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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 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine

The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome—an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'- 0 CG- 1 CA- 2 CG- 3 TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2 CG has very little effect on TCF4 binding, E-box 1 CA modification has a negative influence on binding, while modification of the flanking 0 CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nodal root diameter and node number in maize ( Zea mays L.) interact to influence plant growth under nitrogen stress

Under nitrogen limitation, plants increase resource allocation to root growth relative to shoot growth. The utility of various root architectural and anatomical phenotypes for nitrogen acquisition are not well understood. Nodal root number and root cross-sectional area were evaluated in maize in field and greenhouse environments. Nodal root number and root cross-sectional area were inversely correlated under both high and low nitrogen conditions. Attenuated emergence of root nodes, as opposed to differences in the number of axial roots per node, was associated with substantially reduced root number. Greater root cross-sectional area was associated with a greater stele area and number of cortical cell files. Genotypes that produced few, thick nodal roots rather than many, thin nodal roots had deeper rooting and better shoot growth in low nitrogen environments. Fewer nodal roots offset the respiratory and nitrogen costs of thicker diameter roots, since total nodal root respiration and nitrogen content was similar for genotypes with many, thin and few, thick nodal roots. We propose that few, thick nodal roots may enable greater capture of deep soil nitrogen and improve plant performance under nitrogen stress. Synergistic interactions between an architectural and anatomical trait may be an important strategy for nitrogen acquisition. Understanding trait interactions among different root nodes has important implications in for improving crop nutrient uptake and stress tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

A Proposed Pathway for the Nucleation and Crystal Growth of the Tetragonal Form of Lysozyme

A number of factors, the shape and charge distribution anisotropy, multiple components in the solution (buffer + counter ion, precipitant, protein, and water), conformational flexibility, and large numbers of intermolecular contacts, all serve as complicating variables in understanding the nucleation and growth mechanism for macromolecules. Intermolecular contacts include hydrogen bonds, van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and give specificity while the others are weaker, more prevalent, and more promiscuous, i.e., can lead to a range of possible molecular interactions. We propose that for tetragonal lysozyme, and by extension many other monomeric proteins, there is a solution-phase assembly process to form 4(sub 3) helix structures that are the basic unit for nucleation. The formation of these structures is continuous and concentration dependent. They subsequently also servc as growth units, with that process then being a recapitulation of the nucleation process. The advantages of solution phase assembly are the immediate burying of the strongest interactions, removing them from subsequent participation in the nucleation and growth process, and the introduction of symmetry into the system, which also assists in the assembly process.

Pusey, Marc L.↗
NASA NTRS1994

A workstation based simulator for teaching compressible aerodynamics

A workstation-based interactive flow simulator has been developed to aid in the teaching of undergraduate compressible aerodynamics. By solving the equations found in NACA 1135, the simulator models three basic fluids problems encountered in supersonic flow: flow past a compression corner, flow past two wedges in series, and flow past two opposed wedges. The study can vary the geometry or flow conditions through a graphical user interface and the new conditions are calculated immediately. Various graphical formats present the results of the flow calculations to the student. The simulator includes interactive questions and answers to aid in both the use of the tool and to develop an understanding of some of the complexities of compressible aerodynamics. A series of help screens make the simulator easy to learn and use.

Benson, Thomas J.↗
DOE OSTI2022

Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ

Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Trophic interactions at avian carcasses: Do scavengers feed on vulture carrion?

Scavenging is a pervasive foraging strategy among vertebrates, yet researchers have only recently begun to reveal the complex implications of scavenging dynamics. Scavenging studies have predominantly used lower trophic level (i.e., herbivore) species as carrion bait, and the few studies that have used higher trophic level (i.e., carnivore) carrion have found these carcass types are generally avoided by vertebrates or scavenged by fewer species than similarly sized herbivore carcasses. No studies have assessed the fate of carcasses of obligate scavengers. To investigate potential differences in scavenging dynamics among avian carrion representing different guilds and trophic levels, we conducted scavenging trials using 20 replicates of two obligate scavenger species (i.e. black vulture, Coragyps atratus; turkey vulture, Cathartes aura) and two lower trophic level species, chicken (Gallus gallus domesticus), and mallard (Anas platyrhynchos). Carcass trials were conducted at the Savannah River Site, SC, USA, and monitored with remote cameras. We hypothesized carcasses of vultures would persist longer and have a distinct scavenging community compared to lower trophic level carcasses (mallard and chicken). As expected, turkey and black vulture carcasses persisted in the environment longer, were less likely to be entirely consumed by vertebrate scavengers, and had a different scavenging community than mallard and chicken carcasses. Furthermore, these results contribute to the growing body of evidence suggesting higher trophic level carrion is exploited differently by vertebrate scavengers. Our findings suggest nutrients derived from vulture carcasses are likely largely reincorporated into lower trophic levels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Bacterial expansins and related proteins from the world of microbes

The discovery of microbial expansins emerged from studies of the mechanism of plant cell growth and the molecular basis of plant cell wall extensibility. Expansins are wall-loosening proteins that are universal in the plant kingdom and are also found in a small set of phylogenetically diverse bacteria, fungi, and other organisms, most of which colonize plant surfaces. They loosen plant cell walls without detectable lytic activity. Bacterial expansins have attracted considerable attention recently for their potential use in cellulosic biomass conversion for biofuel production, as a means to disaggregate cellulosic structures by nonlytic means (“amorphogenesis”). Evolutionary analysis indicates that microbial expansins originated by multiple horizontal gene transfers from plants. Crystallographic analysis of BsEXLX1, the expansin from Bacillus subtilis , shows that microbial expansins consist of two tightly packed domains: the N-terminal domain D1 has a double-ψ β-barrel fold similar to glycosyl hydrolase family-45 enzymes but lacks catalytic residues usually required for hydrolysis; the C-terminal domain D2 has a unique β-sandwich fold with three co-linear aromatic residues that bind β-1,4-glucans by hydrophobic interactions. Genetic deletion of expansin in Bacillus and Clavibacter cripples their ability to colonize plant tissues. In this paper, we assess reports that expansin addition enhances cellulose breakdown by cellulase and compare expansins with distantly related proteins named swollenin, cerato-platanin, and loosenin. Finally, we end in a speculative vein about the biological roles of microbial expansins and their potential applications. Advances in this field will be aided by a deeper understanding of how these proteins modify cellulosic structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Protocadherin cis -dimer architecture and recognition unit diversity

Clustered protocadherins (Pcdhs) mediate numerous neural patterning functions, including neuronal self-recognition and non–self-discrimination to direct self-avoidance among vertebrate neurons. Individual neurons stochastically express a subset of Pcdh isoforms, which assemble to form a stochastic repertoire of cis -dimers. We describe herein the structure of a PcdhγB7 cis -homodimer, which includes the membrane-proximal extracellular cadherin domains EC5 and EC6. The structure is asymmetric with one molecule contributing interface surface from both EC5 and EC6, and the other only from EC6. Structural and sequence analyses suggest that all Pcdh isoforms will dimerize through this interface. Site-directed mutants at this interface interfere with both Pcdh cis -dimerization and cell surface transport. The structure explains the known restrictions of cis -interactions of some Pcdh isoforms, including α-Pcdhs, which cannot form homodimers. The asymmetry of the interface approximately doubles the size of the recognition repertoire, and restrictions on cis -interactions among Pcdh isoforms define the limits of the Pcdh recognition unit repertoire.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Basic Research of Intrinsic Tamper Indication Markings Defined by Pulsed Laser Irradiation (Quad Chart) [Poster]

Objective: We will research how short (ns) and ultrashort (fs) laser pulses interact with the surfaces of various materials to create complex color layers and morphological patterns. Method: We are investigating the site-specific, formation of microcolor features. Also, research includes a fundamental study of the physics underlying periodic ripple formation during femtosecond laser irradiation. Status of effort: Laser induced color markings were demonstrated on an increased number of materials (including metal thin films) and investigated for optical properties and microstructure. Technology that allows for marking curved surfaces (and large areas) has been implemented. We have used electro-magnetic solvers to model light-solid interactions leading to periodic surface ripple patterns. This includes identifying the roles of surface plasmon polaritons. Goals/Milestones: Research corrosion resistance of oxide color markings (salt spray, fog, polarization tests); Through modeling, investigate effects of multi-source scattering and interference on ripple patterns; Investigate microspectrophotometry for mapping color; and Investigate new methods for laser color marking curved surfaces and large areas.

36 MATERIALS SCIENCE↗
NASA NTRS1993

Interactive Image-Analysis Program

BLOBTOOL computer program used to prepare image for analysis and generates various quantitative measurements of objects or structures present in images. Includes basic input/output capabilities, option to display built-in color tables, and access to on-line help. Written in C Language.

Leonard, Desiree M.↗
NASA NTRS1997

AOPA Survey Summary of AGATE Concepts Demonstration October 17-19, 1996: Basic Report - Volume 1

An AGATE Concepts Demonstration was conducted at the Annual Aircraft Owners and Pilots Association (AOPA) Convention in 1996. The demonstration consisted of an interactive simulation of a single-pilot, single-engine aircraft in which the participant took off, flew a brief enroute segment and then flew a Global Positioning System (GPS) approach and landing. The participant was provided an advanced 'pathway-in-the-sky' presentation on both a head-up display and a head-down display to follow throughout the flight. A single lever power control and display concept was also provided for control of the engine throughout the flight. A second head-down, multifunction display in the instrument panel provided a moving map display for navigation purposes and monitoring of the status of the aircraft's systems. An estimated 352 people observed or participated in the demonstration, and 144 surveys were collected. The pilot ratings of the participants ranged from student to Air Transport Rating with an average of 1850 hours total flight time. The performance of the participants was surprisingly good, considering the minimal training in a completely new system concept. The overwhelming response was that technologies that simplify piloting tasks are enthusiastically welcomed by pilots of all experience levels. The increase in situation awareness and reduction in pilot workload were universally accepted and lauded as steps in the right direction.

Source record↗
DOE OSTI2012

Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain

The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studies of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Semiconducting Zn x Mo 3 S 13 -GO Chalcocarbogel: A High-Capacity and Stable Sulfur-Equivalent Conversion-Based Electrode for Lithium-Ion Batteries

Lithium–sulfur batteries with a sulfur electrode offer a theoretical capacity of ∼1672 mAh g –1 , but rapid capacity loss mainly constrains their practical application. This work introduces a semiconducting and amorphous Zn x Mo 3 S 13 -GO (x = 0.5) chalcocarbogel sulfur-equivalent electrode with superior capacity and stability for lithium-ion batteries (LIBs). The Zn x Mo 3 S 13 -GO is synthesized in solution under ambient conditions, and its local structure contains S–S, M-Q (M = Mo, Zn; Q = S, O), C–S, and Mo–Mo bonding motifs with Mo coordination environment closely related to Mo 3 S 13 anions, as determined by X-ray photoelectron spectroscopy, synchrotron X-ray scattering, X-ray absorption spectroscopy, and ab initio molecular dynamics simulations. The Li/Zn x Mo 3 S 13 -GO cell offers an initial discharge capacity of 1019 mAh g –1 at a rate of C/3. After the activation cycles, the Li/Zn x Mo 3 S 13 -GO cell demonstrates good cycling stability, retaining a discharge capacity of 519.4 mAh g –1 after 250 cycles with ∼99.98% Coulombic efficiency and excellent rate capabilities. Moreover, it provides an initial discharge capacity of ∼574 mAh g –1 and maintains a retention capacity of 279 mAh g –1 at 1C after 625 cycles. The Lewis acidic Zn 2+ ion enhances the Lewis basic polysulfide anchoring ability and reduces the dissolution of polysulfides produced during the redox process through Zn–S covalent interaction, while the semiconducting and amorphous structure of the chalcocarbogel increases the electrical and ionic conductivity. Furthermore, this work highlights chalcocarbogels’ potential for developing high-capacity and stable electrodes for LIBs.

25 ENERGY STORAGE↗
DOE OSTI2015

A Combined Experimental and Computational Study on the Stability of Nanofluids Containing Metal Organic Frameworks

Computational studies on nanofluids composed of metal organic frameworks (MOFs) were performed using molecular modeling techniques. Grand Canonical Monte Carlo (GCMC) simulations were used to study adsorption behavior of 1,1,1,3,3-pentafluoropropane (R-245fa) in a MIL-101 MOF at various temperatures. To understand the stability of the nanofluid composed of MIL-101 particles, we performed molecular dynamics simulations to compute potentials of mean force between hypothetical MIL-101 fragments terminated with two different kinds of modulators in R-245fa and water. Our computed potentials of mean force results indicate that the MOF particles tend to disperse better in water than in R-245fa. The reasons for this observation were analyzed and discussed. Our results agree with experimental results indicating that the employed potential models and modeling approaches provide good description of molecular interactions and the reliabilities. Work performed by LXD was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Work performed by HVRA, SKN, RKM, and PBM was supported by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

The emergent photophysics and photochemistry of molecular polaritons: a theoretical and computational investigation (Final Technical Report)

When molecules are placed between closely spaced mirrors, they interact strongly with the photons that are trapped between them, generating new quantum states which are no longer exclusively material nor photonic alone, but rather, coherent superpositions of both. These hybrid states are known as molecular polaritons, given that they arise from the strong interaction between the electric field of light and the electrical polarization of the molecules. Recently, experimental advances in nano‐ and microfabrication of molecular polariton architectures have successfully demonstrated their feasibility to control the rate and outcome of a certain class of chemical reactions in condensed phases. Importantly, these reactions proceed in strongly dissipative environments such as liquid solvents and lossy mirrors that allow for photons to escape from their confinement. The purpose of this research is to formulate quantum mechanical theories and computational tools that can elucidate the origin of these intriguing phenomena and simultaneously predict capabilities that this new generation of molecular materials affords. Attention is placed on harnessing polaritons to carry out photophysics and photochemistry that challenge currently existing paradigms, such as the optimization of energy conversion processes in organic solar cell or light‐emitting devices, or unconventional phenomena such as long‐range excitation energy transfer, remote control of chemical reactions, and a new quantum mechanical regime of chemical reactivity due to wavefunction overlaps amongst a large number of molecular polaritons (Bose condensation). This research explores a frontier of Chemistry and Physics where electrons, vibrations, and photons interact strongly with each other to generate emergent behavior that can be creatively exploited to address contemporary challenges in Basic Energy Sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1971

Spaceborne computer executive routine functional design specification. Volume 2: Computer executive design for space station/base

The computer executive functional system design concepts derived from study of the Space Station/Base are presented. Information Management System hardware configuration as directly influencing the executive design is reviewed. The hardware configuration and generic executive design requirements are considered in detail in a previous report (System Configuration and Executive Requirements Specifications for Reusable Shuttle and Space Station/Base, 9/25/70). This report defines basic system primitives and delineates processes and process control. Supervisor states are considered for describing basic multiprogramming and multiprocessing systems. A high-level computer executive including control of scheduling, allocation of resources, system interactions, and real-time supervisory functions is defined. The description is oriented to provide a baseline for a functional simulation of the computer executive system.

Kennedy, J. R.↗