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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Pixel Anomaly Detection Tool : a user-friendly GUI for classifying detector frames using machine-learning approaches

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Macromolecular crystallography and biology at the Linac Coherent Light Source

The Linac Coherent Light Source (LCLS) has significantly impacted the field of biology by providing advanced capabilities for probing the structure and dynamics of biological molecules with high precision. The ultrashort coherent X-ray pulses from the LCLS have enabled ultrafast, time-resolved, serial femtosecond crystallography that is inaccessible at conventional synchrotron light sources. Since the facility's founding, scientists have captured detailed insights into biological processes at atomic resolution and fundamental timescales. The ability to observe these processes in real time and under conditions closely resembling their natural state is transforming our approach to studying biochemical mechanisms and developing new medical and energy applications. This work recounts some of the history of the LCLS, advances in biological research enabled by the LCLS, key biological areas that have been impacted and how the LCLS has helped to unravel complex biological phenomena in these fields.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Beyond integration: modeling every pixel to obtain better structure factors from stills

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (10 4 -10 6 ) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb 3+ L -III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of μNS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448–605 of μNS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP-μNS (448–605) crystallization in Sf9 cells was monitored and verified by several imaging techniques. Cells infected with the EGFP-μNS (448–605) baculovirus formed rod-shaped microcrystals (5–15 µm in length) which were reconstituted in high-viscosity media (LCP and agarose) and investigated by serial femtosecond X-ray diffraction using viscous jets at an X-ray free-electron laser (XFEL). The crystals diffracted to 4.5 Å resolution. A total of 4227 diffraction snapshots were successfully indexed into a hexagonal lattice with unit-cell parameters a = 109.29, b = 110.29, c = 324.97 Å. The final data set was merged and refined to 7.0 Å resolution. Preliminary electron-density maps were obtained. While more diffraction data are required to solve the structure of μNS (448–605) , the current experimental strategy, which couples high-viscosity crystal delivery at an XFEL with in cellulo crystallization, paves the way towards structure determination of the μNS protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exploring 3D leaf anatomical traits for C 4 photosynthesis: chloroplast and plasmodesmata pit field size in maize and sugarcane

Summary Volume and surface area of chloroplasts and surface area of plasmodesmata pit fields are presented for two C 4 species, maize and sugarcane, with respect to cell surface area and cell volume. Serial block face scanning electron microscopy (SBF‐SEM) and confocal laser scanning microscopy with the Airyscan system (LSM) were used. Chloroplast size estimates were much faster and easier using LSM than with SBF‐SEM; however, the results were more variable than SBF‐SEM. Mesophyll cells were lobed where chloroplasts were located, facilitating cell‐to‐cell connections while allowing for greater intercellular airspace exposure. Bundle sheath cells were cylindrical with chloroplasts arranged centrifugally. Chloroplasts occupied c. 30–50% of mesophyll cell volume, and 60–70% of bundle sheath cell volume. Roughly 2–3% of each cell surface area was covered by plasmodesmata pit fields for both bundle sheath and mesophyll cells. This work will aid future research to develop SBF‐SEM methodologies with the aim to better understand the effect of cell structure on C 4 photosynthesis.

3D leaf imaging↗
DOE OSTI2020

Ultrafast structural response to charge redistribution within a photosinthetic reaction centre

This data set contains stream files, difference maps and SVD maps obtained from data processing of time-resolved serial femtosecond crystallography measurements performed at LCLS XFEL, used to construct the images and perform the analysis published in the paper "Ultrafast structural response to charge redistribution within a photosinthetic reaction centre". Two (2) time points plus a dark state from 2015 ('a' label) as well as five (5) time points plus a dark state from 2016 ('b' label) are provided.

CXI↗
DOE OSTI2020

Mechanism and dynamics of fatty acid photodecarboxylase

The deposition contains diffraction patterns after hit-finding of time-resolved serial femtosecond crystallography measurements on fatty acid photodecarboxylase performed at LCLS XFEL (proposal ID: LT59). Five datasets are available. One dataset without pump laser excitation, labeled as "dark" and four time-resolved datasets with pump laser excitation at four different time-points labeled as "20 ps", "900 ps", "300 ns" and "2 μs". Please check the publication for more information about the datasets.

CXI↗
DOE OSTI2022

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

This dataset contains a subset of raw diffraction images for the serial femtosecond crystallography data of S1P5-ONO-5430608 complex. The diffraction data contain a strong systematic background as described in Lyapina et al. No additional background subtraction was applied to the data. In order to avoid its effects, the background subtraction implemented in CrystFEL, was applied (--rings-grad subtraction). The final stream, supplemented with this dataset, was obtained with: indexamajig 0.8.0 Respectively, the hkl file was obtained with: partialator 0.8.0

Human sphingosine-1-phosphate receptor 5 (S1P5) in↗
DOE OSTI2024

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Preventing Bio-Bloopers and XFEL Follies: Best Practices from your Friendly Instrument Staff

Serial Femtosecond Crystallography (SFX) at X-ray Free electron Lasers (XFELs) is a relatively new field promising to deliver unparalleled spatial and temporal resolution on biological systems and there dynamics. Over the past decade, though, there have been a handful of results that have truly delivered on these promises. Why? SFX has many paradigm shifting techniques not seen in typical structural biology arenas, such as creating a concentrated slurry of microcrystals rather than a handful of loopable prisms worthy of a catalog photo. Then taking that slurry and high speed jetting them towards the vacuum or helium interation region to destroy less than 1% of your sample and waste the other 99. The literature is full of techniques and methods promising to cure what ails your experiment, yet as an instrument scientist will tell you –and a first author might admit after a few drinks at the conference happy hour—is that there are a lot more failures than the success we published, results may vary. We will walk through a best practices on how to prepare your sample and chose a sample delivery technique that will amerliorate your studies rather than undermine your hardwork and hopefully lead to better experimental planning and execution, inching you closer to that scientific goal and that call from Stockholm. This will be written in a more editorialized fashion and is meant to give the reader an idea of what to try or how they should be thinking. Welcome to SFX, now what?

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2003

Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss

RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern.

Serial Passage↗
NASA NTRS2002

Spacewire on Earth orbiting scatterometers

The need for a high speed, reliable and easy to implement communication link has led to the development of a space flight oriented version of IEEE 1355 called SpaceWire. SpaceWire is based on high-speed (200 Mbps) serial point-to-point links using Low Voltage Differential Signaling (LVDS). SpaceWIre has provisions for routing messages between a large network of processors, using wormhole routing for low overhead and latency. {additionally, there are available space qualified hybrids, which provide the Link layer to the user's bus}. A test bed of multiple digital signal processor breadboards, demonstrating the ability to meet signal processing requirements for an orbiting scatterometer has been implemented using three Astrium MCM-DSPs, each breadboard consists of a Multi Chip Module (MCM) that combines a space qualified Digital Signal Processor and peripherals, including IEEE-1355 links. With the addition of appropriate physical layer interfaces and software on the DSP, the SpaceWire link is used to communicate between processors on the test bed, e.g. sending timing references, commands, status, and science data among the processors. Results are presented on development issues surrounding the use of SpaceWire in this environment, from physical layer implementation (cables, connectors, LVDS drivers) to diagnostic tools, driver firmware, and development methodology. The tools, methods, and hardware, software challenges and preliminary performance are investigated and discussed.

serial↗
NASA NTRS2022

Effects of Debulking on the Fiber Microstructure and Void Distribution in Carbon Fiber Reinforced Plastics

Carbon Fiber Reinforced Plastics (CFRPs) are widely used due to their high stiffness to weight ratios. A common process manufacturers use to increase the strength to weight ratio is debulking. Debulking is the process of compacting a dry fibrous reinforcement prior to resin infusion. This process is meant to decrease the average inter-fiber distance, effectively increasing the fiber volume fraction of the sample. While this process is widely understood macroscopically its effects on fibrous microstructures have not yet been well characterized. The aim of this work is to compare the microstructures of three CFRP laminates, varying only the debulking step in the manufacturing process. High resolution serial sections of all three laminates were taken for analysis. Using these scans, the fiber positions were reconstructed. Statistical descriptors such as local fiber and void volume fractions, fiber orientation, and void distribution and morphology were then generated for each sample. Fiber clusters present within the material were identified and analyzed for each level of debulking applied. Using these descriptors, the effects of debulking on the morphology and organization of the composite microstructure was evaluated.

carbon fiber↗
DOE OSTI2022

Herpes simplex virus and rates of cognitive decline or whole brain atrophy in the Dominantly Inherited Alzheimer Network

Abstract Objective To investigate whether herpes simplex virus type 1 (HSV‐1) infection was associated with rates of cognitive decline or whole brain atrophy among individuals from the Dominantly Inherited Alzheimer Network (DIAN). Methods Among two subsets of the DIAN cohort (age range 19.6–66.6 years; median follow‐up 3.0 years) we examined (i) rate of cognitive decline ( N = 164) using change in mini‐mental state examination (MMSE) score, (ii) rate of whole brain atrophy ( N = 149), derived from serial MR imaging, calculated using the boundary shift integral (BSI) method. HSV‐1 antibodies were assayed in baseline sera collected from 2009–2015. Linear mixed‐effects models were used to compare outcomes by HSV‐1 seropositivity and high HSV‐1 IgG titres/IgM status. Results There was no association between baseline HSV‐1 seropositivity and rates of cognitive decline or whole brain atrophy. Having high HSV‐1 IgG titres/IgM was associated with a slightly greater decline in MMSE points per year (difference in slope − 0.365, 95% CI: −0.958 to −0.072), but not with rate of whole brain atrophy. Symptomatic mutation carriers declined fastest on both MMSE and BSI measures, however, this was not influenced by HSV‐1. Among asymptomatic mutation carriers, rates of decline on MMSE and BSI were slightly greater among those who were HSV‐1 seronegative. Among mutation‐negative individuals, no differences were seen by HSV‐1. Stratifying by APOE4 status yielded inconsistent results. Interpretation We found no evidence for a major role of HSV‐1, measured by serum antibodies, in cognitive decline or whole brain atrophy among individuals at high risk of early‐onset AD.

Warren‐Gash, Charlotte↗
DOE OSTI2024

Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates

X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A Three-in-One Hybrid Strategy for High-Performance Semiconducting Polymers Processed from Anisole

The development of semiconducting polymers with good processability in green solvents and competitive electrical performance is essential for realizing sustainable large-scale manufacturing and commercialization of organic electronics. A major obstacle is the processability-performance dichotomy that is dictated by the lack of ideal building blocks with balanced polarity, solubility, electronic structures, and molecular conformation. Herein, through the integration of donor, quinoid and acceptor units, an unprecedented building block, namely TQBT, is introduced for constructing a serial of conjugated polymers. The TQBT, distinct in non-symmetric structure and high dipole moment, imparts enhanced solubility in anisole—a green solvent—to the polymer TQBT-T. Furthermore, PTQBT-T possess a highly rigid and planar backbone owing to the nearly coplanar geometry and quinoidal nature of TQBT, resulting in strong aggregation in solution and localized aggregates in film. Remarkably, PTQBT-T films spuncast from anisole exhibit a hole mobility of 2.30 cm 2 V -1 s -1 , which is record high for green solvent-processable semiconducting polymers via spin-coating, together with commendable operational and storage stability. The hybrid building block emerges as a pioneering electroactive unit, shedding light on future design strategies in high-performance semiconducting polymers compatible with green processing and marking a significant stride towards ecofriendly organic electronics.

36 MATERIALS SCIENCE↗