were also found and were attributed to poor seed crystal mounting process. In order to reduce carbon inclusions, several experiments were designed by using a NAURA Advanced Physical Vapor Transport (PVT) System APS130G. A graphite plate separator was inserted into the growth compartment to prevent the carbon particles from transporting to the growth surface. SiC powder materials with larger diameters were selected to reduce source graphitization. Additional clean process was performed to remove carbon particle residuals on graphite parts during seed mounting. The results showed significant improvement of carbon inclusion problems in SiC ingots and thus high-quality SiC wafers were made successfully.

Membrane-protein crystals for neutron diffraction.

Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1. The challenges encountered at the various steps in the process from crystal nucleation and growth to crystal mounting are explored, and it is demonstrated that NMX-compatible membrane-protein crystals can indeed be obtained.

The rise of neutron cryo-crystallography.

The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein crystallography offers the opportunity to significantly broaden the scope of biochemical problems that can be addressed, although care must be taken in assuming that direct extrapolation to room temperature is always valid. Here, the history to date of neutron protein cryo-crystallography and the particular problems and solutions associated with the mounting and cryocooling of the larger crystals needed for neutron crystallography are reviewed. Finally, the outlook for further cryogenic neutron studies using existing and future neutron instrumentation is discussed.

3D Printed Micrometer-Scale Polymer Mounts for Single Crystal Analysis.

3D printed micrometer-scale polymer mounts for single crystal analysis have been prepared by photopolymerization using digital light projection stereolithography (DLP-SLA), with a commercially available digital light projection stereolithography printer (US$4000) and 3DM-ABS resin (US$150 per liter). The polymer mounts were prepared in batches of 49 in 1 h 15 min, which allowed for rapid prototyping and testing of new crystal mounting designs, with a resin cost of 0.2¢ US per mount. The suitability of the 3D printed mounts for single crystal crystallography has been demonstrated through their use in Cu Kα X-ray diffraction experiments of Rochelle salt (sodium potassium tartrate), the protein lysozyme, and has been employed for routine crystallographic analysis of organic and inorganic materials.

Computational characterization of HPGe detectors usable for a wide variety of source geometries by using Monte Carlo simulation and a multi-objective evolutionary algorithm

In this work, we have developed a computational methodology for characterizing HPGe detectors by implementing in parallel a multi-objective evolutionary algorithm, together with a Monte Carlo simulation code. The evolutionary algorithm is used for searching the geometrical parameters of a model of detector by minimizing the differences between the efficiencies calculated by Monte Carlo simulation and two reference sets of Full Energy Peak Efficiencies (FEPEs) corresponding to two given sample geometries, a beaker of small diameter laid over the detector window and a beaker of large capacity which wrap the detector. This methodology is a generalization of a previously published work, which was limited to beakers placed over the window of the detector with a diameter equal or smaller than the crystal diameter, so that the crystal mount cap (which surround the lateral surface of the crystal), was not considered in the detector model. The generalization has been accomplished not only by including such a mount cap in the model, but also using multi-objective optimization instead of mono-objective, with the aim of building a model sufficiently accurate for a wider variety of beakers commonly used for the measurement of environmental samples by gamma spectrometry, like for instance, Marinellis, Petris, or any other beaker with a diameter larger than the crystal diameter, for which part of the detected radiation have to pass through the mount cap. The proposed methodology has been applied to an HPGe XtRa detector, providing a model of detector which has been successfully verificated for different source-detector geometries and materials and experimentally validated using CRMs.