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At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
NASA NTRS1990

The vibrational frequencies of ozone

The singles and doubles coupled-cluster (CCSD) method is used, together with the recently proposed CCSD(T) and CCSDT-1 methods, to determine the equilibrium structure and harmonic frequencies of ozone at various levels, on the basis of large one-particle basis sets. It is demonstrated that f-type functions are required in order to obtain quantitative accuracy for the equilibrium structure and harmonic frequencies. The CCSD(T) level of theory, in conjunction with a (4s 3p 2d 1f) atomic natural orbital set, yields an equilibrium geometry and harmonic frequencies that are in excellent agreement with experimental results; an effort has accordingly been made to determine the cubic and quartic force constants, and evaluate the anharmonic corrections to the fundamental vibrational frequencies.

Lee, Timothy J.↗
NASA NTRS1991

Effect of gravity on the stability and structure of lean hydrogen-air flames

Detailed, time-dependent, 2D numerical simulations with full hydrogen-oxygen chemistry are used to investigate the effects of gravity on the stability and structure of laminar flames in lean, premixed hydrogen-air mixtures. The calculations show that the effects of gravity becomes more important as the lean flammability limit is approached. In a 12 percent hydrogen-air mixture, gravity plays only a secondary role in determining the multidimensional structure of the flame with the stability and structure of the flame controlled primarily by the thermo-diffusive instability mechanism. However, in leaner hydrogen-air mixtures gravity becomes more important. Upward-propagating flames are highly curved and evolve into a bubble rising upwards in the tube. Downward-propagating flames are flat or even oscillate between structures with concave and convex curvatures. The zero-gravity flame shows only cellular structures. Cellular structures which are present in zero gravity can be suppressed by the effect of buoyancy for mixtures leaner than 11 percent hydrogen. These observations are explained on the basis of an interaction between the processes leading to buoyancy-induced Rayleigh-Taylor instability and the thermo-diffusive instability.

Patnaik, G.↗
DOE OSTI2023

Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis

Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M . brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

The near-infrared structure and spectra of the bipolar nebulae M2-9 and AFGL 2688: The role of ultraviolet pumping and shocks in molecular hydrogen excitation

High-resolution near-infrared images and moderate resolution spectra were obtained of the bipolar nebulae M2-9 and AFGL 2688. The ability to spatially and spectrally resolve the various components of the nebulae has proved to be important in determining their physical structure and characteristics. In M2-9, the lobes are found to have a double-shell structure. The inner shell is dominated by emission from hydrogen recombination lines, and the outer shell is primarily emission from H2 lines in teh 2-2.5 micron region. Analysis of H2 line ratios indicates that the H2 emission is radiatively excited. A well-resolved photodissociation region is observed in the lobes. The spectrum of the central source is dominated by H recombination lines and a strong continuum rising toward longer wavelengths consistent with a T = 795 K blackbody. Also present are lines of He I and Fe II. In contrast, the N knot and E lobe of M2-9 show little continuum emission. The N knot spectrum consists of lines of (Fe II) and hydrogen recombination lines. In AGFL 2688, the emission from the bright lobes is mainly continuum reflected from the central star. Several molecular features from C2 and CN are present. In the extreme end of the N lobe and in the E equatorial region, the emission is dominated by lines of H2 in the 2-2.5 region. The observed H2 line ratios indicate that the emission is collisionally excited, with an excitation temperature T(sub ex) approixmately = 1600 +/- 100 K.

Hora, Joseph L.↗
NASA NTRS1975

An assessment of the impact of water impoundment and diversion structures on vegetation in Southern Arizona

High-altitude color infrared photography was used to survey existing conditions, both upstream and downstream, from nineteen diversion structures in Southern Arizona to determine their effect upon vegetation health, vigor, and cover. A diversion structure is defined as a man/made feature constructed to control storm runoff. The results are used to determine the policy for future structure design.

Conn, J. S.↗
DOE OSTI2024

Tunable Magnetic Coupling in Graphene Nanoribbon Quantum Dots

Abstract Carbon‐based quantum dots (QDs) enable flexible manipulation of electronic behavior at the nanoscale, but controlling their magnetic properties requires atomically precise structural control. While magnetism is observed in organic molecules and graphene nanoribbons (GNRs), GNR precursors enabling bottom‐up fabrication of QDs with various spin ground states have not yet been reported. Here the development of a new GNR precursor that results in magnetic QD structures embedded in semiconducting GNRs is reported. Inserting one such molecule into the GNR backbone and graphitizing it results in a QD region hosting one unpaired electron. QDs composed of two precursor molecules exhibit nonmagnetic, antiferromagnetic, or antiferromagnetic ground states, depending on the structural details that determine the coupling behavior of the spins originating from each molecule. The synthesis of these QDs and the emergence of localized states are demonstrated through high‐resolution atomic force microscopy (HR‐AFM), scanning tunneling microscopy (STM) imaging, and spectroscopy, and the relationship between QD atomic structure and magnetic properties is uncovered. GNR QDs provide a useful platform for controlling the spin‐degree of freedom in carbon‐based nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural basis for self-discrimination by neoantigen-specific TCRs

T cell receptors (TCR) are pivotal in mediating tumour cell cytolysis via recognition of mutation-derived tumour neoantigens (neoAgs) presented by major histocompatibility class-I (MHC-I). Understanding the factors governing the emergence of neoAg from somatic mutations is a major focus of current research. However, the structural and cellular determinants controlling TCR recognition of neoAgs remain poorly understood. This study describes the multi-level analysis of a model neoAg from the B16F10 murine melanoma, H2-D b /Hsf2 p.K72N 68-76 , as well as its cognate TCR 47BE7. Through cellular, molecular and structural studies we demonstrate that the p.K72N mutation enhances H2-D b binding, thereby improving cell surface presentation and stabilizing the TCR 47BE7 epitope. Furthermore, TCR 47BE7 exhibited high functional avidity and selectivity, attributable to a broad, stringent, binding interface enabling recognition of native B16F10 despite low antigen density. Our findings provide insight into the generation of anchor-residue modified neoAg, and emphasize the value of molecular and structural investigations of neoAg in diverse MHC-I contexts for advancing the understanding of neoAg immunogenicity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. In C . difficile , MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn 2+ stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn 2+ , which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn 2+ co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

Development of the Learjet 28/29 Wing Using NASTRAN Analysis

The structural development work performed on the Learjet 28/29 wing using NASTRAN analysis is discussed. The work included the basic sizing of primary structural members such as wing skins, wing skin splices, and spar caps, as well as the calculation of preliminary weight estimates utilizing the weight computation routine in NASTRAN. The eight spar redundancy of the Learjet wing made this task somewhat more complex than for more determinate type wing structures. Some of the problems that were encountered and the solutions and methods that were used are described.

Boroughs, R. R.↗
NASA NTRS1988

Deep space tracking in local reference frames

A self-calibrating deep space tracking technique is described which can potentially produce two nanoradian angular spacecraft determinations. The technique uses very long base interferometric observations of a spacecraft and several radio sources. The currently employed single source technique is described as a parameter estimation procedure. Then, the number of parameters and observations leads to the proposed local reference frame technique. Station clock, Earth rotation, and tropospheric parameters are estimated along with spacecraft position from the multisource observation sequence. The contributions to spacecraft angular uncertainty from system noise, tropospheric fluctuations, and uncalibrated radio source structure are evaluated. Of these experimental errors, radio source structure dominates the determination of the spacecraft position in the radio reference frame. It is shown, however, that the sensitivity of relative spacecraft position accuracies to time-invariant radio source structure effects may be on the order of 2 nanoradians.

Treuhaft, R. N.↗
DOE OSTI2021

Ultrafast X-ray scattering offers a structural view of excited-state charge transfer

Intramolecular charge transfer and the associated changes in molecular structure in N,N'-dimethylpiperazine are tracked using femtosecond gas-phase X-ray scattering. The molecules are optically excited to the 3p state at 200 nm. Following rapid relaxation to the 3s state, distinct charge-localized and charge-delocalized species related by charge transfer are observed. The experiment determines the molecular structure of the two species, with the redistribution of electron density accounted for by a scattering correction factor. The initially dominant charge-localized state has a weakened carbon–carbon bond and reorients one methyl group compared with the ground state. Subsequent charge transfer to the charge-delocalized state elongates the carbon–carbon bond further, creating an extended 1.634 Å bond, and also reorients the second methyl group. At the same time, the bond lengths between the nitrogen and the ring-carbon atoms contract from an average of 1.505 to 1.465 Å. The experiment determines the overall charge transfer time constant for approaching the equilibrium between charge-localized and charge-delocalized species to 3.0 ps.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Magnetic structure and exchange interactions in the layered semiconductor CrPS 4

Compounds with two-dimensional (2D) layers of magnetic ions weakly connected by van der Waals bonding offer routes to enhance quantum behavior, stimulating both fundamental and applied interest. CrPS 4 is one such magnetic van der Waals material, however, it has undergone only limited investigation. Here we present a comprehensive series of neutron scattering measurements to determine the magnetic structure and exchange interactions. The observed magnetic excitations allow a high degree of constraint on the model parameters not normally associated with measurements on a powder sample. The results demonstrate the 2D nature of the magnetic interactions, while also revealing the importance of interactions along 1D chains within the layers. The subtle role of competing interactions is observed, which manifest in a nontrivial magnetic transition and a tunable magnetic structure in a small applied magnetic field through a spin-flop transition. Our results on the bulk compound provide insights that can be applied to an understanding of the behavior of reduced layer CrPS 4 .

36 MATERIALS SCIENCE↗
DOE OSTI2022

Giant resonances in topological spin Hall effect due to electron-skyrmion scattering in two-dimensional Rashba spin-orbit ferromagnets

Here we study a topological spin Hall effect where conduction electrons are scattered by Néel-type skyrmions in two-dimensional Rashba spin-orbit ferromagnets. We find the resonance structures in direct and Hall electric conductivities. The resonances strongly depend on the skyrmion size, the Rashba spin-orbit coupling vector value, and the relative direction between magnetization and Rashba vectors. The antiparallel arrangement of the Rashba spin-orbit coupling vector with respect to the magnetization determines the resonance structure and increases the direct conductivity by about two orders of magnitude. For the parallel arrangement the electric conductivities decrease by one to three orders of magnitude and the Hall conductivity changes the sign. The Rashba spin-orbit coupling also modifies electron bands depending on the ratio ε R /J, where ε R is Rashba energy and J is an exchange integral between conduction and localized electrons. If ε R /J ≤ 1, each energy band has the single minimum while for ε R /J > 1 the lower band has the “Mexican-hat” shape with the maximum at k = 0. We focus on the dependencies of direct and Hall electric conductivities on Fermi energy, ε F , skyrmion sizes, and Rashba spin-orbit coupling constant values and its relative direction with the magnetization. Analyzing both types of the energy bands, in general, we find two types of resonances: at the minimum of the upper band and behaviors, we employ the scattering pattern analysis. The resonance dependencies on skyrmion sizes and Rashba, a spin-orbit coupling contestant, can be qualitatively explained in terms of the Ramsauer-Townsend scattering of the upper band electrons by the skyrmion quantum well. The resonance properties can be used in spin transistors. To discover the resonances it is necessary to know the specific range of the parameters. At some values of the parameters the electric conductivity changes by about two orders of magnitude in the narrow range of ε F (< 0.01 eV). To detect the resonances it is also important to identify the relative direction of the Rashba spin-orbit coupling vector with respect to the magnetization.

36 MATERIALS SCIENCE↗
NASA NTRS1993

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Manchester, John I.↗
DOE OSTI2022

Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules

In Saccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside the Saccharomycetaceae family are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure of ScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyond Saccharomycetaceae, e.g. in Schizosaccharomyces pombe or human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix αC in the zf-C3HC and Rsm1 modules, and an extra helix αAB' in the Rsm1 module. Conservation of key residues responsible for its distinct features identifies S. pombe Rsm1 and Homo sapiens NIPA/ZC3HC1 as structural orthologs of ScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function of ScPml39 in S. cerevisiae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures

Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in Toxoplasma gondii, an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite’s long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Overview of density pedestal structure: Role fueling versus transport

How much of the density pedestal structure profile is determined by fueling versus transport is still a valid question. In most current tokamaks, the Scrape-Off Layer is not opaque enough to screen the neutrals and limit their penetration past the separatrix. As such recycled neutrals as well as additional gas puffing can directly affect the pedestal structure through ionization. Yet, in ITER and other future burning plasma magnetic confinement devices, this ionization source will be pushed further out into the Scrape-Off Layer. This poses the question, how much of the pedestal density structure is governed by this edge ionization source versus plasma transport effects. Theoretically, several turbulent modes have been identified which could provide a 'pinch' like up-gradient transport mechanism. Up-gradient transport is necessary in a source-free region to obtain a peaked density profile, which is often observed in the core of tokamaks. In an opaque Scrape-Off Layer, without the existence of such a pinch, the pedestal density structure would eventually disappear. Not only would this limit our ability to fuel a fusion reactor, it would also affect the pedestal stability. In this paper we will give an overview of the state of the art on what sets the pedestal density structure based on experimental observations as well as theoretical models. We will complement these studies with new results from Alcator C-Mod and DIII-D where the opaqueness is increased to reach values similar to those in ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

O 2 -Dependence of reactions of 1,2-dimethoxyethanyl and 1,2-dimethoxyethanylperoxy isomers

Reaction mechanisms of Ṙ and ROȮ radicals derived from low-temperature oxidation of 1,2-dimethoxyethane (CH 3 O(CH 2 ) 2 OCH 3 ) were investigated using speciation from multiplexed photoionization mass spectrometry (MPIMS) measurements via Cl-initiated oxidation, in conjunction with electronic structure calculations. The experiments were conducted at 5 bar, from 450 K – 650 K, and O 2 concentrations from 1 · 10 14 cm –3 – 6 · 10 18 cm –3 to probe the effects on competing reaction channels of 1,2-dimethoxyethanyl (Ṙ) and 1,2-dimethoxyethanylperoxy (ROȮ) isomers. Several species were detected with photoionization spectral fitting – ethene, formaldehyde, methyl vinyl ether, and 2-methoxyacetaldehyde – and, as determined by electronic structure calculations, may form via unimolecular decomposition of 1,2-dimethoxyethanyl or 1,2-dimethoxyethanylperoxy. O 2 -dependent yield ratios show that the formation pathways for all species undergo a competition between O 2 -addition and unimolecular decomposition. Here, adiabatic ionization energies were also calculated and utilized along with exact mass determinations to infer contributions for other species derived exclusively from first- and second-O 2 -addition, including 1,2-dimethoxyethene, cyclic ethers, and dicarbonyls.

1,2-dimethoxyethane↗