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At least 847 records · Page 47

Efficient Cache use for Stencil Operations on Structured Discretization Grids

We derive tight bounds on the cache misses for evaluation of explicit stencil operators on structured grids. Our lower bound is based on the isoperimetrical property of the discrete octahedron. Our upper bound is based on a good surface to volume ratio of a parallelepiped spanned by a reduced basis of the interference lattice of a grid. Measurements show that our algorithm typically reduces the number of cache misses by a factor of three, relative to a compiler optimized code. We show that stencil calculations on grids whose interference lattice have a short vector feature abnormally high numbers of cache misses. We call such grids unfavorable and suggest to avoid these in computations by appropriate padding. By direct measurements on a MIPS R10000 processor we show a good correlation between abnormally high numbers of cache misses and unfavorable three-dimensional grids.

Frumkin, Michael↗

The low-lying electronic states of LiC

The spectroscopic constants for the doublet and quartet states of LiC below about 30,000/cm are determined using an internally contracted multireference configuration-interaction approach in conjunction with a [6s 5p 3d 2f] atomic natural orbital basis sets. All of the strongly bound states, X(sup 4)(SIGMA)(sup -),(1)(sup 2)(DELTA), (1)(sup 2)(SIGMA)(sup +), and (2)(sup 2) II, very ionic in character. The only bound-bound quartet transition in this energy range is (2)(sup 4)SIGMA(sup -) and Franck-Condon factors, Einstein A values, and lifetimes are reported for this transition.

Ricca, Alessandra↗

Making the Impossible Possible: Strategies for Fast POMDP Monitoring

Systems modeled as partially observable Markov decision processes (POMDPs) can be tracked quickly with three restrictions: all actions are grouped together, the out-degree of each system state is bounded by a constant, and the number of non-zero elements in the belief state is bounded by a (different) constant. With these restrictions, the tracking algorithm operates in constant time and linear space. The first restriction assumes that the action itself is unobservable. The second restriction defines a subclass of POMDPs that covers however a wide range of problems. The third restriction is an approximation technique that can lead to a potentially vexing problem: an observation may be received that has probability according to the restricted belief state. This problem of impossibility will cause the belief state to collapse. In this paper we discuss the tradeoffs between the constant bound on the belief state and the quality of the solution. We concentrate on strategies for overcoming the impossibility problem and demonstrate initial experimental results that indicate promising directions.

Washington, Richard↗

A Convex Approach to Fault Tolerant Control

The design of control laws for dynamic systems with the potential for actuator failures is considered in this work. The use of Linear Matrix Inequalities allows more freedom in controller design criteria than typically available with robust control. This work proposes an extension of fault-scheduled control design techniques that can find a fixed controller with provable performance over a set of plants. Through convexity of the objective function, performance bounds on this set of plants implies performance bounds on a range of systems defined by a convex hull. This is used to incorporate performance bounds for a variety of soft and hard failures into the control design problem.

Maghami, Peiman G.↗

Novel Route to Transition Metal Isothiocyanate Complexes Using Metal Powders and Thiourea

A new synthetic route to isothiocyanate-containing materials is presented. Eight isothiocyanate- 4-methylpyridine (y-picoline) compounds were prepared by refluxing metal powders (Mn, Fe, Co, Ni, and Cu) with thiourea in y-picoline. With the exception of compound 5,prepared with Co, the isothiocyanate ligand was generated in situ by the isomerization of thiourea to NH4+SCN- at reflux temperatures. The complexes were characterized by x-ray crystallography. Compounds 1,2, and 8 are the first isothiocyanate- 4-methylpyridine anionic compounds ever prepared and structurally characterized. Compounds 1 and 2 are isostructural with four equatorially bound isothiocyanate ligands and two axially bound y-picoline molecules. Compound 8 is a five-coordinate copper(II) molecule with a distorted square-pyramidal geometry. Coordinated picoline and two isothiocyanates form the basal plane and the remaining isothiocyanate is bound at the apex. Structural data are presented for all compounds.

Harris, Jerry D.↗

Numerical Simulation of High Drag Reduction in a Turbulent Channel Flow with Polymer Additives

The addition of small amounts of long chain polymer molecules to wall-bounded flows can lead to dramatic drag reduction. Although this phenomenon has been known for about fifty years, the action of the polymers and its effect on turbulent structures are still unclear. Detailed experiments have characterized two distinct regimes (Warholic et al. 1999), which are referred to as low drag reduction (LDR) and high drag reduction (HDR). The first regime exhibits similar statistical trends as Newtonian flow: the log-law region of the mean velocity profile remains parallel to that of the Newtonian ow but its lower bound moves away from the wall and the upward shift of the log-region is a function of drag reduction, DR. Although streamwise fluctuations are increased and transverse ones are reduced, the shape of the rms velocity profiles is not qualitatively modified. At higher drag reductions, of the order of 40-50%, the ow enters the HDR regime for which the slope of the log-law is dramatically augmented and the Reynolds shear stress is small (Warholic et al. 1999; Ptasinski et al. 2001). The drag reduction is eventually bounded by a maximum drag reduction (MDR) (Virk & Mickley 1970) which is a function of the Reynolds number. While several experiments report mean velocity profiles very close to the empirical profile of Virk & Mickley (1970) for MDR conditions, the observations regarding the structure of turbulence can differ significantly. For instance, Warholic et al. (1999) measured a near-zero Reynolds shear stress, whereas a recent experiment (Ptasinski et al. 2001) shows evidence of non-negligible Reynolds stress in their MDR flow. To the knowledge of the authors, only the LDR regime has been documented in numerical simulations (Sureshkumar et al. 1997; Dimitropoulos et al. 1998; Min et al. 2001; Dubief & Lele 2001; Sibilla & Baron 2002). This paper discusses the simulation of polymer drag reduced channel ow at HDR using the FENE-P (Finite Elastic non-linear extensibility-Peterlin) model which was used for the first LDR simulation by Sureshkumar et al. (1997). Flow and polymer parameters are close to realistic polymer drag reducing conditions. High drag reductions are achieved by using finite differences and a robust time stepping technique. A minimal channel flow is also used as a numerical experiment to investigate the effect of the outer region turbulent structures on the overall drag at HDR. The drag reducing action of the model is finally studied through the structure of energy transfers from the polymers to the velocity components. This investigation sheds some light on the details of polymer drag reduction.

Dubief, Yves↗

Electron-Hydrogen Elastic Scattering

Scattering by single-electron systems is always of interest because the wave function of the target is known exactly. Various approximations have been employed to take into account distortion produced in the target. Among them are the method of polarized orbitals and the close coupling approximation. Recently, e-H and e-He+ S-wave scattering in the elastic region has been studied using the Feshbach projection operator formalism. In this approach, the usual Hartree-Fock and exchange potentials are augmented by an optical potential and the resulting phase shifts have rigorous lower bounds. Now this method is being applied to the e-H P-wave scattering in the elastic region. The number of terms in the Hylleraas-type wave function for the 1,3 P phase shifts is 84 and the resulting phase shifts (preliminary) are given. The results have been given up to five digits because to that accuracy they are rigorous lower bounds. They are in general agreement with the variational (VAR) results of Armstead, and those obtained from the intermediate energy R-matrix method (RM) of Scholz et al., and the finite element method (FEM) of Botero and Shertzer. The later two methods do not provide any bounds on phase shifts.

Bhatia, A. K.↗

AveBoost2: Boosting for Noisy Data

AdaBoost is a well-known ensemble learning algorithm that constructs its constituent or base models in sequence. A key step in AdaBoost is constructing a distribution over the training examples to create each base model. This distribution, represented as a vector, is constructed to be orthogonal to the vector of mistakes made by the pre- vious base model in the sequence. The idea is to make the next base model's errors uncorrelated with those of the previous model. In previous work, we developed an algorithm, AveBoost, that constructed distributions orthogonal to the mistake vectors of all the previous models, and then averaged them to create the next base model s distribution. Our experiments demonstrated the superior accuracy of our approach. In this paper, we slightly revise our algorithm to allow us to obtain non-trivial theoretical results: bounds on the training error and generalization error (difference between training and test error). Our averaging process has a regularizing effect which, as expected, leads us to a worse training error bound for our algorithm than for AdaBoost but a superior generalization error bound. For this paper, we experimented with the data that we used in both as originally supplied and with added label noise-a small fraction of the data has its original label changed. Noisy data are notoriously difficult for AdaBoost to learn. Our algorithm's performance improvement over AdaBoost is even greater on the noisy data than the original data.

Oza, Nikunj C.↗

Environment Partitioning and Reactivity of Polybrominated Diphenylethers

Polybrominated diphenyl ethers (PBDEs) are an important class of flame retardants. Annual global demand for these compounds was over 67,000 metric tons in 2001. PBDEs have recently been extensively investigated as environmental contaminants because they have been detected in air, sediment, and tissue samples from urban and remote areas. Important issues include quantifying PBDE partitioning in various environmental compartments, and elucidating transformation pathways. The partitioning of PBDE congeners to aerosols was estimated for 16 sites in the United States, Canada, and Mexico. The aerosol particles were PM2.5, the total suspended particle (TSP) concentration varied between 3.0 - 55.4 micro g/cubic meter, and the organic fraction ranged from 11 - 41%; these data are published values for each site. It is estimated that the largest fraction of each PBDE associated with the aerosol particles occurs in Mexico City, and the smallest fraction in Colorado Plateau. Although the organic fraction in Mexico City is about 60% of that observed in the Colorado Plateau, the TSP is larger by a factor of about 18.5, and it is the difference in TSP that strongly influences the fraction of particle-bound PBDE in this case. PBDE partitioning to PM2.5 particles also varies seasonally because of temperature variations. For the less brominated congeners the percentage that is particle-bound is relatively low, regardless of air temperature. In contrast, the heavier congeners exhibit a significant temperature dependence: as the temperature decreases (fall, winter) the percentage of PBDE that is particle-bound increases. The partitioning calculations complement experimental data indicating that decabromodiphenyl ether (DBDE) dissolved in hexane transforms very rapidly when irradiated with solar light. DBDE is the most highly brominated PBDE congener (10 bromine atoms) and occurs in the commercial formulation which is subject to the largest global demand.

Hua, Inez↗

Lipid Biomarkers for a Hypersaline Microbial Mat Community

The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. Various lipids associated with specific microbial groups can serve as biomarkers for establishing organism source and function in contemporary microbial ecosystems (membrane lipids), and by analogy, potential relevance to ancient organic-rich sedimentary rocks (geolipids). As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments. Our recent work has focused on lipid biomarker analysis of a potential analogue for such ancient mats growing in a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. The aerobic, surface layer of this mat (0 to 1 mm) contained a variety of ester-bound fatty acids (FA) representing a diverse bacterial population including cyanobacteria, sulphate reducers (SRB) and heterotrophs. Biomarkers for microeukaryotes detected in this layer included sterols, C-20 polyunsaturated FA and a highly branched isoprenoid, diagnostic for diatoms. Cyanobacteria were also indicated by the presence of a diagnostic set of mid-chain methylalkanes. C-28, to C-34 wax esters (WXE) present in relatively small amounts in the upper 3 mm of the mat are considered biomarkers for green non-sulphur bacteria. Ether-bound isoprenoids were also identified although in considerably lower abundance than ester-bound FA (approx. 1:l0). These complex ether lipids included archatol, hydroxyarchaeol and a C-40 tetraether, all in small amounts. After ether cleavage with boron tribromide, the major recovered isoprenyl was a C-30:1. This C(sub 30;1) yelded squalane after hydrogenation, a known geobiomarker for hypersaline environments in ancient oils and sediments. In this mat, it represents the dominant Archaeal population. The carbon isotopic composition of biomarker lipids were generally depleted relative to the bulk organic material (delta C-13 TOC -10%). Most depleted were the cyanobacterial methylalkanes at -27% with FA such as the SRB biomarker, 10- methyl C-I6, somewhat heavier at -16%, and WXE at -17%. The C-30:1 isoprenyl was most enriched with delta C-13 in the -7 to -11% range, much too heavy to represent the methanogen population responsible for mat methane values measured at -60%.

Jahnke, Linda↗

The purification and properties of a cd-cytochrome nitrite reductase from Paracoccus halodenitrificans

Paracoccus halodenitrificans, grown anaerobically in the presence of nitrite, contained membrane and cytoplasmic nitrite reductases. When assayed in the presence of phenazine methosulfate and ascorbate, the membrane-bound enzyme produced nitrous oxide whereas the cytoplasmic enzyme produced nitric oxide. When both enzymes were assayed in the presence of methyl viologen and dithionite, the cytoplasmic enzyme produced ammonia. Following solubilization, the membrane-bound enzyme behaved like the cytoplasmic enzyme, producing nitric oxide in the presence of phenazine methosulfate and ascorbate, and ammonia when assayed in the presence of methyl viologen and dithionite. The cytoplasmic and membrane-bound enzymes were purified to essentially the same specific activity. Only a single nitrite-reductase activity was detected on electrophoretic gels and the electrophoretic behavior of both enzymes suggested they were identical. The spectral properties of both enzymes suggested they were cd-type cytochromes. These data suggest that the products of nitrite reduction by the cd-cytochrome nitrite reductase are determined by the location of the enzyme and the redox potential of the electron donor.

NASA Center ARC↗

Integrated approaches to terminal Proterozoic stratigraphy: an example from the Olenek Uplift, northeastern Siberia

In the Olenek Uplift of northeastern Siberia, the Khorbusuonka Group and overlying Kessyusa and Erkeket formations preserve a significant record of terminal Proterozoic and basal Cambrian Earth history. A composite section more than 350 m thick is reconstructed from numerous exposures along the Khorbusuonka River. The Khorbusuonka Group comprises three principal sedimentary sequences: peritidal dolomites of the Mastakh Formation, which are bounded above and below by red beds; the Khatyspyt and most of the overlying Turkut formations, which shallow upward from relatively deep-water carbonaceous micrites to cross-bedded dolomitic grainstones and stromatolites; and a thin upper Turkut sequence bounded by karst surfaces. The overlying Kessyusa Formation is bounded above and below by erosional surfaces and contains additional parasequence boundaries internally. Ediacaran metazoans, simple trace fossils, and vendotaenids occur in the Khatyspyt Formation; small shelly fossils, more complex trace fossils, and acritarchs all appear near the base of the Kessyusa Formation and diversify upward. The carbon-isotopic composition of carbonates varies stratigraphically in a pattern comparable to that determined for other terminal Proterozoic and basal Cambrian successions. In concert, litho-, bio-, and chemostratigraphic data indicate the importance of the Khorbusuonka Group in the global correlation of terminal Proterozoic sedimentary rocks. Stratigraphic data and a recently determined radiometric date on basal Kessyusa volcanic breccias further underscore the significance of the Olenek region in investigations of the Proterozoic-cambrian boundary.

Non-NASA Center↗

A role for cysteine 3635 of RYR1 in redox modulation and calmodulin binding

Oxidation of the skeletal muscle Ca(2+) release channel (RYR1) increases its activity, produces intersubunit disulfide bonds, and blocks its interaction with calmodulin. Conversely, bound calmodulin protects RYR1 from the effects of oxidants (Zhang, J.-Z., Wu, Y., Williams, B. Y., Rodney, G., Mandel, F., Strasburg, G. M., and Hamilton, S. L. (1999) Am. J. Physiol. 276, Cell Physiol. C46-C53). In addition, calmodulin protects RYR1 from trypsin cleavage at amino acids 3630 and 3637 (Moore, C. P., Rodney, G., Zhang, J.-Z., Santacruz-Toloza, L., Strasburg, G. M., and Hamilton, S. L. (1999) Biochemistry 38, 8532-8537). The sequence between these two tryptic sites is AVVACFR. Alkylation of RYR1 with N-ethylmaleimide (NEM) blocks both (35)S-apocalmodulin binding and oxidation-induced intersubunit cross-linking. In the current work, we demonstrate that both cysteines needed for the oxidation-induced intersubunit cross-link are protected from alkylation with N-ethylmaleimide by bound calmodulin. We also show, using N-terminal amino acid sequencing together with analysis of the distribution of [(3)H]NEM labeling with each sequencing cycle, that cysteine 3635 of RYR1 is rapidly labeled by NEM and that this labeling is blocked by bound calmodulin. We propose that cysteine 3635 is located at an intersubunit contact site that is close to or within a calmodulin binding site. These findings suggest that calmodulin and oxidation modulate RYR1 activity by regulating intersubunit interactions in a mutually exclusive manner and that these interactions involve cysteine 3635.

Non-NASA Center↗

CCAAT/enhancer-binding protein delta is a critical regulator of insulin-like growth factor-I gene transcription in osteoblasts

Insulin-like growth factor-I (IGF-I) plays a major role in promoting skeletal growth by stimulating bone cell replication and differentiation. Prostaglandin E2 and other agents that induce cAMP production enhance IGF-I gene transcription in cultured rat osteoblasts through a DNA element termed HS3D, located in the proximal part of the major rat IGF-I promoter. We previously determined that CCAAT/enhancer-binding protein delta (C/EBPdelta) is the key cAMP-stimulated regulator of IGF-I transcription in these cells and showed that it transactivates the rat IGF-I promoter through the HS3D site. We now have defined the physical-chemical properties and functional consequences of the interactions between C/EBPdelta and HS3D. C/EBPdelta, expressed in COS-7 cells or purified as a recombinant protein from Escherichia coli, bound to HS3D with an affinity at least equivalent to that of the albumin D-site, a known high affinity C/EBP binding sequence, and both DNA elements competed equally for C/EBPdelta. C/EBPdelta bound to HS3D as a dimer, with protein-DNA contact points located on guanine residues on both DNA strands within and just adjacent to the core C/EBP half-site, GCAAT, as determined by methylation interference footprinting. C/EBPdelta also formed protein-protein dimers in the absence of interactions with its DNA binding site, as indicated by results of glutaraldehyde cross-linking studies. As established by competition gel-mobility shift experiments, the conserved HS3D sequence from rat, human, and chicken also bound C/EBPdelta with similar affinity. We also found that prostaglandin E2-induced expression of reporter genes containing human IGF-I promoter 1 or four tandem copies of the human HS3D element fused to a minimal promoter and show that these effects were enhanced by a co-transfected C/EBPdelta expression plasmid. Taken together, our results provide evidence that C/EBPdelta is a critical activator of IGF-I gene transcription in osteoblasts and potentially in other cell types and species.

NASA Discipline Musculoskeletal↗

Complex high affinity interactions occur between MHCI and superantigens

Staphylococcal enterotoxins A and C1 (SEA or SEC1) bound to major histocompatibility-I (MHCI) molecules with high affinity (binding constants ranging from 1.1 microM to 79 nM). SEA and SEC1 directly bound MHCI molecules that had been captured by monoclonal antibodies specific for H-2Kk, H-2Dk, or both. In addition, MHCI-specific antibodies inhibited the binding of SEC1 to LM929 cells and SEA competitively inhibited SEC1 binding; indicating that the superantigens bound to MHCI on the cell surface. The affinity and number of superantigen binding sites differed depending on whether MHCI was expressed in the membrane of LM929 cells or whether it was captured. These data support the hypothesis that MHCI molecules can serve as superantigen receptors.

NASA Discipline Cell Biology↗

Ceruloplasmin copper induces oxidant damage by a redox process utilizing cell-derived superoxide as reductant

Oxidative damage by transition metals bound to proteins may be an important pathogenic mechanism. Ceruloplasmin (Cp) is a Cu-containing plasma protein thought to be involved in oxidative modification of lipoproteins. We have previously shown that Cp increased cell-mediated low-density lipoprotein (LDL) oxidation by a process requiring cell-derived superoxide, but the underlying chemical mechanism(s) is (are) unknown. We now show that superoxide reduction of Cp Cu is a critical reaction in cellular LDL oxidation. By bathocuproine disulfonate (BCS) binding and by superoxide utilization, we showed that exogenous superoxide reduces a single Cp Cu atom, the same Cu required for LDL oxidation. The Cu atom remained bound to Cp during the redox cycle. Three avenues of evidence showed that vascular cells reduce Cp Cu by a superoxide-dependent process. The 2-fold higher rate of Cp Cu reduction by smooth muscle cells (SMC) compared to endothelial cells (EC) was consistent with their relative rates of superoxide release. Furthermore, Cp Cu reduction by cells was blocked by Cu,Zn superoxide dismutase (SOD1). Finally, the level of superoxide produced by EC and SMC was sufficient to cause the amount of Cu reduction observed. An important role of Cp Cu reduction in LDL oxidation was suggested by results showing that SOD1 inhibited Cp Cu reduction and LDL oxidation by SMC with equal potency, while tumor necrosis factor-alpha stimulated both processes. In summary, these results show that superoxide is a critical cellular reductant of divalent transition metals involved in oxidation, and that protein-bound Cu is a substrate for this reaction. The role of these mechanisms in oxidative processes in vivo has yet to be defined.

NASA Discipline Regulatory Physiology↗

Program Monitoring with LTL in EAGLE

We briefly present a rule-based framework called EAGLE, shown to be capable of defining and implementing finite trace monitoring logics, including future and past time temporal logic, extended regular expressions, real-time and metric temporal logics (MTL), interval logics, forms of quantified temporal logics, and so on. In this paper we focus on a linear temporal logic (LTL) specialization of EAGLE. For an initial formula of size m, we establish upper bounds of O(m(sup 2)2(sup m)log m) and O(m(sup 4)2(sup 2m)log(sup 2) m) for the space and time complexity, respectively, of single step evaluation over an input trace. This bound is close to the lower bound O(2(sup square root m) for future-time LTL presented. EAGLE has been successfully used, in both LTL and metric LTL forms, to test a real-time controller of an experimental NASA planetary rover.

Barringer, Howard↗

Gas Motion in a Local Supersonic Region and Conditions of Potential-Flow Breakdown

For a certain Mach number of the oncoming flow, the local velocity first reaches the value of the local velocity of sound (M = 1) at some point on the surface of the body located within the flow. This Mach number is designated the critical Mach number M(sub cr). By increasing the flow velocity, a supersonic local region is formed bounded by the body contour and the line of transition from subsonic to supersonic velocity. As is shown by observations with the Toepler apparatus, at a certain flow Mach number M > M(sub cr) a shock wave is formed near the body that closes the local supersonic region from behind. The formation of the shock wave is associated with the appearance of an additional resistance defined as the wave drag. In this paper, certain features are described of the flow in the local supersonic region, which is bounded by the contour of the body and the transition line, and conditions are sought for which the potential flow with the local supersonic region becomes impossible and a shock wave occurs. In the first part of the paper, the general properties of the potential flow in the local supersonic region, bounded by the contour of the profile and the transition line, are established. It is found that at the transition line, if it is not a line of discontinuity, the law of monotonic variation of the angle of inclination of the velocity vector holds (monotonic law). An approximation is given for the change in velocity at the contour of the body. The flow about a contour having a straight part is studied. In the second part of the paper, an approximation is given of the magnitudes of the accelerations at the interior points of the supersonic region. With the aid of these approximations, it is shown that for profiles convex to the flow the breakdown of the potential flow,associated with an increase of the Mach number of the oncoming flow, cannot be due to the formation of an envelope of the characteristics within the supersonic region. On the basis of the monotonic law, the transitional Mach number M is found, beyond which the potential flow with local supersonic region becomes impossible.

Nikolskii, A. A.↗