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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

In this paper, we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. Finally, we used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

dCache – Efficient Message Encoding For Inter-Service Communication in dCache: Evaluation of Existing Serialization Protocols as a Replacement for Java Object Serialization

As a well established, large-scale distributed storage system, dCache is used to manage and serve huge amounts of data collected by high energy physics, astrophysics and photon science experiments. Based on a microservices-like architecture, dCache is built as a modular distributed system, where each component provides a different core functionality. These services communicate by passing serialized messages to each other, a core behavior whose performance properties can consequently affect the entire system.This paper compares and evaluates different data serialization protocols in computer science with the objective of replacing and improving upon Java Object Serialization (JOS), which has increasingly presented itself as no longer being sufficiently performant for encoding messages. The criteria for choosing a new framework are collected, analyzed and formalized. The primary motivation for replacing Java serialization for encoding dCache messages is increasing the general speed of message-passing and thereby reducing the round-trip time for user requests. Emphasis is also placed on schema evolution capabilities and framework usability. Approaches for generalizing (de)serialization speed and size measurements based on data structure complexity are introduced, criteria for measuring documentation, learning curve, maintainability and introduction effort are defined. Finally, several selected serialization protocols are evaluated and compared accordingly, concluding with a recommendation for a suitable JOS replacement.

Morschel, Lea↗
DOE OSTI2015

Data Exploration Toolkit for serial diffraction experiments

This paper describes a set of tools allowing experimentalists insight into the variation present within large serial data sets. Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the ‘diffraction before destruction’ nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, roomtemperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 A ° . The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.

serial crystallography, free-electron lasers, memb↗
DOE OSTI2015

A novel inert crystal delivery medium for serial femtosecond crystallography

Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5Å resolution using 300µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

Conrad, Chelsie E.↗
DOE OSTI2015

Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Adapting the serial Alpgen parton-interaction generator to simulate LHC collisions on millions of parallel threads

As the LHC moves to higher energies and luminosity, the demand for computing resources increases accordingly and will soon outpace the growth of the World- wide LHC Computing Grid. To meet this greater demand, event generation Monte Carlo was targeted for adaptation to run on Mira, the supercomputer at the Argonne Leadership Computing Facility. Alpgen is a Monte Carlo event generation application that is used by LHC experiments in the simulation of collisions that take place in the Large Hadron Collider. This paper details the process by which Alpgen was adapted from a single-processor serial-application to a large-scale parallel-application and the performance that was achieved.

HEP↗
DOE OSTI2017

High-speed fixed-target serial virus crystallography

Here, we report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injection molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquid flow conservation. Finally, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

A Serially-Connected Compensator for Eliminating the Unbalanced Three-Phase Voltage Impact on Wind Turbine Generators

Untransposed transmission lines, unbalanced tap changer operations, and unbalanced loading in weak distribution lines can cause unbalanced-voltage conditions. The resulting unbalanced voltage at the point of interconnection affects proper gird integration and reduces the lifetime of wind turbines due to power oscillations, torque pulsations, mechanical stresses, energy losses, and uneven and overheating of the generator stator winding. This work investigates the dynamic impact of unbalanced voltage on the mechanical and electrical components of integrated Fatigue, Aerodynamics, Structures, and Turbulence (FAST) wind turbine generation systems (WTGs) of Type 1 (squirrel-cage induction generator) and Type 3 (doubly-fed induction generator). To alleviate this impact, a serially-connected compensator for a three-phase power line is proposed to balance the wind turbine-side voltage. Dynamic simulation studies are conducted in MATLAB/Simulink to compare the responses of these two types of wind turbine models under normal and unbalanced-voltage operation conditions and demonstrate the effectiveness of the proposed compensator.

17 WIND ENERGY↗
DOE OSTI2021

Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison

For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

We report that angiotensin II type 1 receptor (AT 1 R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT 1 R blockers (ARBs), the structural basis for AT 1 R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT 1 R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. The AT 1 R-ZD7155 complex structure revealed key structural features ofAT 1 R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT 1 R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT 1 R structure-function relationship and structure-based drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin

We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C 10 H 16 N 2 O 3 S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously. Diffraction patterns from Se-B SA were recorded to a resolution of 1.9 Å. The dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) and also on LCLS compute nodes as a resource for research and algorithm development.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

59 BASIC BIOLOGICAL SCIENCES↗