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Results for “affine approximation”

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At least 55 records · Page 3

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NASA NTRS1991

Purification and characterization of ornithine transcarbamylase from pea (Pisum sativum L.)

Pea (Pisum sativum) ornithine transcarbamylase (OTC) was purified to homogeneity from leaf homogenates in a single-step procedure, using delta-N-(phosphonacetyl)-L-ornithine-Sepharose 6B affinity chromatography. The 1581-fold purified OTC enzyme exhibited a specific activity of 139 micromoles citrulline per minute per milligram of protein at 37 degrees C, pH 8.5. Pea OTC represents approximately 0.05% of the total soluble protein in the leaf. The molecular weight of the native enzyme was approximately 108,200, as estimated by Sephacryl S-200 gel filtration chromatography. The purified protein ran as a single molecular weight band of 36,500 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results suggest that the pea OTC is a trimer of identical subunits. The overall amino acid composition of pea OTC is similar to that found in other eukaryotic and prokaryotic OTCs, but the number of arginine residues is approximately twofold higher. The increased number of arginine residues probably accounts for the observed isoelectric point of 7.6 for the pea enzyme, which is considerably more basic than isoelectric point values that have been reported for other OTCs.

Non-NASA Center↗

DOE OSTI2025

Effect of activation temperature on quantum efficiency and lifetime of NEA truncated nanocone array GaAs photocathode

This study investigates the quantum efficiency (QE) and operational lifetime of a negative electron affinity GaAs truncated nanocone array (TNCA) photocathode benchmarked against a conventional flat GaAs photocathode under varying activation temperatures. The TNCA structure demonstrated a QE of up to 13.6% at 590 nm with room temperature (RT) activation—approximately 1.5 times higher than its flat counterpart. This enhancement is due to Mie resonance effects within the nanostructure, as confirmed by finite-difference time-domain simulations. Moreover, the TNCA photocathode exhibits significantly extended charge lifetime, with enhancement factors of ∼6.1 and ∼19.8 under RT and 50 °C activations, respectively. These gains are primarily attributed to increased effective surface area and optimized dipole layer formation at elevated temperatures. In addition, shorter excitation wavelengths further contribute to lifetime improvements. These findings underscore the TNCA GaAs photocathode’s potential as a high QE, long lifetime electron source for many large-scale electron accelerators.

Cs-NF3 activation↗

DOE OSTI2022

Formation of a Strong Heterogeneous Aluminum Lewis Acid on Silica

Abstract Al(OC(CF 3 ) 3 )(PhF) reacts with silanols present on partially dehydroxylated silica to form well‐defined ≡SiOAl(OC(CF 3 ) 3 ) 2 (O(Si≡) 2 ) ( 1 ). 27 Al NMR and DFT calculations with a small cluster model to approximate the silica surface show that the aluminum in 1 adopts a distorted trigonal bipyramidal coordination geometry by coordinating to a nearby siloxane bridge and a fluorine from the alkoxide. Fluoride ion affinity (FIA) calculations follow experimental trends and show that 1 is a stronger Lewis acid than B(C 6 F 5 ) 3 and Al(OC(CF 3 ) 3 )(PhF) but is weaker than Al(OC(CF 3 ) 3 ) and i Pr 3 Si + . Cp 2 Zr(CH 3 ) 2 reacts with 1 to form [Cp 2 ZrCH 3 ][≡SiOAl(OC(CF 3 ) 3 ) 2 (CH 3 )] ( 3 ) by methide abstraction. This reactivity pattern is similar to reactions of organometallics with the proposed strong Lewis acid sites present on Al 2 O 3 .

Samudrala, Kavyasripriya K.↗

DOE OSTI2022

Formation of a Strong Heterogeneous Aluminum Lewis Acid on Silica

Samudrala, Kavyasripriya K.↗

NASA NTRS1989

Photodetachment cross sections of negative ions - The range of validity of the Wigner threshold law

The threshold behavior of the photodetachment cross section of negative ions as a function of photon frequency is usually described by the Wigner law. This paper reports the results of a model calculation using the zero-core-contribution (ZCC) approximation. Theoretical expressions for the leading correction to the Wigner law are developed, giving the range of validity of the Wigner law and the expected accuracy. The results are relevant to extraction of electron affinities from experimental photodetachment data.

Farley, John W.↗

NASA NTRS1999

Localization of the human 64kD autoantigen D1 to myofibrils in a subset of extraocular muscle fibers

PURPOSE. To evaluate the tissue-specific expression pattern of the 64kD human autoantigen D1, a tropomodulin-related protein that may be involved in thyroid-associated ophthalmopathy. METHODS. Recombinant 64kD human autoantigen D1 was generated in a bacterial expression system and used to immunize rabbits. Specific antibodies were affinity-purified and used for Western blots on normal and hyperthyroid rat and rabbit tissue, and immunofluorescence localization on cryosections of rat tissue. RESULTS. Anti-64kD human autoantigen D1 antibodies recognize specifically a approximately 70kD polypeptide in western blots of extraocular muscle, sternothyroid muscle, and smooth muscle. Immunofluorescence staining demonstrates that the 64kD human autoantigen D1 localizes to myofibrils in slow fibers from rat extraocular and sternothyroid muscle. The level of this protein is not altered in extraocular muscles from hyperthyroid rabbits. CONCLUSIONS. The 64kD human autoantigen D1 is expressed in slow fibers of extraocular and sternothyroid muscles as a component of myofibrils, and is not upregulated in conditions of hyperthyroidism.

Proteins/genetics/immunology/metabolism↗

DOE OSTI2022

Interaction of Th with H 0/–/+ : Combined Experimental and Theoretical Thermodynamic Properties

In this work, high-level electronic structure calculations of the lowlying energy electronic states for ThH, ThH – , and ThH + are reported and compared to experimental measurements. The inclusion of spin–orbit coupling is critical to predict the ground-state ordering as inclusion of spin–orbit switches the coupled-cluster CCSD(T) ordering of the two lowest energy states for ThH and ThH + . At the multireference spin–orbit SO-CASPT2 level, the ground states of ThH, ThH – , and ThH + are predicted to be the 2 Δ 3/2 , 3 Φ 2 , and 3 Δ 1 states, respectively. The adiabatic electron affinity is calculated to be 0.820 eV, and the vertical detachment energy is calculated to be 0.832 eV in comparison to an experimental value of 0.87 ± 0.02 eV. The observed ThH – photoelectron spectrum has many transitions, which approximately correlate with excitations of Th + and/or Th. The adiabatic ionization energy of ThH including spin–orbit corrections is calculated to be 6.181 eV. The natural bond orbital results are consistent with a significant contribution of the Th + H – ionic configuration to the bonding in ThH. The bond dissociation energies for ThH, ThH – , and ThH + using the Feller–Peterson–Dixon approach were calculated to be similar for all three molecules and lie between 259 and 280 kJ/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Sulfonyl PIM–1: A diverse separation membrane with dilation resistance

A sulfone modified variant (soPIM–1) of the first polymer of intrinsic microporosity has been studied through molecular simulations to analyze its applicability for adsorption–based separations of diverse nonpolar, quadrupolar, and dipolar adsorbate species. Single component gas phase adsorption isotherms of each adsorbate are provided. Here, the adsorptive properties of soPIM–1 are reported from the application of two methods: (a) traditional grand canonical Monte Carlo (GCMC) simulations and (b) a combination of Monte Carlo and molecular dynamics (GCMC/MD) techniques, which accounts for sorption–induced polymer dynamics. The calculated isosteric heats of adsorption are compared to those from the parent PIM–1 structure and reveals increased CO2 affinity with relatively no change in hydrocarbon affinity. Moreover, to quantify soPIM–1's resistance to dilation the evolution of the microporous structure across the adsorption isotherm loading pressures has been evaluated. Relatedly, nonequilibrium MD simulations have been utilized to determine that soPIM–1 is approximately twice as stiff as PIM–1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

Streptococcus pneumoniae PstS production is phosphate responsive and enhanced during growth in the murine peritoneal cavity

Differential display-PCR (DDPCR) was used to identify a Streptococcus pneumoniae gene with enhanced transcription during growth in the murine peritoneal cavity. Northern dot blot analysis and comparative densitometry confirmed a 1.8-fold increase in expression of the encoded sequence following murine peritoneal culture (MPC) versus laboratory culture or control culture (CC). Sequencing and basic local alignment search tool analysis identified the DDPCR fragment as pstS, the phosphate-binding protein of a high-affinity phosphate uptake system. PCR amplification of the complete pstS gene followed by restriction analysis and sequencing suggests a high level of conservation between strains and serotypes. Quantitative immunodot blotting using antiserum to recombinant PstS (rPstS) demonstrated an approximately twofold increase in PstS production during MPC from that during CCs, a finding consistent with the low levels of phosphate observed in the peritoneum. Moreover, immunodot blot and Northern analysis demonstrated phosphate-dependent production of PstS in six of seven strains examined. These results identify pstS expression as responsive to the MPC environment and extracellular phosphate concentrations. Presently, it remains unclear if phosphate concentrations in vivo contribute to the regulation of pstS. Finally, polyclonal antiserum to rPstS did not inhibit growth of the pneumococcus in vitro, suggesting that antibodies do not block phosphate uptake; moreover, vaccination of mice with rPstS did not protect against intraperitoneal challenge as assessed by the 50% lethal dose.

Non-NASA Center↗

DOE OSTI2021

A contorted nanographene shelter

Nanographenes have kindled considerable interest in the fields of materials science and supramolecular chemistry as a result of their unique self-assembling and optoelectronic properties. Encapsulating the contorted nanographenes inside artificial receptors, however, remains challenging. Herein, we report the design and synthesis of a trigonal prismatic hexacationic cage, which has a large cavity and adopts a relatively flexible conformation. It serves as a receptor, not only for planar coronene, but also for contorted nanographene derivatives with diameters of approximately 15 Å and thicknesses of 7 Å. A comprehensive investigation of the host-guest interactions in the solid, solution and gaseous states by experimentation and theoretical calculations reveals collectively an induced-fit binding mechanism with high binding affinities between the cage and the nanographenes. Notably, the photostability of the nanographenes is improved significantly by the ultrafast deactivation of their excited states within the cage. Encapsulating the contorted nanographenes inside the cage provides a noncovalent strategy for regulating their photoreactivity.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2017

Assessing the Behavior of Typically Lithophile Elements Under Highly Reducing Conditions Relevant to the Planet Mercury

With the data returned from the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) mission, there are now numerous constraints on the physical and chemical properties of Mercury, including its surface composition. The high Sand low FeO contents observed from MESSENGER suggest a low oxygen fugacity of the present materials on the planet's surface. Most of our understanding of elemental partitioning behavior comes from observations made on terrestrial rocks, but Mercury's oxygen fugacity is far outside the conditions of those samples, estimated at approximately 3-7 log units below the Iron-Wtistite (lW) oxygen buffer, several orders of magnitude more reducing than other terrestrial bodies we have data from. With limited oxygen available, lithophile elements may instead exhibit chalcophile, halophile, or siderophile behaviors. Furthermore, very few natural samples of rocks that formed under reducing conditions (e.g., enstatite chondrites, achondrites, aubrites) are available in our collections for examination of this change in geochemical affinity. Our goal is to determine the elemental partitioning behavior of typically lithophile elements at lower oxygen fugacity as a function of temperature and pressure. Experiments were conducted at I GPa in a 13 mm QUICKpress piston cylinder and at 4 GPa in an 880-ton multianvil press, at temperatures up to 1850degC. The composition of starting materials for the experiments were designed so the final run products contained metal, silicate melt, and sulfide melt phases. Oxygen fugacity was controlled in the experiments by adding silicon metal to the samples, in order to utilize the Si-Si02 buffer, which is approximately 5 log units more reducing than the IW buffer at our temperatures of interest. The target silicate melt composition was diopside (CaMgSi206) because measured surface compositions indicate partial melting of a pyroxene-rich mantle. The results of our experiments will aid in our understanding of the fate of elements during the differentiation and thermal evolution of Mercury and other highly reducing planetary bodies.

Rowland, Rick, II↗

NASA NTRS1989

Purification and identification of the fusicoccin binding protein from oat root plasma membrane

Fusicoccin (FC), a fungal phytotoxin, stimulates the H(+) -ATPase located in the plasma membrane (PM) of higher plants. The first event in the reaction chain leading to enhanced H(+) -efflux seems to be the binding of FC to a FC-binding protein (FCBP) in the PM. We solubilized 90% of the FCBP from oat (Avena sativa L. cv Victory) root PM in an active form with 1% octyl-glucoside. The FCBP was stabilized by the presence of protease inhibitors. The FCBP was purified by affinity chromatography using FC-linked adipic acid dihydrazide agarose (FC-AADA). Upon elution with 8 molar urea, two major protein bands on sodium dodecyl sulfate-polyaerylamide gel electrophoresis with molecular weights of 29,700 and 31,000 were obtained. Successive chromatography on BBAB Bio-Gel A, hexyl agarose, and FC-AADA resulted in the same two bands when the FC-AADA was eluted with sodium dodecyl sulfate. A direct correlation was made between 3H-FC-binding activity and the presence of the two protein bands. The stoichiometry of the 29,700 and 31,000 molecular weight bands was 1:2. This suggests that the FCBP occurs in the native form as a heterotrimer with an apparent molecular weight of approximately 92,000.

NASA Discipline Number 29-20↗

NASA NTRS1981

Application of HCMM data to regional geologic analysis for mineral and energy resource evaluation

Experimentation with several potentially promising techniques led to the selection of a fairly simple scheme for registration of data from the HCMM using an affine transformation. A method based solely on remote sensing was developed to estimate those meteorological effects which are required for thermal inertia mapping. It assumes that the atmospheric fluxes are spatially invariant and that the solar, sky and sensible heat fluxes can be approximated by a simple mathematical form. Coefficients are determined from least squares method by fitting observational data to the thermal model.

Watson, K.↗

NASA NTRS1987

On self-similarity of crack layer

The crack layer (CL) theory of Chudnovsky (1986), based on principles of thermodynamics of irreversible processes, employs a crucial hypothesis of self-similarity. The self-similarity hypothesis states that the value of the damage density at a point x of the active zone at a time t coincides with that at the corresponding point in the initial (t = 0) configuration of the active zone, the correspondence being given by a time-dependent affine transformation of the space variables. In this paper, the implications of the self-similarity hypothesis for qusi-static CL propagation is investigated using polystyrene as a model material and examining the evolution of damage distribution along the trailing edge which is approximated by a straight segment perpendicular to the crack path. The results support the self-similarity hypothesis adopted by the CL theory.

Botsis, J.↗

DOE OSTI2024

A weighted shifted boundary method for immersed moving boundary simulations of Stokes' flow

The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods, and relies on reformulating the original boundary value problem over a surrogate (approximate) computational domain. The surrogate domain is constructed so as to avoid cut cells and the associated problematic implementation and numerical integration issues. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions: hence the name of the method, that shifts the location and values of the boundary conditions. Here, in this article, we extend the SBM to the simulation of incompressible Stokes flow, by appropriately weighting its variational form with the elemental volume fraction of active fluid. This approach allows to drastically reduce spurious pressure oscillations in time, which are produced if the total volume of active fluid were to change abruptly over a time step. The proposed Weighted SBM (W-SBM) exactly preserves states of hydrostatic equilibrium, and induces small mass and momentum conservation errors, which converge as the grid is refined. This is in analogy to cutFEMs and related unfitted approaches, which rely on an affine representation of cut boundaries. We demonstrate the robustness and accuracy of the proposed method with an extensive suite of two-dimensional tests.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

RrA, an enzyme from Rhodospirillum rubrum , is a prototype of a new family of short‐chain L‐asparaginases

Abstract L‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum , reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

CCAAT/enhancer-binding protein delta activates insulin-like growth factor-I gene transcription in osteoblasts. Identification of a novel cyclic AMP signaling pathway in bone

Insulin-like growth factor-I (IGF-I) plays a key role in skeletal growth by stimulating bone cell replication and differentiation. We previously showed that prostaglandin E2 (PGE2) and other cAMP-activating agents enhanced IGF-I gene transcription in cultured primary rat osteoblasts through promoter 1, the major IGF-I promoter, and identified a short segment of the promoter, termed HS3D, that was essential for hormonal regulation of IGF-I gene expression. We now demonstrate that CCAAT/enhancer-binding protein (C/EBP) delta is a major component of a PGE2-stimulated DNA-protein complex involving HS3D and find that C/EBPdelta transactivates IGF-I promoter 1 through this site. Competition gel shift studies first indicated that a core C/EBP half-site (GCAAT) was required for binding of a labeled HS3D oligomer to osteoblast nuclear proteins. Southwestern blotting and UV-cross-linking studies showed that the HS3D probe recognized a approximately 35-kDa nuclear protein, and antibody supershift assays indicated that C/EBPdelta comprised most of the PGE2-activated gel-shifted complex. C/EBPdelta was detected by Western immunoblotting in osteoblast nuclear extracts after treatment of cells with PGE2. An HS3D oligonucleotide competed effectively with a high affinity C/EBP site from the rat albumin gene for binding to osteoblast nuclear proteins. Co-transfection of osteoblast cell cultures with a C/EBPdelta expression plasmid enhanced basal and PGE2-activated IGF-I promoter 1-luciferase activity but did not stimulate a reporter gene lacking an HS3D site. By contrast, an expression plasmid for the related protein, C/EBPbeta, did not alter basal IGF-I gene activity but did increase the response to PGE2. In osteoblasts and in COS-7 cells, C/EBPdelta, but not C/EBPbeta, transactivated a reporter gene containing four tandem copies of HS3D fused to a minimal promoter; neither transcription factor stimulated a gene with four copies of an HS3D mutant that was unable to bind osteoblast nuclear proteins. These results identify C/EBPdelta as a hormonally activated inducer of IGF-I gene transcription in osteoblasts and show that the HS3D element within IGF-I promoter 1 is a high affinity binding site for this protein.

NASA Discipline Musculoskeletal↗