Numerical modelling and visualization of the evolution of extensional fault systems

The purpose of this work is split into two categories, the first was to analyse the application of real-time Physics Engine software libraries for use in calculating a geological numerical model. Second was the analysis of the applicability of glyph and implicit surface based visualization techniques to explore fault systems produced by the model. The current state of the art in Physics Engines was explored by redeveloping a Discrete Element Model to be calculated using NVIDIA's PhysX engine. Analyses regarding the suitability of the engine in terms of numerical accuracy and developmental capabilities is given, as well as the definition of a specialised and bespoke parallelisation technique. The use of various glyph based visualizations is explored to define a new standardised taxonomy for geological data and the MetaBall visualization technique was applied to reveal three dimensional fault structures as an implicit surface. Qualitative analysis was undertaken in the form of a user study, comprising of interviews with expert geologists. The processing pipeline used by many Physics Engines was found to be comparable to the design of Discrete Element Model software, however, aspects of their design, such as integration accuracy, limitation to single precision floating point and imposed limits on the scale of n-body problem means their suitability is restricted to specific modelling cases. Glyph and implicit surface based visualization have been shown to be an effective way to present a geological Discrete Element Model, with the majority of experts interviewed able to perceive the fault structures that it contained. Development of a new engine, or modification of one that exists in accordance with the findings of this thesis would result in a library extremely well suited to the problem of rigid-body simulation for the sciences.EThOS - Electronic Theses Online ServiceNERCGBUnited Kingdo

Porting TELEMAC-MASCARET to OPENPOWER and experimenting GPU offloading to accelerate the TOMAWAC module

Hydrodynamic

Mikrocytids Are a Broadly Distributed and Divergent Radiation of Parasites in Aquatic Invertebrates

publisher: Elsevier articletitle: Mikrocytids Are a Broadly Distributed and Divergent Radiation of Parasites in Aquatic Invertebrates journaltitle: Current Biology articlelink: http://dx.doi.org/10.1016/j.cub.2014.02.033 content_type: article copyright: Copyright © 2014 The Authors. Published by Elsevier Ltd.The file attached is the Published/publisher’s pdf version of the articl

The effect of octopaminergic compounds on the behaviour and transmission of Gyrodactylus

Background: The high transmission potential of species belonging to the monogenean parasite genus Gyrodactylus, coupled with their high fecundity, allows them to rapidly colonise new hosts and to increase in number. One gyrodactylid, Gyrodactylus salaris Malmberg, 1957, has been responsible for devastation of Altantic salmon (Salmo salar L.) populations in a number of Norwegian rivers. Current methods of eradicating G. salaris from river systems centre around the use of non-specific biocides, such as rotenone and aluminium sulphate. Although transmission routes in gyrodactylids have been studied extensively, the behaviour of individual parasites has received little attention. Specimens of Gyrodactylus gasterostei Gläser, 1974 and G. arcuatus Bychowsky, 1933, were collected from the skin of their host, the three-spined stickleback (Gasterosteus aculeatus L.), and permitted to attach to the substrate. The movements of individual parasites were recorded and analysed. Results: The behaviour patterns of the two species were similar and parasites were more active in red light and darkness than in white light. Four octopaminergic compounds were tested and all four inhibited the movements of parasites. Treatment ultimately led to death at low concentrations (0.2 μM), although prolonged exposure was necessary in some instances. Conclusions: Octopaminergic compounds may affect the parasite's ability to locate and remain on its host and these or related compounds might provide alternative or supplementary treatments for the control of G. salaris infections. With more research there is potential for use of octopaminergic compounds, which have minimal effects on the host or its environment, as parasite-specific treatments against G. salaris infections

The Magnitude of Global Marine Species Diversity

Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century

Ultrastructural characterisation of Marteilia species (Paramyxea) from Ostrea edulis, Mytilus edulis and Mytilus galloprovincialis in Europe

6 pages, 1 figure, 2 tables.A focused ultrastructural study of Marteilia spp. found in cultured Ostrea edulis, Mytilus edulis and Mytilus galloprovincialis from France and Spain was conducted with emphasis placed on haplosporosomes, striated plate-like inclusions and spore wall morphology. Two types of haplosporosome were identified, sphaeroid and oblate, which were common to the parasite in all 3 host species. A total of 492 haplosporosomes were measured; those from the Marteilia sp. in Mytilus spp. were marginally smaller than those in Ostrea edulis. Spore wall morphology was found to vary depending on the state of maturity of the parasite‹the more mature the parasite, the thicker the wall surrounding it. It is suggested that the current criteria used to distinguish M. maurini from M. refringens are invalid and that M. maurini was relegated to a junior synonym of M. refringens.This work was supported by European Union FAIR contract 94C 85/13.Peer reviewe

Susceptibility of a number of bivalve species to the protozoan parasite Bonamia ostreae and their ability to act as vectors for this parasite

8 pages, 1 figure, 7 tables.The protozoan parasite Bonamia ostreae (Pichot et al., 1980) is a serious pathogen of the native European flat oyster Ostrea edulis. Field and laboratory based experiments were carried out in Ireland and Spain to investigate the susceptibility to this protozoan of the Pacific oyster Crassostrea gigas, the mussels Mytilus edulis and Mytilus galloprovincialis, the European native clam Ruditapes decussatus and the Manila clam Ruditapes philippinarum. Their ability to act as vectors or intermediate hosts was also investigated. The study corroborated previous findings that demonstrated that flat oysters can be successfully infected both naturally in the field and experimentally in the laboratory, and the pathogen can be transmitted directly between flat oysters in the laboratory. However, the other bivalves tested could not be infected with the parasite either naturally or experimentally, and these bivalves did not appear to act as vectors or intermediate hosts for the parasite. These results have implications for movements of bivalves between areas within the European Union.This work was supported by European Union FAIR contract 94C 85/13.Peer reviewe

Simulating Slosh Induced Damping, with Application to Aircraft Wing-like Structures

: The added damping generated by liquid sloshing in a tank has been utilized in a number of civil applications, including aviation, to reduce the vibration of the system. As part of a wider EU H2020 project called SLOWD (Sloshing Wing Dynamics), the presented study performed numerical simulations on the slosh-induced damping of liquid in tanks that were under free decay oscillations and embedded in an aircraft wing-like structure. A new open-source partitioned fluid–structure interaction software framework is presented and employed for the numerical simulations. Periodic sloshing waves and violent vertical fluid motions are observed in the study. These demonstrate the effects of slosh-induced damping under different excitation amplitudes of the structure and a varying number of baffled regions within the tank. Various sloshing patterns caused by different combinations of the excitation amplitude and compartment numbers lead to different induced dampings of the free decay motion. We observed a distinctly non-monotonic function on the slosh damping when the initial excitation amplitude is small (i.e., 0.25), with a 59% reduction when we increase the number of baffled compartments from one to four, and a 153% increase when moving from one to eight compartments. This is due to the change in the sloshing wave frequency, resulting in a significant change in the impact of the fluid between the tank ceiling and the wave crests. When the initial excitation amplitude is large (i.e., 1.0), there is no significant change in the slosh-induced damping when changing the number of compartments in the tank, for the range of parameters considered, due to the highly turbulent fluid motion. This work is expected to form the basis of further, more detailed studies within the context of the SLOWD project and its ever-expanding experimental data output