A mixed directed-undirected data structure for a parallel implementation of a domain decomposition algorithm

The choice of data structures influences the parallelization, efficiency and the manageability of a mesh refinement program. We introduce a mixed directed-undirected graph that combines both communication and scheduling needs. An inverted index is maintained for the directed graph to improve code performance and readability.This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.     

Vinyl‐type polymerization of norbornene by nickel(II) bisbenzimidazole catalysts

Novel nickel(II) bisbenzimidazole complexes were prepared via a three‐step synthetic procedure consisting of aniline/diacid condensation, ligand N‐alkylation, and metal complexation. The complexes were characterized by X‐ray crystallography and found to possess a pseudotetrahedral geometry. Upon activation with methylaluminoxane, these nickel bisbenzimidazoles did not polymerize simple olefins (e.g., ethylene, propylene, and 1‐butene) but were found to carry out the rapid and efficient polymerization of norbornene. The polynorbornene products were characterized by gel permeation chromatography/light scattering, ¹³C NMR, and IR, and their Mark–Houwink and dn/dc parameters were determined. The molecular weights of the polynorbornenes were very high (weight‐average molecular weight = 587,000–797,000 g/mol). ¹³C NMR suggested that the polymerization occurred via vinyl addition (i.e., a 2,3‐linked polymer); no ring‐opened product was observed. Thermogravimetric analysis indicated that the polynorbornenes were stable up to 400 °C under nitrogen. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2095–2106, 2003     

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Synthesis and structural characterisation of a novel tris-methylene bridged compound (NO) 4Fe2 Se(μ-CH2)3

The tris-methylene bridged compound (NO)₄Fe₂Se(μ-CH₂)₃ has been isolated. It has been characterised by IR and ¹H, ¹³C, and ⁷⁷Se NMR spectroscopy. Its structure has been determined by single-crystal X-ray diffraction methods. The structure consists of a heavy atom triangle consisting of one Se and two Fe atoms. The Fe-Fe and the two Fe-Se edges are bridged by methylene groups.     

Potential of electrophilic epoxide reactions for the monitoring of acid gases in the environment

Mineral and short-chain carboxylic acid vapours and NO(x) gases were reacted with cyclohexene oxide (1,2-epoxycyclohexane) to quantitatively produce specific, thermally stable cyclohexyl derivatives. Subsequent analysis of these derivatives by gas chromatography with mass spectroscopy and flame ionisation detection afforded a multi analyte method for the assay of these gaseous acidic atmospheric species. Derivatisation was found to be quantitative for the derivatives tested and the method highly sensitive (to 0.3 mg/m3 for a 30 l sample), accurate, precise and free from apparent interferences. The technique has been applied to "acid stack gases" and a number of other acid rich atmospheres and the results obtained show good agreement with the single analyte wet chemical determinations indicating that the approach has considerable potential as a routine analytical method for measuring such atmospheric pollutants. The high specificity of the reaction mechanism and its potential for the analysis of analyte mixtures is illustrated in the assay of nitric acid and its acid anhydride, dinitrogen pentoxide.     

EXCISION OF CYCLOBUTANE DIMERS IN GENOMIC AND EPISOMAL DNA IN HUMAN CELLS

Abstract Direct determination has been made of cyclobutyl pyrimidine dimer induction and excision repair in an episomal SV40 DNA population in vivo . Maintaining SV40-transformed human (GM637) cells in confluent culture results in amplification of a mutant SV40 episome to high copy number. T4 endonuclease V was used to quantify the induction and repair of cyclobutane dimers in the SV40 episome and genomic DNA of the same cells. Differences in both parameters were observed cyclobutane dimers were induced at 1.5–2-fold greater frequency in episomal DNA and excised at a reduced rate compared to genomic DNA in the host cells.     

A single-site model for divalent transition and heavy metal adsorption over a range of metal concentrations

Metal adsorption data over a range of surface coverages typically are characterized by curvilinear metal adsorption isotherms. These isotherms generally have a slope of 1 at low surface coverage and a shallower slope at higher surface coverages. The curvature of metal adsorption isotherms with increasing surface coverage is frequently interpreted in terms of sequential adsorption onto different types of surface sites, multinuclear surface complexation, or nonideality of metal adsorption. We demonstrate that the curvature of metal adsorption isotherms can also be attributed to changes in surface charge and potential that depend on the predominant type of metal surface complex. A single-site extended triple-layer model is used to reinterpret previously studied metal adsorption isotherms and pH edges for a wide variety of metals (Cd2+, Co2+, Cu2+, Pb2+, and Zn2+) and solids (goethite, hydrous ferric oxide, corundum, and magnetite) in different electrolyte solutions (NaNO3 and NaClO4). Only metal adsorption on ferrihydrite at very low surface coverages is not consistent with the single-site triple-layer model. This discrepancy might be explained if ferrihydrite is in fact not a single phase but a mixture of two or more phases. Metal surface coverages ranging from 10(-4) to 10.2 mmol/m2 on the other minerals can be accounted for with a single-site extended triple-layer model if appropriate metal adsorption reactions are chosen. In addition, several examples suggest that, within the context of the model, surface complexation schemes can be established that describe metal adsorption over both a wide range of surface coverage and a wide range of ionic strength.     

A two-directional synthesis of (+/-)-perhydrohistrionicotoxin

An entirely two-directional synthesis of (+/-)-perhydrohistrionicotoxin is presented, utilizing a tandem oxime formation/Michael addition/[3 + 2] cycloaddition as the key step. This approach also constitutes formal syntheses of (+/-)-histrionicotoxin and (+/-)-histrionicotoxin 235A.     

Salmonella in foods: new enrichment procedure for TECRA Salmonella Visual Immunoassay using a single rv(R10) only, TT only, or dual rv(R10) and TT selective enrichment broths (AOAC official method 998.09): collaborative study

A collaborative study was conducted to compare a new enrichment procedure for the TECRA Salmonella Visual Immunoassay (TSVIA) with the reference method given in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (7th Ed.). Three food types (milk powder, pepper, and soy flour) were analyzed in Australia and 3 food types (milk chocolate, dried egg, and raw turkey) were analyzed in the United States. Thirty-eight collaborators participated in the study. The TECRA method was evaluated using both Rappaport-Vassiliadis R10 (RV(R10)) and tetrathionate (TT) broths for selective enrichment. M broth cultures arising from each of the 2 selective enrichment broths were tested in the TSVIA using 2 individual wells, one for each selective broth, and a single well to test the pooled selective enrichment broths. The results for the pooled enrichment broths were reported elsewhere. This study presents the results for the use of single enrichment broths, i.e., RV(R10) only or TT only, with the TSVIA. No significant differences (p > 0.05) were observed for the pairwise comparison of the proportion of positive samples for either RV(R10) or TT used as a single enrichment broth for the TSVIA with that for the reference method.     

Fast folding of a four-helical bundle protein

The FK506-FKBP12 binding-domain of the kinase FRAP (FRB) forms a classic up-down four-helical bundle. The folding pathway of this protein has been investigated using a combination of equilibrium and kinetic studies. The native state of the protein is stable with respect to the unfolded state by some 7 kcal mol(-1) at pH 6.0, 10 degrees C. A kinetic analysis of unfolding and refolding rate constants as a function of chemical denaturant concentration suggests that an intermediate state may be populated during folding at low concentrations of denaturant. The presence of this intermediate state is confirmed by refolding experiments performed in the presence of the hydrophobic dye 8-anilinonaphthalene-1 sulfonate (ANS). ANS binds to the partially folded intermediate state populated during the folding of FRB and undergoes a large change in fluorescence that can be detected using stopped-flow techniques. Analysis of the kinetic data suggests that the intermediate state is compact and it may even be a misfolded species that has to partially unfold before it can reach the transition state. Folding and unfolding rate constants in water are approximately 150-200 s(-1) and 0.005-0.06 s(-1), respectively, at neutral pH and 10 degrees C. The folding of FRB is somewhat slower than for other all-helical proteins, probably as a consequence of the formation of a metastable intermediate state. The folding rate constant in the absence of any populated intermediate can be estimated to be 8800 s(-1). Despite the presence of an intermediate state, which effectively slows folding, the protein still folds rapidly with a half-life of 5 ms at 10 degrees C. The dependence of the rate constants on denaturant concentration indicates that the transition state for folding is compact with some 80% of the surface area exposed in the unfolded state buried in the transition state. Data presented for FRB is compared with kinetic data obtained for other all-helical proteins.