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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Pink-beam serial crystallography

Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, “pink”, beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Chemical crystallography by serial femtosecond X-ray diffraction

Abstract Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction 2,3 and electron microdiffraction 4–11 . Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation 12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach 14 , the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data 15–17 . We describe the ab initio structure solutions of mithrene (AgSePh) 18–20 , thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties 20 . We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs

Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT 1 R and CysLT 2 R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing. A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Elucidating metal–organic framework structures using synchrotron serial crystallography

Metal organic frameworks (MOFs) are porous crystalline materials that display a wide variety of physical and chemical properties. Their single crystal structure determination is often challenging because in most cases micro- or nano-sized crystals spontaneously form upon MOF synthesis, which cannot be recrystallized. The production of larger single crystals for structure determination involves optimizing, and thus modifying, the conditions of synthesis, in which success cannot be guaranteed. Failure to produce crystals suitable for single-crystal X-ray diffraction leaves the 3D structure of the MOF compound unknown, and scientists must resort to more challenging structure solution methods based on X-ray powder or electron diffraction data. These laborious tasks can be avoided by using serial crystallography techniques which merge data collected on many micro-crystals. Here, we report the application of three synchrotron serial crystallography methods. We call these “mesh”, “grid” and “mesh&collect” scans. “Still” images (no rotation) are collected in the mesh scan approach, whereas small rotational wedges are collected in the grid scan method. The third protocol, mesh&collect, combines the acquisition of still images and rotational wedges. Using these means, we determine the ab initio structure of benchmark MOFs, MIL-100(Fe) and ZIF-8, that differ largely in unit cell size. These methods are expected to be widely applicable and facilitate structure determination of many MOF microcrystalline systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals

The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.

Lahey-Rudolph, J. Mia (ORCID:0000000152797267)↗
DOE OSTI2018

Improving signal strength in serial crystallography with DIALS geometry refinement

The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A 24-Channel Digitizer With a JESD204B-Compliant Serial Interface for High-Speed Detectors

In this report a 24-channel application-specific integrated circuit (ASIC) for the readout of high-speed CMOS active pixel sensors for charged particle detection is presented. The chip comprises 24 preamplifiers, 24 distinct 12-bit, 25 MSPS Pipelined analog-to-digital converters (ADCs) with self-calibration, an internal phase-locked loop (PLL), and a 3 Gbps serial interface that conforms to the JESD204B standard. To simplify interfacing with a variety of sensors, the ASIC also includes an automatic offset calibration loop. The high level of integration of the ASIC reduces overall system cost and area, and exploiting the signal characteristics of the image sensor allows the ADC to be optimized for reduced power dissipation. The use of an integrated serializer and an industry standard protocol simplifies integration of the ASIC into a complete camera system. The ASIC, called the High-Speed Image Preprocessor Targeted for Electron Readout, or HIPSTER, with a die area of 64.26 mm 2 , is packaged in a 480-ball grid array (BGA) and is fabricated in 180-nm CMOS technology. HIPSTER achieves typical differential nonlinearity (DNL) < 0.55 LSB, input-referred thermal noise of $114.5 μV-rms, and a bit error rate (BER) of better than 10-14. The power dissipation is 98 mW/channel.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

serial-log-replayer

The code records or logs serial input along with a timestamp to a binary file. The code can then read this log file and replay the serial data with the same relative timings.

Sikkema, Isaac [Oak Ridge National Laboratory (ORN↗
DOE OSTI2023

3-D reconstruction and microstructural characterization of neutron-irradiated U-10Zr fuel using FIB-SEM serial sectioning

Herein, focused ion beam-scanning electron microscopy serial sectioning was applied to characterize the three-dimensional (3-D) porosity and phase regions of a neutron-irradiated U-10 wt% Zr fuel. The specimen was removed from an intermediate radial region of a fuel pin irradiated to 5.7 at.% burn-up. Backscattered electron imaging and energy-dispersive spectroscopy were performed on each serial section, allowing for the characterization of microstructural morphology and composition. Porosity size followed a lognormal distribution, ranging from 1.46 × 10 –4 to 25.58 µm 3 with a total porosity volume fraction of 13.02%. Distinctive microstructural regions were identified by composition and porosity: (1) a Zr-rich region with an average composition of 28.4 wt% Zr and a local porosity fraction of 6.88%, and (2) a U-rich region with an average composition of 97.0 wt% U and a local porosity fraction of 14.11%; subdivided into U-rich—high porosity (16.68%) and U-rich—low porosity (8.04%) regions. The detailed 3-D compositional and porosity regions can improve nuclear fuel performance codes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2017

Multi-static Serial LiDAR for Surveillance and Identification of Marine Life at MHK Installations

Final Report for project DE-EE0006787: Multi-static Serial LiDAR for Surveillance and Identification of Marine Life at MHK Installations. This project developed and tested an optical monitoring system prototype that will be suitable for marine and hydrokinetic (MHK) full project lifecycle observation (baseline, commissioning, and decommissioning), with automated real-time classification of marine animals. This system can be deployed to collect pre-installation baseline species observations at a proposed deployment site with minimal post-processing overhead. To satisfy deployed MHK project species of concern (e.g. Endangered Species Act-listed) monitoring requirements, the system provides automated tracking and notification of the presence of managed animals within established perimeters of MHK equipment and provides high resolution imagery of their behavior through a wide range of conditions. During a project’s decommissioning stage, the system can remain installed to provide resource managers with post-installation data. Our technology, known as an Unobtrusive Multi-static Serial LiDAR Imager (UMSLI), is a technology transfer of underwater distributed LiDAR imaging technology that preserves the advantages of traditional optical and acoustic solutions while overcoming associated disadvantages for MHK environmental monitoring applications. This new approach is a purposefully-designed, reconfigurable adaptation of an existing technology that can be easily mounted on or around different classes of MHK equipment. The system uses low average power red (638nm) laser illumination to be invisible and eye-safe to marine animals and is compact and cost effective. The equipment is designed for long term, maintenance-free operations, to inherently generate a sparse primary dataset that only includes detected anomalies (animal presence information), and to allow robust real-time automated animal classification/identification with a low data bandwidth requirement. Advantages of the technology over others currently being used or being considered for MHK monitoring include: Unlike a conventional camera, the depth of field is near-infinite and limited by attenuation (approximately 5-8 m) rather than focal properties of a lens; Operation in an adaptive mode which can project a sparse grid of pulses with higher peak power for longer range detection (>10 meters) and track animals within a zone of interest with high resolution imagery for identification of marine life at closer range (<5m); System detection limit and Signal-to-Noise-Ratio is superior to a camera, due to rejection of both backscattering component and ambient solar background; Multiple wide-angle pulsed laser illuminators and bucket detectors can be flexibly configured to cover a 4pi steradian (i.e. omnidirectional) scene volume, while also retrieving 3D features of animal targets from timing information; Process and classification framework centered around a novel active learning and incremental classification classifier that enables accurate identification of a variety of marine animals automatically; A two-tiered monitoring architecture and invisible watermarking-based data archiving and retrieving approach ensures significant data reduction while preserving high fidelity monitoring. A methodology to train and optimize the classifier for target species of concern to optimize site monitoring effectiveness. This technological innovation addresses a high priority regulatory requirement to observe marine life interaction near MHK projects. Our solution improves resource manager confidence that any interactions between marine animals and equipment are observed in a cost-effective and automated manner. Without EERE funding, this novel application of multi-static LiDAR would not have been available to the MHK community for environmental monitoring.

16 TIDAL AND WAVE POWER↗
NASA NTRS1969

Reidentifying hardware after loss of serial number

System traces fabrication and inspection records of special hardware back to the raw material. Reidentification of hardware, after loss of serial numbers, is established by X raying all parts again and comparing the new film with the original, whose numbers were previously recorded on serialized documents.

Wells, R. J.↗
NASA NTRS1977

A serial digital data communications device

A general purpose computer peripheral device which is used to provide a full-duplex, serial, digital data transmission link between a Xerox Sigma computer and a wide variety of external equipment, including computers, terminals, and special purpose devices is reported. The interface has an extensive set of user defined options to assist the user in establishing the necessary data links. This report describes those options and other features of the serial communications interface and its performance by discussing its application to a particular problem.

Fetter, J. L.↗
NASA NTRS1988

Experiences with serial and parallel algorithms for channel routing using simulated annealing

Two algorithms for channel routing using simulated annealing are presented. Simulated annealing is an optimization methodology which allows the solution process to back up out of local minima that may be encountered by inappropriate selections. By properly controlling the annealing process, it is very likely that the optimal solution to an NP-complete problem such as channel routing may be found. The algorithm presented proposes very relaxed restrictions on the types of allowable transformations, including overlapping nets. By freeing that restriction and controlling overlap situations with an appropriate cost function, the algorithm becomes very flexible and can be applied to many extensions of channel routing. The selection of the transformation utilizes a number of heuristics, still retaining the pseudorandom nature of simulated annealing. The algorithm was implemented as a serial program for a workstation, and a parallel program designed for a hypercube computer. The details of the serial implementation are presented, including many of the heuristics used and some of the resulting solutions.

Brouwer, Randall Jay↗
NASA NTRS1988

Development of gallium arsenide high-speed, low-power serial parallel interface modules: Executive summary

Final report to NASA LeRC on the development of gallium arsenide (GaAS) high-speed, low power serial/parallel interface modules. The report discusses the development and test of a family of 16, 32 and 64 bit parallel to serial and serial to parallel integrated circuits using a self aligned gate MESFET technology developed at the Honeywell Sensors and Signal Processing Laboratory. Lab testing demonstrated 1.3 GHz clock rates at a power of 300 mW. This work was accomplished under contract number NAS3-24676.

Source record↗
NASA NTRS1988

DFT algorithms for bit-serial GaAs array processor architectures

Systems and Processes Engineering Corporation (SPEC) has developed an innovative array processor architecture for computing Fourier transforms and other commonly used signal processing algorithms. This architecture is designed to extract the highest possible array performance from state-of-the-art GaAs technology. SPEC's architectural design includes a high performance RISC processor implemented in GaAs, along with a Floating Point Coprocessor and a unique Array Communications Coprocessor, also implemented in GaAs technology. Together, these data processors represent the latest in technology, both from an architectural and implementation viewpoint. SPEC has examined numerous algorithms and parallel processing architectures to determine the optimum array processor architecture. SPEC has developed an array processor architecture with integral communications ability to provide maximum node connectivity. The Array Communications Coprocessor embeds communications operations directly in the core of the processor architecture. A Floating Point Coprocessor architecture has been defined that utilizes Bit-Serial arithmetic units, operating at very high frequency, to perform floating point operations. These Bit-Serial devices reduce the device integration level and complexity to a level compatible with state-of-the-art GaAs device technology.

Mcmillan, Gary B.↗