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26 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Design of a robot-automated flat plate/reflection geometry x-ray diffraction setup for accelerated materials discovery and structural screening

Here, we report the design, construction, and automation of a flat plate sample loading, alignment, and data acquisition system for X-ray diffraction measurements in reflection geometry implemented at the Stanford Synchrotron Radiation Lightsource. The system is built onto a single platform, enabling facile transferability, and is compartmentalized into sample storage, sample transfer, and sample position/alignment segments. The core feature of this system is a six-axis robotic arm that offers a large range of highly reproducible and programable movements. The degrees of freedom of the robot arm enable adaptability in which movements can be modified to fit various beamline environments and sample configurations. Samples are housed on 3D printed sample mounts, which are arranged onto a 6 × 2 array of sample cassettes capable of holding 7 samples. Using sample mounts designed for solid oxide electrolysis button cells (SOECs), the maximum tray capacity is 84 samples, which can be aligned and run in ~ 24 hours with long exposure scans. The sample array is additionally capable of accommodating a range of sample sizes and geometries due to the rapid 3D printed fabrication. The components of the setup will be described in detail and performance will be demonstrated with a set of representative SOEC and XRD standard samples. Opportunities for future developments and integration with the automated setup are summarized.

08 HYDROGEN↗
NASA NTRS2006

Fluorescent Applications to Crystallization

By covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and tests with model proteins have shown that labeling u to 5 percent of the protein molecules does not affect the X-ray data quality obtained . The presence of the trace fluorescent label gives a number of advantages. Since the label is covalently attached to the protein molecules, it "tracks" the protein s response to the crystallization conditions. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a darker background. Non-protein structures, such as salt crystals, do not show up under fluorescent illumination. Crystals have the highest protein concentration and are readily observed against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. Preliminary tests, using model proteins, indicates that we can use high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that more rapid amorphous precipitation kinetics may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Experiments are now being carried out to test this approach using a wider range, of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.

Pusey, Marc L.↗
DOE OSTI2024

A general Bayesian algorithm for the autonomous alignment of beamlines

Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high-dimensional expensive-to-sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks. In this paper, we present a basic formulation of Bayesian inference and Gaussian process models as they relate to multi-objective Bayesian optimization, as well as the practical challenges presented by beamline alignment. We show that the same general implementation of Bayesian optimization with special consideration for beamline alignment can quickly learn the dynamics of particular beamlines in an online fashion through hyperparameter fitting with no prior information. We present the implementation of a concise software framework for beamline alignment and test it on four different optimization problems for experiments on X-ray beamlines at the National Synchrotron Light Source II and the Advanced Light Source, and an electron beam at the Accelerator Test Facility, along with benchmarking on a simulated digital twin. We discuss new applications of the framework, and the potential for a unified approach to beamline alignment at synchrotron facilities.

47 OTHER INSTRUMENTATION↗
NASA NTRS2006

Fluorescent Approaches to High Throughput Crystallography

We have shown that by covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and the presence of the probe at low concentrations does not affect the X-ray data quality or the crystallization behavior. The presence of the trace fluorescent label gives a number of advantages when used with high throughput crystallizations. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a dark background. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Brightly fluorescent crystals are readily found against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. We are now testing the use of high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that kinetics leading to non-structured phases may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Preliminary experiments with test proteins have resulted in the extraction of a number of crystallization conditions from screening outcomes based solely on the presence of bright fluorescent regions. Subsequent experiments will test this approach using a wider range of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.

Pusey, Marc L.↗
NASA NTRS2005

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, 51%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear hits. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Pusey, Marc L.↗
NASA NTRS2004

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically can not reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Pusey, Marc L.↗
NASA NTRS2004

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of a macromolecules purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals will show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "bits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Minamitani, Elizabeth Forsythe↗
NASA NTRS2006

NASA Tech Briefs, October 2006

Topics covered include: Protein Sensors Based on Optical Ring Resonators; Phase Sensor for Aligning a Segmented Telescope Mirror; Control Software for Advanced Video Guidance Sensor; Generating Control Commands From Gestures Sensed by EMG; Multiple-Flat-Panel System Displays Multidimensional Data; 3D X-Ray Luggage-Screening System; Probe Station and Near-Field Scanner for Testing Antennas; Photodetector Arrays for Multicolor Visible/Infrared Imaging; Semiconductor Bolometers Give Background-Limited Performance; Multichannel X-Band Dielectric-Resonator Oscillator; Automatic Alignment of Displacement-Measuring Interferometer; Earth Observing System Data Gateway; Power User Interface; Mercury Shopping Cart Interface; Cassini Archive Tracking System; Architecture Adaptive Computing Environment; Computing Fault Displacements from Surface Deformations; Oxygen-Permeable, Hydrophobic Membranes of Silanized alpha-Al2O3; SiC Composite Turbine Vanes; Retaining Device for the Interior Structure of a Spacecraft Payload; Tool for Torquing Circular Electrical-Connector Collars; System for Continuous Deaeration of Hydraulic Oil; Solar-Powered Cooler and Heater for an Automobile Interior; Improved Oxygen-Beam Texturing of Glucose-Monitoring Optics; Tool for Two Types of Friction Stir Welding; Stationary Apparatus Would Apply Forces of Walking to Feet; Instrument Would Detect and Collect Biological Aerosols; Boundary Condition for Modeling Semiconductor Nanostructures; Miniature Distillation Column for Producing LOX From Air; Even Illumination from Fiber-Optic-Coupled Laser Diodes; Optically Driven Deformable Mirrors; Algorithm for Automated Detection of Edges of Clouds; Exploiting Quantum Resonance to Solve Combinatorial Problems; Hybrid Terrain Database; On Release of Microbe-Laden Particles from Mars Landers; A Concept for Run-Time Support of the Chapel Language; Thermoelectric Inhomogeneities in (Ag(sub 1-y)SbTe2)(sub x)(PbTe)(sub 1-x); and Spacecraft Escape Capsule.

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