A computational study of shock speeds in high-performance shock tubes

This paper describes U2DE, a finite-volume code that numerically solves the Euler equations. The code was used to perform multi-dimensional simulations of the gradual opening of a primary diaphragm in a shock tube. From the simulations, the speed of the developing shock wave was recorded and compared with other estimates. The ability of U2DE to compute shock speed was confirmed by comparing numerical results with the analytic solution for an ideal shock tube. For high initial pressure ratios across the diaphragm, previous experiments have shown that the measured shock speed can exceed the shock speed predicted by one-dimensional models. The shock speeds computed with the present multi-dimensional simulation were higher than those estimated by previous one-dimensional models and, thus, were closer to the experimental measurements. This indicates that multi-dimensional flow effects were partly responsible for the relatively high shock speeds measured in the experiments.

Mechanistic aspects of proton chain transfer: A computational study for the green fluorescent protein chromophore

We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging “water” that already has substantial negative charge.

Synthesis and structure elucidation of kappa-casein (45-87) - A two dimensional nuclear magnetic resonance study

We have shown that 44 amino acid residues N-terminal segment of kappa-casein exhibits considerable a-helical structure. This prompted us to investigate the structures of the remaining segments of kappa-casein. Thus, in this study the chemical synthesis and structure elucidation of the peptide 45-87 amino acid residues of kappa-casein is reported. The peptide was assembled using solid phase peptide synthesis methodology on pam resin, cleaved via HF, freeze dried and, after purification, characterised by mass spectrometry (observed m/z 4929; calculated mit 4929.83). The amino acid sequence of the peptide is: CKPVALINNQFLPYPYYAKPAAVRSPAQILQWQVLSNTVPAKA Its structure elucidation has been carried out using circular dichroism (CD) and nuclear magnetic resonance (NMR) techniques. CD spectrum of the peptide shows it to be a random structure in water but in 30% trifluoroethanol the peptide exhibits considerable structure. The 1D and 2D NMR spectra corroborated the results of CD. The structure elucidation of the peptide using TOCSY and NOESY NMR techniques will be discussed.

Computational tools for the study of allergens

Allergy is a major cause of morbidity worldwide. The number of characterized allergens and related information is increasing rapidly creating demands for advanced information storage, retrieval and analysis. Bioinformatics provides useful tools for analysing allergens and these are complementary to traditional laboratory techniques for the study of allergens. Specific applications include structural analysis of allergens, identification of B- and T-cell epitopes, assessment of allergenicity and cross-reactivity, and genome analysis. In this paper, the most important bioinformatic tools and methods with relevance to the study of allergy have been reviewed.

A synthesis of the findings from the Quake Impact Study: A two year investigation of the psychosocial sequelae of the 1989 Newcastle earthquake

This paper summarises the major findings from the Quake Impact Study (QIS), a four-phase longitudinal project that was conducted in the aftermath of the 1989 Newcastle (Australia) earthquake. A total of 3,484 subjects participated in at least one component of the QIS, comprising a stratified sample of 3,007 drawn from community electoral rolls and 477 from specially targeted supplementary samples (the injured, the displaced, the owners of damaged businesses, and the helpers). Subjects' initial earthquake experiences were rated in terms of weighted indices of exposure to threat and disruption. Psychological morbidity was measured at each phase using the General Health Questionnaire (GHQ-12) and the Impact of Event Scale (IES). Selected findings and key conclusions are presented for each of six areas of investigation: service utilisation during the first 6 months post-disaster; patterns of earthquake experience and short-term (6-month) psychosocial outcome; earthquake exposure and medium term (2-year) psychosocial outcome; vulnerability factors and medium-term psychosocial outcome: specific community groups at increased risk (e.g., the elderly and immigrants from non-English-speaking backgrounds); the effects of stress debriefing for helpers. Threshold morbidity (i.e., likely caseness) rates are also presented for a broad range of subgroups. In addition to presenting an overview of the QIS, this paper synthesises the major findings and discusses their implications for future disaster management and research from a mental health perspective.

Embracing ligands. Synthesis, characterisation and the correlation between 59Co NMR and ligand field parameters of Co(III) complexes with a new class of nitrogen-thioether multidentate ligand

The syntheses of the hexadentate ligands 2,2,10,10-tetra(methyleneamine)-4,8-dithiaundecane (PrN(4)S(2)amp), 2,2,11,11-tetra(methyleneamine)-4,9-dithiadodecane (BuN(4)S(2)amp), and 1,2-bis(4,4-methyleneamine)-2-thiapentyl)benzene (XyN(4)S(2)amp) are reported and the complexes [Co(RN(4)S(2)amp)](3+) (R = Pr, Bu, Xy) characterised by single crystal X-ray study. The low-temperature (11 K) absorption spectra have been measured in Nafion films. From the observed positions of both spin-allowed (1)A(1g) --> T-1(1g) and (1)A(1g) --> T-1(2g) and spin forbidden (1)A(1g) --> T-3(1g) and (1)A(1g) --> T-3(2g) bands, octahedral ligand-field parameters (10D(q), B and C) have been determined. DFT calculations suggest that significant interaction between the d-d and CT excitations occurs for the complexes. The calculations offer an explanation for the observed deviations from linearity of the relationship between Co-59 magnetogyric ratio and beta(DeltaE)(-1) (beta = the nephelauxetic ratio; DeltaE the energy of the (1)A(1g) --> T-1(1g) transition) for a series of amine and mixed amine/thioether donor complexes.

Synthesis, characterization and DFT studies of the cobalt(III) complex of a tetrapodal pentadentate N4S donor ligand

The synthesis of the pentadentate ligand 2,6-bis(3,3-dimethyl-2,4-dioxocyclohexanyl)-4-thiaheptane (N(4)Samp) is described. The synthetic pathway involves the coupling of two 1,3-(dimethylenedioxy)-2-methyl-2-(methylene-p-toluenesulfonyl)propane moieties with sodium sulfide and subsequent synthetic elaboration to prepare the final N4S donor system. The cobalt(III) complex [Co(N(4)Samp)Cl](2+) has been prepared and subsequently crystallized as the tetrachlorozincate salt. The X-ray structure analysis confirms the pentadentate nature of the ligand and shows the thioether donor occupying one apex with four equivalent amine donors effectively occupying the equatorial plane of the molecule. The sixth coordination site is occupied by a chloro ligand. The electronic absorption and C-13 NMR spectra have been studied. DFT calculations have been employed to explore structural and mechanistic comparisons between [Co(N(4)Samp)Cl](2+) and an analogous pentaamine complex.

Study of flow behaviour in a three-product cyclone using computational fluid dynamics

Simplicity in design and minimal floor space requirements render the hydrocyclone the preferred classifier in mineral processing plants. Empirical models have been developed for design and process optimisation but due to the complexity of the flow behaviour in the hydrocyclone these do not provide information on the internal separation mechanisms. To study the interaction of design variables, the flow behaviour needs to be considered, especially when modelling the new three-product cyclone. Computational fluid dynamics (CFD) was used to model the three-product cyclone, in particular the influence of the dual vortex finder arrangement on flow behaviour. From experimental work performed on the UG2 platinum ore, significant differences in the classification performance of the three-product cyclone were noticed with variations in the inner vortex finder length. Because of this simulations were performed for a range of inner vortex finder lengths. Simulations were also conducted on a conventional hydrocyclone of the same size to enable a direct comparison of the flow behaviour between the two cyclone designs. Significantly, high velocities were observed for the three-product cyclone with an inner vortex finder extended deep into the conical section of the cyclone. CFD studies revealed that in the three-product cyclone, a cylindrical shaped air-core is observed similar to conventional hydrocyclones. A constant diameter air-core was observed throughout the inner vortex finder length, while no air-core was present in the annulus. (c) 2006 Elsevier Ltd. All rights reserved.

Catalytic effects of subsurface carbon in the chemisorption of hydrogen on a Mg(0001) surface: an ab-initio study

Ab initio density functional theory (DFT) calculations are performed to explore possible catalytic effects on the dissociative chemisorption of hydrogen on a Mg(0001) surface when carbon is incorporated into Mg materials. The computational results imply that a C atom located initially on a Mg(0001) surface can migrate into the subsurface and occupy an fcc interstitial site, with charge transfer to the C atom from neighboring Mg atoms. The effect of subsurface C on the dissociation of H-2 on the Mg(0001) surface is found to be relatively marginal: a perfect sublayer of interstitial C is calculated to lower the barrier by 0.16 eV compared with that on a pure Mg(0001) surface. Further calculations reveal, however, that sublayer C may have a significant effect in enhancing the diffusion of atomic hydrogen into the sublayers through fcc channels. This contributes new physical understanding toward rationalizing the experimentally observed improvement in absorption kinetics of H2 when graphite or single walled carbon nanotubes (SWCNT) are introduced into the Mg powder during ball milling.