Atomistic modelling of diffusion

This thesis describes the dimer method, which is an algorithm that can be used to find state transitions in an atomistic system, and the application of this method to two different atomistic diffusion problems. The dimer method is an algorithm that locates the saddle points of a potential field of arbitrary dimensionality. These saddle points correspond to the points of transition between metastable states of an atomistic system. A number of improvements to the algorithm of the dimer method have been described and implemented in this work. The first atomistic problem to be described is the diffusion of Au adatoms on a face-centred cubic Au(100) surface. By applying the dimer method to this system, a number of state transitions involving varying numbers of atoms are discovered, from the initial configuration of a single adatom on the surface and from configurations of two adatoms close together. [Continues.

Does biased gene conversion influence polymorphism in the circumsporozoite protein-encoding gene of Plasmodium vivax?

Variation between North Korean and Latin American isolates in the circumsporozoite (CS) protein encoding gene of the human malaria parasite Plasmodium vivax was studied. Polymorphic positions are confined to the central tandemly repeated sequences. Nucleotide substitutions in the tandem repeats produce variants; these substituted positions within the repeat array tend to be conserved between genes. The North Korean CS gene has a short insertion after the repeats encoding a 4-amino acid repeat (Ala-Gly-Gly-Asn) not found in the New World P. vivax genes. This sequence is found both flanking and within the tandem repeats of the CS genes of several strains of the Southeast Asian simian malaria parasite, Plasmodium cynomolgi. The intraspecific conservation of positions of variants within tandem repeat arrays and the interspecific conservation of probably ancestral repeat motifs at the end of these arrays are consistent with the occurrence of nonreciprocal genetic exchanges between the tandem repeats of these genes. However, a striking asymmetry in strand nucleotide composition within the tandem repeats of all CS genes leads us to suggest that biased correction of heteroduplexes formed during recombination plays a role in the evolution of these genes

The suitability of N2 to replace SF6 in a triggered spark-gap switch for pulsed power applications

The high dielectric strength of sulphur hexafluoride (SF6) when compared with other gases, coupled with safety benefits such as non-flammability and non-toxicity, has seen the widespread use of SF6 for the insulation of switching components. However, SF6 is now widely recognised as a highly damaging greenhouse gas, and investigations of the switching properties of alternative gases to replace SF6 within the bounds of existing system topologies are required. In the present paper, a comparative study has been carried out on a triggered spark-gap of type presently deployed in industrial pulsed-power machines, to determine the suitability of nitrogen (N2) to replace SF6 as the switching medium, without compromising on functionality. Experiments were performed with fast-rising trigger pulses to minimise the delay time to breakdown and jitter, and three distinct operational regimes have been identified for both gases as the pressure inside the switch is increased. The static breakdown characteristics and upper pressure boundaries of operation have been determined for both gases at a range of dc charging voltages. Measurements of the time to breakdown have shown jitters as low as 1.3 ns when operating in N2, highlighting the potential of N2 to replace SF6 without the need for re-design or replacement of the presently used switch

Distribution, Habitat, and Productivity of Tundra Swans on Victoria Island, King William Island, and Southwestern Boothia Peninsula, N.W.T.

Data on tundra swans (Cygnus columbianus columbianus) were recorded in the central and eastern Canadian Arctic, south of 77 N latitude, and on Southampton Island during the summers of 1980-85. Swans were seen on Victoria, Royal Geographical Society, King William, Stanley, and Southampton islands and on southwestern Melville and Boothia peninsulas. Most swans inhabited low-lying areas that were inundated by the sea following glaciation and are now dotted with shallow tundra ponds. Breeding swans were common in the Minto Inlet, Lady Franklin Point, and Cambridge Bay areas of Victoria Island and on King William Island and southwestern Boothia Peninsula. In August, 52-89% of the adults and subadults in these areas were seen as potential breeders, and the remainder were in nonbreeding flocks. Between 17 and 33% of the pairs had cygnets, and 10-13% of all swans were cygnets. With brood sizes of 1-3 (1.5 ±0.7 [mean ±SD] to 1.6 ±0.5), the apparent breeding success was low relative to other northern swan populations. However, these breeding populations are significant and should be considered in management plans for the eastern population of the tundra swan.Key words: arctic birds, Canada, Cygnus columbianus columbianus, distribution, habitat, Northwest Territories, productivityMots clés: oiseaux arctiques, Canada, Cygnus columbianus columbianus, distribution, habitat, Territoires du Nord-Ouest, productivit&eacute

Adverse Effects Associated With The Use Of South African Traditional Folk Remedies

A CAJM article on alternatives to western medical science.At least 80% of people in the South African black community use folk remedies obtained from traditional healers.1'2 The reasons for use of these remedies include community pressure, spiritual needs and lack of access to physicians. Because of the large numbers of people using them, most remedies are not likely to be harmful, but as with western medicine, folk remedies are associated with “iatrogenic” complications. Information about the potential toxicity of folk remedies is limited however, because of secrecy surrounding their use, so making the systematic study of the spectrum of clinical presentations and the nature of any toxic substances difficult. Studies from all over Africa are hampered by similar problems, but it is clear that the use of folk remedies is associated with significant morbidity and mortality across the continent

Maternal obesity is associated with the formation of small dense LDL and hypoadiponectinemia in the third trimester

Context: Maternal obesity is associated with high plasma triglyceride, poor vascular function, and an increased risk for pregnancy complications. In normal-weight pregnant women, higher triglyceride is associated with increased small, dense low-density lipoprotein (LDL). Hypothesis: In obese pregnancy, increased plasma triglyceride concentrations result in triglyceride enrichment of very low-density lipoprotein-1 particles and formation of small dense LDL via lipoprotein lipase. Design: Women (n = 55) of body mass index of 18–46 kg/m2 were sampled longitudinally at 12, 26, and 35 weeks' gestation and 4 months postnatally. Setting: Women were recruited at hospital antenatal appointments, and study visits were in a clinical research suite. Outcome Measures: Plasma concentrations of lipids, triglyceride-rich lipoproteins, lipoprotein lipase mass, estradiol, steroid hormone binding globulin, insulin, glucose, leptin, and adiponectin were determined. Results: Obese women commenced pregnancy with higher plasma triglyceride, reached the same maximum, and then returned to higher postnatal levels than normal-weight women. Estradiol response to pregnancy (trimester 1–3 incremental area under the curve) was positively associated with plasma triglyceride response (r2 adjusted 25%, P < .001). In the third trimester, the proportion of small, dense LDL was 2-fold higher in obese women than normal-weight women [mean (SD) 40.7 (18.8) vs 21.9 (10.9)%, P = .014], and 35% of obese, 14% of overweight, and none of the normal-weight women displayed an atherogenic LDL subfraction phenotype. The small, dense LDL mass response to pregnancy was inversely associated with adiponectin response (17%, P = .013). Conclusions: Maternal obesity is associated with an atherogenic LDL subfraction phenotype and may provide a mechanistic link to poor vascular function and adverse pregnancy outcome

A Q-methodological investigation into the meanings of cigarette consumption

This Q-methodological study identified shared subjective explanations of smoking among non-smokers, current smokers and ex-smokers, to consider whether some representations were protective or facilitated quitting. Four factors were identified: named independent addiction; independent non-addiction; anti-smoking; and social addiction. The first two factors were dominated by current and ex-smokers, and the last two by non-smokers. Differences emerged on the use of the 'addiction' concept, the use of smoking as a tool for affect management, the role of image manipulation and the general positive and negative perceptions of smoking. The functional use of the different shared smoking representations is discussed. Copyright © 2009 SAGE Publications

Tectonic evolution of the Plymouth Bay Basin

A synthesis of offshore seismic data in the Plymouth Bay and Western Approaches, and onshore basement structures and mineralisation history has allowed new constraints to be placed on the structural evolution of the late Carboniferous- Triassic Plymouth Bay Basin. These data have been combined to produce a model for the late- and post- Variscan tectonics of the Plymouth Bay area. Additional controls on the timing and magnitude of Variscan uplift and late-Variscan low-angle extensional deformation onshore are used to infer a late Carboniferous age for the earliest basin fill. These sediments were accommodated in a northeast — south-west oriented basin formed during late-orogenic extension. A change in the orientation of the depocentre in the early Permian signalled a switch to a north-west — south-east, strike-slip dominated tectonic environment

Diffusion dynamics of defects in Fe and Fe-P systems

The dimer method with the Ackland EAM potential has been used to determine the diffusion mechanisms of isolated defects in the bulk of α-Fe. Three defect systems were studied, an isolated vacancy, a P-vacancy complex and a P interstitial defect. Using an event table consisting of the transitions found using the dimer method, the kinetic Monte Carlo method has been used to simulate the diffusion of these defects. Periodic boundary conditions were used to simulate Fe crystals with finite concentrations of P atoms between 0.006 at. % and 0.038 at. %. At lower temperatures of around 350 K, substitutional P atoms in Fe act as centers of attraction for vacancy defects, such that the defect moves as a P-vacancy complex for most of the time. However, as the temperature is increased, the phosphorus atom and the vacancy spend greater amounts of time dissociated. We found that P interstitial defects can also diffuse through the lattice. Diffusion constants have been calculated for these systems at various temperatures and P concentrations. These showed that an Fe-P dumbbell is the most mobile of these defect systems and a P-vacancy complex the least mobile. For the isolated vacancy and P interstitial defect systems, the diffusion constant was found to satisfy the Arrhenius relation; the P-vacancy complex, however, showed a deviation from this relation