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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 415 records · Page 23

High-order limiting methods using maximum principle bounds derived from the Boltzmann equation I: Euler equations

The use of limiting methods for high-order numerical approximations of hyperbolic conservation laws generally requires defining an admissible region/bounds for the solution. In this work, we present a novel approach for computing solution bounds and limiting for the Euler equations through the kinetic representation provided by the Boltzmann equation, which allows for extending limiters designed for linear advection directly to the Euler equations. Given an arbitrary set of solution values to compute bounds over (e.g., numerical stencil) and a desired linear advection limiter, the proposed approach yields an analytic expression for the admissible region of particle distribution function values, which may be numerically integrated to yield a set of bounds for the density, momentum, and total energy. Further, these solution bounds are shown to preserve positivity of density/pressure/internal energy and, when paired with a limiting technique, can robustly resolve strong discontinuities while recovering high-order accuracy in smooth regions without any ad hoc corrections (e.g., relaxing the bounds). This approach is demonstrated in the context of an explicit unstructured high-order discontinuous Galerkin/flux reconstruction scheme for a variety of difficult problems in gas dynamics, including cases with extreme shocks and shock-vortex interactions. Furthermore, this work presents a foundation for limiting techniques for more complex macroscopic governing equations that can be derived from an underlying kinetic representation for which admissible solution bounds are not well-understood.

42 ENGINEERING↗

Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex

The 22nd genetically encoded amino acid, pyrrolysine, plays a unique role in the key step in the growth of methanogens on mono-, di-, and tri-methylamines by activating the methyl group of these substrates for transfer to a corrinoid cofactor. Previous crystal structures of the Methanosarcina barkeri monomethylamine methyltransferase elucidated the structure of pyrrolysine and provide insight into its role in monomethylamine activation. Herein, we report the second structure of a pyrrolysine-containing protein, the M. barkeri trimethylamine methyltransferase MttB, and its structure bound to sulfite, a substrate analog of trimethylamine. We also report the structure of MttB in complex with its cognate corrinoid protein MttC, which specifically receives the methyl group from the pyrrolysine-activated trimethylamine substrate during methanogenesis. Together these structures provide key insights into the role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in MttC.

60 APPLIED LIFE SCIENCES↗

Quantitative Separation of Unknown Organic–Metal Complexes by Liquid Chromatography–Inductively Coupled Plasma-Mass Spectrometry

Dissolved organic matter (DOM) is widely recognized to control the solubility and reactivity of trace metals in the environment. However, the mechanisms that govern metal-DOM complexation remain elusive, primarily due to the analytical challenge of fractionating and quantifying metal–organic species within the complex mixture of organic compounds that comprise DOM. Here, we describe a quantitative method for fractionation and element-specific detection of organic–metal complexes using liquid chromatography with online inductively coupled plasma mass spectrometry (LC–ICP-MS). The method implements a post-column compensation gradient to stabilize ICP–MS elemental response across the LC solvent gradient, thereby overcoming a major barrier to achieving quantitative accuracy with LC–ICP-MS. With external calibration and internal standard correction, the method yields concentrations of organic–metal complexes that were consistently within 6% of their true values, regardless of the complex’s elution time. We used the method to evaluate the effects of four stationary phases (C18, phenyl, amide, and pentafluoroylphenyl propyl) on the recovery and separation of environmentally relevant trace metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, and Pb) in Suwannee River Fulvic Acid and Suwannee River Natural Organic Matter. The C18, amide, and phenyl phases generally yielded optimal metal recoveries (>75% for all metals except Pb), with the phenyl phase separating polar species to a greater extent than C18 or amide. We also fractionated organic-bound Fe, Cu, and Ni in oxidized and reduced soils, revealing divergent metal-DOM speciation across soil redox environments. Finally, by enabling quantitative fractionation of DOM-bound metals, our method offers a means for advancing a mechanistic understanding of metal–organic complexation throughout the environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Good trellises for IC implementation of viterbi decoders for linear block codes

This paper investigates trellis structures of linear block codes for the IC (integrated circuit) implementation of Viterbi decoders capable of achieving high decoding speed while satisfying a constraint on the structural complexity of the trellis in terms of the maximum number of states at any particular depth. Only uniform sectionalizations of the code trellis diagram are considered. An upper bound on the number of parallel and structurally identical (or isomorphic) subtrellises in a proper trellis for a code without exceeding the maximum state complexity of the minimal trellis of the code is first derived. Parallel structures of trellises with various section lengths for binary BCH and Reed-Muller (RM) codes of lengths 32 and 64 are analyzed. Next, the complexity of IC implementation of a Viterbi decoder based on an L-section trellis diagram for a code is investigated. A structural property of a Viterbi decoder called ACS-connectivity which is related to state connectivity is introduced. This parameter affects the complexity of wire-routing (interconnections within the IC). The effect of five parameters namely: (1) effective computational complexity; (2) complexity of the ACS-circuit; (3) traceback complexity; (4) ACS-connectivity; and (5) branch complexity of a trellis diagram on the VLSI complexity of a Viterbi decoder is investigated. It is shown that an IC implementation of a Viterbi decoder based on a non-minimal trellis requires less area and is capable of operation at higher speed than one based on the minimal trellis when the commonly used ACS-array architecture is considered.

Moorthy, H. T.↗

Good trellises for IC implementation of viterbi decoders for linear block codes

This paper investigates trellis structures of linear block codes for the IC (integrated circuit) implementation of Viterbi decoders capable of achieving high decoding speed while satisfying a constraint on the structural complexity of the trellis in terms of the maximum number of states at any particular depth. Only uniform sectionalizations of the code trellis diagram are considered. An upper bound on the number of parallel and structurally identical (or isomorphic) subtrellises in a proper trellis for a code without exceeding the maximum state complexity of the minimal trellis of the code is first derived. Parallel structures of trellises with various section lengths for binary BCH and Reed-Muller (RM) codes of lengths 32 and 64 are analyzed. Next, the complexity of IC implementation of a Viterbi decoder based on an L-section trellis diagram for a code is investigated. A structural property of a Viterbi decoder called ACS-connectivity which is related to state connectivity is introduced. This parameter affects the complexity of wire-routing (interconnections within the IC). The effect of five parameters namely: (1) effective computational complexity; (2) complexity of the ACS-circuit; (3) traceback complexity; (4) ACS-connectivity; and (5) branch complexity of a trellis diagram on the VLSI complexity of a Viterbi decoder is investigated. It is shown that an IC implementation of a Viterbi decoder based on a non-minimal trellis requires less area and is capable of operation at higher speed than one based on the minimal trellis when the commonly used ACS-array architecture is considered.

Lin, Shu↗

Phosphine Ligand Binding and Catalytic Activity of Group 10–14 Heterobimetallic Complexes

We report heterobimetallic complexes have attracted much interest due to their broad range of structures and reactivities as well as unique catalytic abilities. Additionally, these complexes can be utilized as single-source precursors for the synthesis of binary intermetallic compounds. An example is the family of bis(pyridine-2-thiolato)dichloro-germanium and tin complexes of group 10 metals (Pd and Pt). The reactivity of these heterobimetallic complexes is highly tunable through substitution of the group 14 element and the neutral ligand bound to the transition metal. Here, we study the binding energies of three different phosphorous-based ligands, PR 3 (R = Bu, Ph, and OPh) by density functional theory and restricted Hartree–Fock methods. The PR 3 ligand-binding energies follow the trend of PBu 3 > PPh 3 > P(OPh) 3 , in agreement with their sigma-bonding ability. These results are confirmed by ligand exchange experiments monitored with 31 P NMR spectroscopy, in which a weaker binding PR 3 ligand is replaced with a stronger one. Furthermore, we demonstrate that the heterobimetallic complexes are active catalysts in the Negishi coupling reaction, where stronger binding PR 3 ligands inhibit access to an active site at the metal center. Similar strategies could be applied to other complexes to better understand their ligand-binding energetics and predict their reactivity as both precursors and catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dehydration of UO 2 Cl 2 ·3H 2 O and Nd(NO 3 ) 3 ·6H 2 O with a Soft Donor Ligand and Comparison of Their Interactions through X-ray Diffraction and Theoretical Investigation [plus Supplemental Information]

Herein we investigated whether the relatively Lewis basic imidazole-2-thiones could be used to substitute water ligands bound to f-element cations and generate f-element soft donor complexes. Reactions of 1,3-diethylimidazole-2-thione (C 2 C 2 ImT) with Nd(NO 3 ) 3 ·6H 2 O and UO 2 Cl 2 ·3H 2 O led to the isolation of the anhydrous thione complexes Nd(NO 3 ) 3 (C 2 C 2 ImT) 3 and UO 2 Cl 2 (C 2 C 2 ImT) 2 , characterized by single crystal X-ray diffraction. Differences in the strength of metal–thione interactions have been examined by means of the crystal structure analysis and density functional theory (DFT) calculations. The C 2 C 2 ImT ligands were found to be affected by both coordination and noncovalent interactions, making it impossible to deconvolute the effects of one from the other. Calculated partial atomic charges indicated greater ligand-to-metal charge transfer in the [UO 2 ] 2+ complex, indicative of a stronger interaction. The reactivity of C 2 C 2 ImT demonstrates its usefulness in the preparation of f-element soft donor complexes from readily available hydrates that could be useful intermediates for promoting the coordination and studying the effects of soft donor anions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

SALSAA: a statistical approach to line shapes from an average atom

Ion-Stark line broadening is a key density diagnostic for hot dense plasmas relevant to inertial fusion and astrophysics. It is caused by interactions of a radiating ion with nearby perturbing ions, whose electric microfields lead to changes in bound-bound transition energies. Ion-Stark broadening becomes increasingly difficult to compute for complex, many-electron ions with myriad transitions. In this paper, we propose a simplified approach to ion-Stark broadening based on self-consistent ion distributions and electronic structure from an average-atom model. We find that this approach reproduces the line shape predictions of one traditional method for high-n K-shell emission lines in aluminum ions with accuracy sufficient for density diagnostics in thermal plasmas with equal ion and electron temperatures. We expect that this approach can be extended to provide a reasonable picture of ion-Stark broadening in many-electron ions, enabling rapid calculations of line profiles in complex spectra.

average-atom↗

Virtual-Voltage Partition-Based Approach to Optimal Transmission Switching

This article deals with optimal transmission switching (OTS) problems involving binary decisions about network topology and nonconvex power flow constraints. We adopt a semidefinite programming formulation for the optimal power flow (OPF) problem that, however, remains nonconvex due to the presence of discrete variables and bilinear products between the decision variables. To tackle the latter, we introduce a physically inspired, virtual-voltage approximation that leads to provable lower and upper bounds on the solution of the original problem. To deal with the exponential complexity caused by the discrete variables, we introduce a graph partition-based algorithm that breaks the problem into several parallel mixed-integer subproblems of smaller size. Simulations on the IEEE bus test cases demonstrate the high degree of accuracy and affordable computational requirements of our approach.

42 ENGINEERING↗

Charm meson and charm-meson molecule in an expanding hadron gas

We present our studies on the evolution of charm mesons after the kinetic freeze-out of the expanding hadron gas produced in a heavy-ion collision and the thermal correction to a loosely bound charm-meson molecule in a pion gas. The πD* → πD* reaction rates have t-channel singularities that give contributions inversely proportional to the thermal width of the D. The ratio of the D 0 and D + production rate can differ significantly from those predicted using the measured D* branching fractions. The thermal correction to a loosely bound charm-meson molecule in a pion gas comes primarily from the complex thermal energy shift of the charm-meson constituents.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture

Cell density signaling drives tendon morphogenesis by regulating both procollagen production and cell proliferation. The signal is composed of a small, highly conserved protein (SNZR P) tightly bound to a tissue-specific, unique lipid (SNZR L). This allows the complex (SNZR PL) to bind to the membrane of the cell and locally diffuse over a radius of ~1 mm. The cell produces low levels of this signal but the binding to the membrane increases with the number of tendon cells in the local environment. In this article SNZR P was produced in E.coli and SNZR L was chemically synthesized. The two bind together when heated to 60 °C in the presence of Ca ++ and Mg ++ and the synthesized SNZR PL at ng/ml levels can replace serum. Adding SNZR PL to the medium was also tested on primary tendon cells from adult roosters. The older cells were in a maintenance state in vivo and in cell culture they proliferate more slowly than embryonic cells. Nevertheless, after reaching a moderately high cell density, they produced high levels of procollagen similar to the embryonic cells. This data was not expected from older cells but suggests that adult tendon cells can regenerate the tissue after injury when given the correct signals.

59 BASIC BIOLOGICAL SCIENCES↗

Synsedimentary deformation and thrusting on the eatern margin of the Barberton Greenstone belt, Swaziland

Mapping on the eastern margin of the 3.6 to 3.3 Ga Barberton Greenstone Belt NW Swaziland has revealed a tectonic complex which is more than 5 km thick. The area consists of fault bound units made up of three lithological associations. Some of these were affected by four phases of deformation. Fold structures, foliations, and lineations are associated with the deformation. Sedimentation, geological structures, and evolutionary history of the area are explained.

Lamb, S. H.↗

A microarray immunoassay for simultaneous detection of proteins and bacteria

We report the development and characterization of an antibody microarray biosensor for the rapid detection of both protein and bacterial analytes under flow conditions. Using a noncontact microarray printer, biotinylated capture antibodies were immobilized at discrete locations on the surface of an avidin-coated glass microscope slide. Preservation of capture antibody function during the deposition process was accomplished with the use of a low-salt buffer containing sucrose and bovine serum albumin. The slide was fitted with a six-channel flow module that conducted analyte-containing solutions over the array of capture antibody microspots. Detection of bound analyte was subsequently achieved using fluorescent tracer antibodies. The pattern of fluorescent complexes was interrogated using a scanning confocal microscope equipped with a 635-nm laser. This microarray system was employed to detect protein and bacterial analytes both individually and in samples containing mixtures of analytes. Assays were completed in 15 min, and detection of cholera toxin, staphylococcal enterotoxin B, ricin, and Bacillus globigii was demonstrated at levels as low as 8 ng/mL, 4 ng/mL, 10 ng/mL, and 6.2 x 10(4) cfu/mL, respectively. The assays presented here are very fast, as compared to previously published methods for measuring antibody-antigen interactions using microarrays (minutes versus hours).

Non-NASA Center↗

An improved approach to the analysis of drug-protein binding by distance geometry

The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard C-C distance representations.

NASA Discipline Exobiology↗

Method bacterial endospore quantification using lanthanide dipicolinate luminescence

A lanthanide is combined with a medium to be tested for endospores. The dipicolinic acid released from the endospores binds the lanthanides, which have distinctive emission (i.e., luminescence) spectra, and are detected using photoluminescence. The concentration of spores is determined by preparing a calibration curve generated from photoluminescence spectra of lanthanide complex mixed with spores of a known concentration. A lanthanide complex is used as the analysis reagent, and is comprised of lanthanide ions bound to multidentate ligands that increase the dipicolinic acid binding constant through a cooperative binding effect with respect to lanthanide chloride. The resulting combined effect of increasing the binding constant and eliminating coordinated water and multiple equilibria increase the sensitivity of the endospore assay by an estimated three to four orders of magnitude over prior art of endospore detection based on lanthanide luminescence.

Ponce, Adrian↗

Compressing branch-and-bound trees

A branch-and-bound (BB) tree certifies a dual bound on the value of an integer program. In this work, we introduce the tree compression problem (TCP): Given a BB tree T that certifies a dual bound, can we obtain a smaller tree with the same (or stronger) bound by either (1) applying a different disjunction at some node in T or (2) removing leaves from T? Here we believe such post-hoc analysis of BB trees may assist in identifying helpful general disjunctions in BB algorithms. We initiate our study by considering computational complexity and limitations of TCP. We then conduct experiments to evaluate the compressibility of realistic branch-and-bound trees generated by commonly-used branching strategies, using both an exact and a heuristic compression algorithm.

97 MATHEMATICS AND COMPUTING↗

Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism

Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.

59 BASIC BIOLOGICAL SCIENCES↗