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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS1989

Locating Damaged Members in a Truss Structure Using Modal Test Data: a Demonstration Experiment

On-orbit assessment of large flexible space truss structures can be accomplished, in principle, with dynamic response information, structural identification methods, and model correlation techniques which produce an adjusted mathematical model. In a previously developed approach for damage location, an optimal update of the structure model is formed using the response data, then examined to locate damaged members. An experiment designed to demonstrate and verify the performance of the on-orbit assessment approach uses a laboratory scale model truss structure which exhibits characteristics expected for large space truss structures. Vibration experiments were performed to generate response data for the damaged truss. The damage location approach, analytical work performed in support of the vibration tests, the measured response of the test article, and some preliminary results are described.

Smith, Suzanne Weaver↗
NASA NTRS1999

Protein crystal growth and the International Space Station

Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

STS Shuttle Project↗
DOE OSTI2022

An approach to nearest neighbor analysis of pigment-protein complexes using chemical cross-linking in combination with mass spectrometry

Herein, protein cross-linking is the process of chemically joining two amino acids in a protein or protein complex by a covalent bond. When combined with mass spectrometry, it becomes one of the structural mass spectrometry techniques gaining in importance for deriving valuable three-dimensional structural information on proteins and protein complexes. This platform complements existing structural methods, such as NMR spectroscopy, X-ray crystallography, and cryo-EM. Photosynthetic pigment protein complexes serve as light-energy harvesting systems and perform photochemical conversion as part of the “early events” of photosynthesis. This chapter outlines how to prepare cross-linking pigment protein complex samples for LC-MS/MS analysis, including identification of the cross-linked species, network analysis in a protein complex, and structural modeling and justification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry

The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background gas can cause structural changes ranging from unfolding to subunit dissociation. Additionally, recent studies have highlighted the role of charge in such structural changes, but the mechanism is not completely understood. In this study, native top down (native TD) mass spectrometry was used to probe gas-phase structural changes of alcohol dehydrogenase (ADH, 4mer) under varying degrees of in-source activation. Changes in covalent backbone fragments produced by electron capture dissociation (ECD) or 193 nm ultraviolet photodissociation (UVPD) were correlated to structural changes of the ADH 4mer. ECD fragments indicated unfolding started at the N-terminus, and the charge states of UVPD fragments enabled monitoring of charge migration to the unfolded regions. Interestingly, UVPD fragments also indicated that the charge at the “unfolding” N-terminus of ADH decreased at high in-source activation energies after the initial increase. We proposed a possible “refolding-after-unfolding” mechanism, as further supported by monitoring hydrogen elimination from radical a-ions produced by UVPD at the N-terminus of ADH. However, “refolding-after-unfolding” with increasing in-source activation was not observed for charge-reduced ADH, which likely adopted compact structures that are resistant to both charge migration and unfolding. Combined, these results support a charge-directed unfolding mechanism for protein complexes. Overall, an experimental framework was outlined for utilizing native TD to generate structure-informative mass spectral signatures for protein complexes that complement other structure characterization techniques, such as ion mobility spectrometry and computational modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Bioremediation of Chlorinated Volatile Organic Compounds: DOE Experiences and Lessons Learned

From the mid-1980s to the present, the Department of Energy (DOE) has developed, tested, and deployed diverse bioremediation strategies for chlorinated volatile organic compounds (cVOCs). A systematic review of these projects after decades of activity provides an opportunity to identify crosscutting themes and lessons learned. The knowledge provided by a DOE bioremediation retrospective represents a resource to support current and future bioremediation operations, and future decisions related to cVOC bioremediation. This systematic review examined the design, objectives, performance and outcomes for remediation projects at DOE sites including Savannah River, Hanford, Idaho, Mound and Pinellas. The results were used to identify emergent themes to provide actionable insights. The bioremediation retrospective technical team first developed standardized criteria to support the systematic review. Then, the evaluation was performed using a sequential process that was informed by local technical experts who identified and provided the structured information that served as the basis for the evaluation. The participation of these experts was invaluable to the effort. Importantly, DOE cVOC bioremediation efforts were implemented based on the foundational knowledge developed by U.S. Department of Defense (DoD) strategic and applied environmental technology development and certification programs, as well as technical, policy and regulatory guidance from the U.S. Environmental Protection Agency (EPA), Interstate Technology and Regulatory Council (ITRC), U.S. Geological Survey (USGS), industry, and universities. To maximize the value of the DOE cVOC bioremediation retrospective, the systematic review strategy focused on identifying important DOE-specific experiences, trends and lessons learned that would extend the knowledge available from these other key entities.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1988

Object-oriented fault tree evaluation program for quantitative analyses

Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

Patterson-Hine, F. A.↗
NASA NTRS1982

Attitude control of the space construction base: A modular approach

A planar model of a space base and one module is considered. For this simplified system, a feedback controller which is compatible with the modular construction method is described. The systems dynamics are decomposed into two parts corresponding to base and module. The information structure of the problem is non-classical in that not all system information is supplied to each controller. The base controller is designed to accommodate structural changes that occur as the module is added and the module controller is designed to regulate its own states and follow commands from the base. Overall stability of the system is checked by Liapunov analysis and controller effectiveness is verified by computer simulation.

Oconnor, D. A.↗
DOE OSTI2022

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

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

Differentiating Three-Dimensional Molecular Structures Using Laser-Induced Coulomb Explosion Imaging

Coulomb explosion imaging (CEI) with x-ray free electron lasers has recently been shown to be a powerful method for obtaining detailed structural information of gas-phase planar ring molecules [R. Boll et al., X-ray multiphoton-induced Coulomb explosion images complex single molecules, Nat. Phys. 18, 423 (2022).]. In this Letter, we investigate the potential of CEI driven by a tabletop laser and extend this approach to differentiating three-dimensional structures. We study the static CEI patterns of planar and nonplanar organic molecules that resemble the structures of typical products formed in ring-opening reactions. Here, our results reveal that each molecule exhibits a well-localized and distinctive pattern in three-dimensional fragment-ion momentum space. We find that these patterns yield direct information about the molecular structures and can be qualitatively reproduced using a classical Coulomb explosion simulation. Our findings suggest that laser-induced CEI can serve as a robust method for differentiating molecular structures of organic ring and chain molecules. As such, it holds great promise as a method for following ultrafast structural changes, e.g., during ring-opening reactions, by tracking the motion of individual atoms in pump-probe experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1996

Monitoring Data-Structure Evolution in Distributed Message-Passing Programs

Monitoring the evolution of data structures in parallel and distributed programs, is critical for debugging its semantics and performance. However, the current state-of-art in tracking and presenting data-structure information on parallel and distributed environments is cumbersome and does not scale. In this paper we present a methodology that automatically tracks memory bindings (not the actual contents) of static and dynamic data-structures of message-passing C programs, using PVM. With the help of a number of examples we show that in addition to determining the impact of memory allocation overheads on program performance, graphical views can help in debugging the semantics of program execution. Scalable animations of virtual address bindings of source-level data-structures are used for debugging the semantics of parallel programs across all processors. In conjunction with light-weight core-files, this technique can be used to complement traditional debuggers on single processors. Detailed information (such as data-structure contents), on specific nodes, can be determined using traditional debuggers after the data structure evolution leading to the semantic error is observed graphically.

Sarukkai, Sekhar R.↗
NASA NTRS2018

Mapping Pine Plantations in the Southeastern U.S. Using Structural, Spectral, and Temporal Remote Sensing Data

The southeastern U.S. produces the most industrial roundwood in the U.S. each year, largely from commercial pine plantations. The extent of plantation forests and management dynamics can be difficult to ascertain from periodic forest inventories, yet short-rotation tree plantations also present challenges for remote sensing. Here, we integrated spectral, temporal, and structural information from airborne and satellite platforms to distinguish pine plantations from natural forests and evaluate the contribution from planted forests to regional forest coverin the southeastern U.S. Within flight lines from NASA Goddard's Lidar, Hyperspectral, and Thermal (G-LiHT) Airborne Imager, lidar metrics of forest structure had the highest overall accuracy for pine plantations among single-source classifications (90%), but the combination of spectral and temporal metrics from Landsat generated comparable accuracy (91%). Combined structural, temporal, and spectral information from G-LiHT and Landsat had the highest accuracy for plantations (92%) and natural forests (88%). At a regional scale, classifications using Landsat spectral and temporal metrics had between 74 and 82% mean class accuracy for plantations.Regionally, plantations accounted for 28% of forest cover in the southeastern U.S., a result similar to plot-based estimates, albeit with greater spatial detail. Regional maps of plantation forests differed from existing map products, including the National Land Cover Database. Combining plantation extent in 2011 with Landsat based forest change data identified strong regional gradients in plantation dynamics since 1985, with distinct spatial patterns of rotation age (east-west) and plantation expansion (interior). Our analysis demonstrates the potential to improve the characterization of dynamic land cover classes, including economically important timber plantations, by integrating diverse remote sensing datasets. Critically, multi-source remote sensing provides an approach to leverage periodic forest inventory data for annual monitoring of managed forest landscapes.

Fagan, M. E.↗
DOE OSTI2025

Supramolecular Support of Cuprophilic Network Bonding in 2-D Copper n -Alkanethiolates

Here, the development of heterogeneous materials, catalysts, and semiconductors is often reliant on precise control of self-assembly and crystal packing. Many new materials are initially synthesized as microcrystalline powders, making them incompatible with typical methods of structure determination, such as single-crystal X-ray diffraction. This resultant lack of structural information has made thorough investigation into the effect of metal substitution on crystal structure in metal-organic chalcogenolates (MOChas) challenging. Here, we use small molecule serial femtosecond crystallography (smSFX) to present the structures of four copper n-alkanethiolates: CuSC4, CuSC5, CuSC6, and CuSC7. Divergent patterns of alkyl chain packing are identified from microcrystalline powders via smSFX. An odd-even effect in crystal packing has been identified and attributed to different orientations of symmetry elements in the even- and odd-numbered chains. This results in minute changes in the azimuthal organization of the even-numbered chains and the network of cuprophilic interactions. Additionally, we present a synthesis of crystalline gold n-alkanethiolates to provide the first comparison between three d 10 coinage metals (Cu, Ag, and Au) and their resultant n-alkanethiolates.

Willson, Maggie C. [Univ. of Connecticut, Storrs, ↗
DOE OSTI2020

Structural basis for divergent C–H hydroxylation selectivity in two Rieske oxygenases

Biocatalysts that perform C–H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Rapid sensing of hidden objects and defects using a single-pixel diffractive terahertz sensor

Abstract Terahertz waves offer advantages for nondestructive detection of hidden objects/defects in materials, as they can penetrate most optically-opaque materials. However, existing terahertz inspection systems face throughput and accuracy restrictions due to their limited imaging speed and resolution. Furthermore, machine-vision-based systems using large-pixel-count imaging encounter bottlenecks due to their data storage, transmission and processing requirements. Here, we report a diffractive sensor that rapidly detects hidden defects/objects within a 3D sample using a single-pixel terahertz detector, eliminating sample scanning or image formation/processing. Leveraging deep-learning-optimized diffractive layers, this diffractive sensor can all-optically probe the 3D structural information of samples by outputting a spectrum, directly indicating the presence/absence of hidden structures or defects. We experimentally validated this framework using a single-pixel terahertz time-domain spectroscopy set-up and 3D-printed diffractive layers, successfully detecting unknown hidden defects inside silicon samples. This technique is valuable for applications including security screening, biomedical sensing and industrial quality control.

Li, Jingxi (ORCID:0000000165958680)↗
DOE OSTI2020

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

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

Structure-aware annotation of leucine-rich repeat domains

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.

Xu, Boyan↗