The semi-automatic parallelisation of scientific application codes using a computer aided parallelisation toolkit

The shared-memory programming model can be an effective way to achieve parallelism on shared memory parallel computers. Historically however, the lack of a programming standard using directives and the limited scalability have affected its take-up. Recent advances in hardware and software technologies have resulted in improvements to both the performance of parallel programs with compiler directives and the issue of portability with the introduction of OpenMP. In this study, the Computer Aided Parallelisation Toolkit has been extended to automatically generate OpenMP-based parallel programs with nominal user assistance. We categorize the different loop types and show how efficient directives can be placed using the toolkit's in-depth interprocedural analysis. Examples are taken from the NAS parallel benchmarks and a number of real-world application codes. This demonstrates the great potential of using the toolkit to quickly parallelise serial programs as well as the good performance achievable on up to 300 processors for hybrid message passing-directive parallelisations.

Vibrational spectroscopy and DFT calculations of di-amino acid cyclic peptides. Part I: cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(t-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C-2 and C-1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cydo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cydo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ~ 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring.

Cyclic voltammetry and spectroelectrochemical study of nickel and cobalt diphenyltetraazaannulene complexes

The absorption spectra. cyclic voltammetry and spectroelectrochemistry of [Ni(II)DPTAA] and [Co(II)DPTAA] (DPTAA = 6,13-diphenyldibenzo[b,i][1,4,8,11] tetraaza[14]annulene) complexes in DMF are reported in detail. The ligand oxidation is observed for [Ni(II)DPTAA] at +0.70 V vs. SCE whereas Ni2(+/+) occurs at - 1.60 V. For [Co(II)DPTAA], a ligand oxidation redox couple is seen at +0.56 V while the Co2+/+ and Co2+/3+ redox couples appear at -1.21 and +0.24 V, respectively. All observed redox couples are assigned to reversible one-electron processes on account of peak separations and scan-rate dependency. These processes were further investigated by spectroelectrochemistry for [Co(II)DPTAA]. For [Co(II)DPTAA], axial ligation of pyridine was found to shift the Co2+/3+ redox couple more negative. while the ligand oxidation was shifted to more positive potentials. From a spectrophotometric titration of [Co(II)DPTAA] with pyridine an equilibrium constant, K-f, was determined for the binding of pyridine to [Co(II)DPTAA]. This was found to be 10.2 dm(3) mol(-1), slightly lower than that of [Co(II)TAA], indicating the influence of the phenyl groups. From this value and shifts in the Co2+/3+ redox couple upon ligation, an equilibrium constant for the binding of pyridine to [Co(III)DPTAA], K'(f), was found to be 5.06 x 10(6) dm(3) mol(-1). (c) 2007 Elsevier B.V. All rights reserved.

Physiological Adaptation Of Mytilus-Edulis To Cyclic Temperatures

Mytilus edulis adapted to cyclic temperatures by reducing the amplitude of response of oxygen consumption and filtration rate over a period of approximately two weeks, and thereby increasing their independence of temperature within the range of the fluctuating regime. When acclimated to cyclic temperature regimes within the range from 6 to 20°C, the metabolic and feeding rates, measured at different temperatures in the cycle, were not significantly different from the adapted response to equivalent constant temperatures. Physiological adaptation ofMytilus edulis to different thermal environments was reflected in their metabolic and feeding rate-temperature curves. Animals subjected to marked diel fluctuations in environmental temperature showed an appropriate region of temperature-independence, whereas animals from a population not experiencing large diel temperature fluctuations showed no region of temperature-independence. In a fluctuating thermal environment which extended above the normal environmental maxima, respiratory adaptation occurred at higher temperatures than was possible in a constant thermal environment. The feeding rate was also maintained at higher temperatures in a cyclic regime than was possible under constant thermal conditions. This represented a shortterm extension of the zone of activity in a fluctuating thermal environment. The net result of these physiological responses to high cyclic and constant temperatures has been assessed in terms of ‘scope for growth’. Animals acclimated to cyclic temperatures between 21 and 29°C had a higher scope for growth at 29°C and were less severely stressed than those maintained at the constant temperature of 29°C.

Effects of the novel (Pro(3))GIP antagonist and exendin(9-39)amide on GIP- and GLP-1-induced cyclic AMP generation, insulin secretion and postprandial insulin release in obese diabetic (ob/ob) mice: evidence that GIP is the major physiological incretin

AIMS/HYPOTHESIS: This study examined the biological effects of the GIP receptor antagonist, (Pro3)GIP and the GLP-1 receptor antagonist, exendin(9-39)amide.

METHODS: Cyclic AMP production was assessed in Chinese hamster lung fibroblasts transfected with human GIP or GLP-1 receptors, respectively. In vitro insulin release studies were assessed in BRIN-BD11 cells while in vivo insulinotropic and glycaemic responses were measured in obese diabetic ( ob/ ob) mice.

RESULTS: In GIP receptor-transfected fibroblasts, (Pro(3))GIP or exendin(9-39)amide inhibited GIP-stimulated cyclic AMP production with maximal inhibition of 70.0+/-3.5% and 73.5+/-3.2% at 10(-6) mol/l, respectively. In GLP-1 receptor-transfected fibroblasts, exendin(9-39)amide inhibited GLP-1-stimulated cyclic AMP production with maximal inhibition of 60+/-0.7% at 10(-6) mol/l, whereas (Pro(3))GIP had no effect. (Pro(3))GIP specifically inhibited GIP-stimulated insulin release (86%; p<0.001) from clonal BRIN-BD11 cells, but had no effect on GLP-1-stimulated insulin release. In contrast, exendin(9-39)amide inhibited both GIP and GLP-1-stimulated insulin release (57% and 44%, respectively; p<0.001). Administration of (Pro(3))GIP, exendin(9-39)amide or a combination of both peptides (25 nmol/kg body weight, i.p.) to fasted (ob/ob) mice decreased the plasma insulin responses by 42%, 54% and 49%, respectively (p<0.01 to p<0.001). The hyperinsulinaemia of non-fasted (ob/ob) mice was decreased by 19%, 27% and 18% (p<0.05 to p<0.01) by injection of (Pro3)GIP, exendin(9-39)amide or combined peptides but accompanying changes of plasma glucose were small.

CONCLUSIONS/INTERPRETATION: These data show that (Pro(3))GIP is a specific GIP receptor antagonist. Furthermore, feeding studies in one commonly used animal model of obesity and diabetes, (ob/ob) mice, suggest that GIP is the major physiological component of the enteroinsular axis, contributing approximately 80% to incretin-induced insulin release.

2,4-dinitrophenol as an activating reagent in a facile preparation of cyclic phosphate trimesters

Abstract 2,4-Dinitrophenol was employed with benzyloxy-bis-(diisopropylamino)phosphine to synthesise the cyclic phosphate derivatives of a series of alkane diols (HO–(CH2)n–OH, n=2–6) in good isolated yields. Tetrazole and DNP were compared by 31P NMR spectroscopy for their ability to catalyse the cyclisation at the P(III) stage. Investigation of the phosphate triester stability under various oxidation and chromatographic conditions resulted in the optimisation of the isolation procedures of the chemically unstable cyclic compounds. Conditions for debenzylation were developed to yield the corresponding cyclic phosphodiesters quantitatively. The methodology was further applied to the preparation and isolation of the cyclic phosphate derivative of a carbohydrate.