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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Center for Tokamak Transients Simulations

The major goals for the Center for Tokamak Transients Simulations (CTTS) were to develop detailed numerical simulations of disruptive transients in tokamak experiments and to use them in theoretical studies of the thermal-quench (TQ) and current-quench (CQ) phases of disruption. The University of Wisconsin-Madison component of CTTS contributed relevant development for the NIMROD code (https://nimrodteam.org) and applied it to disruptions that involve global vertical displacement. Code-development contributions include boundary conditions that represent sheath effects which occur when tokamak plasma is in contact with the surrounding vessel wall during vertical displacement events (VDEs). We also implemented a reduced model of energetic runaway electrons (REs) to simulate the effect of these energetic electrons on the CQ phase of tokamak disruptions. Our computations of VDEs include 2D and 3D verification through benchmarks with two other widely used macroscale plasma simulation codes, M3D-C1 and JOREK. Over nonlinear evolution to the final termination of plasma current, the 2D simulation results on magnetic axis location, toroidal current, and halo current track each other well. With the 3D benchmark computation, all three codes found the same qualitative behavior of the asymmetric instabilities having increasing growth rate after contact with the wall, followed by nonlinear excitation of other toroidal harmonics. Our NIMROD computations for an idealized configuration show agreement with an analytical assessment by V. D. Pustovitov [Nucl. Fusion 55, 113032 (2015)] that the plasma and non-ideal wall remain in force-balance such that net forces only result from magnetic stresses over the outer surface of the wall. Our study of the influence of boundary conditions on VDEs shows that extended-MHD simulations of VDEs are sensitive to electron energy transport to the wall and that boundary conditions on flow are only significant to the extent that they influence the electron energy transport. Resistive-MHD NIMROD simulations of the tokamak discharges in the Madison Symmetric Torus show that magnetic perturbations of poloidal wavenumber m=3 lead to chaotic magnetic topology over the edge region, which helps deconfine energetic electrons. A second area of RE study shows that the coupled resistive MHD/reduced RE model reproduces the resistive-hose particle-beam instability. With respect to educational opportunities, this effort involved and supported four graduate students at the University of Wisconsin-Madison and one postdoctoral associate. The results of this study have been disseminated through journal publications, conference presentations, technical reports, and PhD dissertations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Structure of LARP7 Protein p65–telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR

La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). Here, in Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains—N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65–TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65–TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3' terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5' end. Our results reveal the extensive p65–TER interactions that promote TER 3'-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Node-Accessible Zirconium MOFs

High-stability, zirconium-based metal–organic frameworks are attractive as heterogeneous catalysts and as model supports for uniform arrays of subsequently constructed heterogeneous catalysts—for example, MOF-node-grafted metal–oxy and metal–sulfur clusters. For hexa-Zr(IV)-MOFs characterized by nodes that are less than 12-connected, sites not used for linkers are ideally occupied by reactive and displaceable OH/H 2 O pairs. Here, the desired pairs are ideal for grafting the aforementioned catalytic clusters, while aqua-ligand lability renders them effective for exposing highly Lewis-acidic Zr(IV) sites (catalytic sites) to candidate reactants. New single-crystal X-ray studies of an eight-connected Zr-MOF, NU-1000, reveal that conventional activation fully removes modulator ligands, but replaces them with three node-blocking formate ligands (from solvent decomposition) and only one OH/H 2 O pair, not four—a largely overlooked complication that now appears to be general for Zr-MOFs. Here we describe an alternative activation protocol that effectively removes modulators, avoids formate, and installs the full complement of terminal OH/H 2 O pairs. It does so via an unusual isolatable intermediate featuring eight aqua ligands and four non-ligated chlorides—again as supported by single-crystal X-ray data. We find that complete replacement of node-blocking modulators/formate with the originally envisioned OH/OH 2 pairs has striking consequences; here we touch upon just three. First, elimination of unrecognized formate renders aqua ligands much more thermally labile, enabling open Zr(IV) sites to be obtained at lower temperature. Second, in the absence of formate, which otherwise links and locks pairs of node Zr(IV) ions, reversible removal of aqua ligands engenders reversible contraction of MOF meso- and micropores, as evidenced by X-ray diffraction. Third, formate replacement with OH/OH 2 pairs renders NU-1000 ca.10× more active for catalytic hydrolytic degradation of a representative simulant of G-type chemical warfare agents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining the results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.

03 NATURAL GAS↗
DOE OSTI2018

The N-terminal domain of gastrulation brain homeobox 2 (Gbx2) is required for iridophore specification in zebrafish

Highlights: • Iridophore formation is suppressed by gbx2 knockdown in zebrafish. • gbx2 is expressed in neural crest cells and iridophores during development. • gbx2 knockdown leads to apoptosis of neural crest cells. • The N-terminal domain of Gbx2 rescues the phenotype of gbx2 knockdown. Although body color pattern formation by pigment cells plays critical roles in animals, pigment cell specification has not yet been fully elucidated. In zebrafish, there are three chromatophores: melanophore, iridophore, and xanthophore, that are derived from neural crest cells (NCCs). A recent study has reported the differentially expressed genes between melanophores and iridophores. Based on transcriptome data, we identified that Gbx2 is required for iridophore specification during development. In support of this, iridophore formation is suppressed by gbx2 knockdown by morpholino antisense oligonucleotide, at 72 h post fertilization (hpf) in zebrafish. Moreover, gbx2 is expressed in sox10-expressing NCCs and guanine crystal plates-containing iridophores during development at 24 and 48 hpf, respectively. In gbx2 knockdown zebrafish embryos, apoptosis of sox10-expressing NCCs was detected at 24 hpf without any effect on the formation of melanophores and xanthophores at 48 hpf. We further observed that the N-terminal domain of Gbx2 is able to rescue the iridophore formation defect caused by gbx2 knockdown. Our study provides insights into the requirement of N-terminal domain of Gbx2 for iridophore specification in zebrafish.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The linear rheological responses of wedge‐type polymers

ABSTRACT The linear rheological responses of a series of specially designed wedge‐type polymers synthesized by the polymerization of large molecular weight monomers have been measured. These wedge polymers contained large side groups which contained three flexible branch chains per polymer chain unit. The master curves for these polymers were obtained by time temperature superposition of dynamic data at different temperatures from the terminal flow regime to well below the glass transition temperature, T g . While these polymers maintained a behavior similar to that of linear polymers, the influence of the large side group structure lead to low entanglement densities and extremely low rubbery plateau modulus values, being near to 13 kPa. The viscosity molecular weight dependence was also somewhat higher than that normally observed for linear polymers, tending toward a power law near to 4.2 rather than the typical 3.4 found in entangled linear chains. The glassy modulus of these branched polymers is also found to be extremely low, being less than 100 MPa at T g −60 °C. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53 , 899–906

Hu, Miao↗
DOE OSTI2017

Spectroscopic Characterization, Computational Investigation, and Comparisons of ECX – (E = As, P, and N; X = S and O) Anions

Three newly-synthesized [Na+(221-kryptofix)] salts containing AsCO–, PCO–, and PCS– anions were successfully electrosprayed into the vacuum, and the ECX– (E = As, P; X = O, S) anions were investigated by negative ion photoelectron spectroscopy (NIPES) and high resolution photoelectron imaging spectroscopy. For each ECX– anion, a well-resolved NIPE spectrum was obtained, in which every major peak is split into a doublet. The splittings are attributed to spin-orbit coupling (SOC) in the ECX• radicals. Vibrational progressions in the NIPE spectra of ECX– were assigned to the symmetric and antisymmetric stretching modes in ECX• radicals. The electron affinities (EAs) and SOC splittings of ECX• are determined from the NIPE spectra to be: AsCO•: EA = 2.414 ± 0.002 eV, SOC splitting = 988 cm-1; PCO•: EA = 2.670 ± 0.005 eV, SOC splitting = 175 cm-1; PCS•: EA = 2.850 ± 0.005 eV, SOC splitting = 300 cm-1. Calculations using the B3LYP, CASPT2, and CCSD(T) methods all predict linear geometries for both the anions and neutral radicals. The calculated EAs and SOC splittings for ECX• are in excellent agreement with the experimentally-measured values. The simulated NIPE spectra, based on the calculated Franck-Condon factors, and SOC splittings nicely reproduce all of the observed spectral peaks, thus allowing unambiguous spectral assignments. The finding that PCS has the greatest EA of the three triatomic molecules considered here is counterintuitive based upon electronegativity considerations, but understandable in terms of the HOMO of PCS– having the greatest degree of delocalization onto both terminal atoms.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A Hybrid Index for Characterizing Drought Based on a Nonparametric Kernel Estimator

This study develops a nonparametric multivariate drought index, namely, the nonparametric multivariate standardized drought index (NMSDI), by considering the variations of both precipitation and streamflow. Building upon previous efforts in constructing nonparametric multivariate drought index, the nonparametric kernel estimator is used to derive the joint distribution of precipitation and streamflow, thus providing additional insights into drought-index development. The proposed NMSDI is applied in the Wei River basin (WRB), on the basis of which the drought-evolution characteristics are investigated. Three main results were found: 1) In general, NMSDI captures drought onset in a way that is similar to that of the standardized precipitation index and captures drought termination and persistence in a way that is similar to that of the standardized streamflow index. We report the drought events identified by NMSDI match well with historical drought records in the WRB. Performance is also consistent with that of an existing multivariate standardized drought index at various time scales, confirming the validity of the newly constructed NMSDI in drought detections. 2) An increasing risk of drought has been detected for past decades and will persist to a certain extent in the future in most areas of the WRB. 3) The identified changepoints of annual NMSDI are mainly concentrated in the early 1970s and mid-1990s, coincident with extensive water use and soil conservation practices. In summary, this study highlights a nonparametric multivariable drought index that can efficiently and comprehensively be used for drought detections and predictions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Computationally Robust Line Outage Detection and Identification in Three-Phase Networks

Detection and identification of individual phase outages remains a challenging problem due to insufficient metering in three-phase unbalanced power networks. This problem was tackled for the transmission systems in our previous work as documented in [1]. In this paper, this work is extended to detect phase outages in three-phase unbalanced systems using only the sparse estimation method. In addition, further improvements are introduced to increase the estimation accuracy for the virtual power injections at the terminal buses of disconnected lines, once the disconnected line is identified by sparse estimation methods. Simulation results are provided to experimentally validate the increased accuracy in detecting phase outages while decreasing the computational time by using the proposed approach.

Sparse Estimation, Line Outage, Phase Outage, LASS↗
DOE OSTI2014

In Situ SIMS and IR Spectroscopy of Well-Defined Surfaces Prepared by Soft Landing of Mass-Selected Ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3]2+, onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.

in situ↗
DOE OSTI2017

Comparison of Virtual Oscillator and Droop Control: Preprint

Virtual oscillator control and droop control are two techniques that can be used to ensure synchronization and power sharing of parallel inverters in islanded operation. VOC relies on the implementation of non-linear Van der Pol oscillator equations in the control system of the inverter, acting upon the time-domain instantaneous inverter current and terminal voltage. On the other hand, DC explicitly computes active and reactive power produced by the inverter and relies on limited bandwidth low-pass filters. Even though both methods can be engineered to produce the same steady-state characteristics, their dynamic performances are significantly different. This paper presents analytical and experimental results that aim to compare both methods. It is shown that VOC is inherently faster and enables minimizing the circulating currents. The results are verified using three 120V, 1kW inverters.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2014

Crystal structures of sialyltransferase from Photobacterium damselae

Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae α2–6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of α2–6-linked sialosides. In this paper, we report three crystal structures of this enzyme. Two structures with and without a donor substrate analog CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks the Ig-domain. Finally, comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Structure of an integrin with an [alpha]I domain, complement receptor type 4

We report the structure of an integrin with an {alpha}I domain, {alpha}{sub X}{beta}{sub 2}, the complement receptor type 4. It was earlier expected that a fixed orientation between the {alpha}I domain and the {beta}-propeller domain in which it is inserted would be required for allosteric signal transmission. However, the {alpha}I domain is highly flexible, enabling two {beta}I domain conformational states to couple to three {alpha}I domain states, and greater accessibility for ligand recognition. Although {alpha}{sub X}{beta}{sub 2} is bent similarly to integrins that lack {alpha}I domains, the terminal domains of the {alpha}- and {beta}-legs, calf-2 and {beta}-tail, are oriented differently than in {alpha}I-less integrins. Linkers extending to the transmembrane domains are unstructured. Previous mutations in the {beta}2-tail domain support the importance of extension, rather than a deadbolt, in integrin activation. The locations of further activating mutations and antibody epitopes show the critical role of extension, and conversion from the closed to the open headpiece conformation, in integrin activation. Differences among 10 molecules in crystal lattices provide unprecedented information on interdomain flexibility important for modelling integrin extension and activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life

Abstract Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S 0 )-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S 0 reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

First-principles studies on molecular beam epitaxy growth of GaAs 1-x Bi x

We investigate the molecular beam epitaxy (MBE) growth of GaAs 1-x Bi x film using density functional theory with spin-orbit coupling to understand the growth of this film, especially the mechanisms of Bi incorporation. We study the stable adsorption structures and kinetics of the incident molecules (As₂ molecule, Ga atom, Bi atom, and Bi₂ molecule) on the (2 x 1)-Ga sub ||Bi surface and a proposed q (1 x 1)-Ga sub ||AsAs surface has a quasi-(1 x 1) As layer above the Ga-terminated GaAs substrate and a randomly oriented As dimer layer on top. We obtain the desorption and diffusion barriers of the adsorbed molecules and also the reaction barriers of three key processes related to Bi evolution, namely, Bi incorporation, As/Bi exchange, and Bi clustering. The results help explain the experimentally observed dependence of Bi incorporation on the As/Ga ratio and growth temperature. Furthermore, we find that As₂ exchange with Bi of the (2 x 1)-Ga sub ||Bi surface is a key step controlling the kinetics of the Bi incorporation. Finally, we explore two possible methods to enhance the Bi incorporation, namely, replacing the MBE growth mode from codeposition of all fluxes with a sequential deposition of fluxes and applying asymmetric in-plane strain to the substrate.

Luo, Guangfu↗