Bibliography: leaves 217-238. / ix, 238 leaves ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Applied Mathematics, 1995?

Bibliography: leaves 132-153. / viii, 153 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Spatially explicit models and computer intensive analysis were employed to explore how processes acting at the individual level scale up to population dynamics when processes are variable in space as well as the consequences of sampling spatially complex variability for drawing conclusions from limited ecological data. Dispersal and variation in marsupial mortality and development in relation to habitat selection and quality were studied, while evaluating spatially explicit models. The study of dynamics models of tick populations on sleepy lizards considered the effect of spatial and temporal variability, and demonstrated that counting ticks is a poor indicator of tick abundance. The "virtual ecologist" model is a useful method for linking the output of spatially explicit population models to reality, and will be a valuable approach for improving the design of ecological field research on spatially complex landscapes. / Thesis (Ph.D.)--University of Adelaide, Dept. of Environmental Science and Management, 1999?

Bibliography: leaves 132-153. Spatially explicit models and computer intensive analysis were employed to explore how processes acting at the individual level scale up to population dynamics when processes are variable in space as well as the consequences of sampling spatially complex variability for drawing conclusions from limited ecological data. Dispersal and variation in marsupial mortality and development in relation to habitat selection and quality were studied, while evaluating spatially explicit models. The study of dynamics models of tick populations on sleepy lizards considered the effect of spatial and temporal variability, and demonstrated that counting ticks is a poor indicator of tick abundance. The "virtual ecologist" model is a useful method for linking the output of spatially explicit population models to reality, and will be a valuable approach for improving the design of ecological field research on spatially complex landscapes.

Ever since Maynard-Smith and Price first introduced the concept of an evolutionary stable strategy (ESS) in 1973, there has been a growing amount of work in and around this field. Many new concepts have been introduced, quite often several times over, with different acronyms by different authors. This led to other authors trying to collect and collate the various terms (for example Lessard, 1990 & Eshel, 1996) in order to promote better understanding ofthe topic. It has been noticed that dynamic selection did not always lead to the establishment of an ESS. This led to the development ofthe concept ofa continuously stable strategy (CSS), and the claim that dynamic selection leads to the establishment of an ESSif it is a CSS. It has since been proved that this is not always the case, as a CSS may not be able to displace its near neighbours in pairwise ecological competitions. The concept of a neighbourhood invader strategy (NIS) was introduced, and when used in conjunction with the concept of an ESS, produced the evolutionary stable neighbourhood invader strategy (ESNIS) which is an unbeatable strategy. This work has tried to extend what has already been done in this field by investigating the dynamics of coexisting species, concentrating on systems whose dynamics are governed by Lotka-Volterra competition models. It is proved that an ESNIS coalition is an optimal strategy which will displace any size and composition of incumbent populations, and which will be immune to invasions by any other mutant populations, because the ESNIS coalition, when it exists, is unique. It has also been shown that an ESNIS coalition cannot exist in an ecologically stable state with any finite number of strategies in its neighbourhood. The equilibrium population when the ESNIS coalition is the only population present is globally stable in a n-dimensional system (for finite n), where the ESNIS coalition interacts with n - 2 other strategies in its neighbourhood. The dynamical behaviour of coexisting species was examined when the incumbent species interacted with various invading species. The different behaviour ofthe incumbent population when invaded by a coalition using either an ESNIS or an NIS phenotype underlines the difference in the various strategies. Similar simulations were intended for invaders who were using an ESS phenotype, but unfortunately the ESS coalition could not be found. If the invading coalition use NIS phenotypes then the outcome is not certain. Some, but not all of the incumbents might become extinct, and the degree to which the invaders flourish is very dependent on the nature ofthe incumbents. However, if the invading species form an ESNIS coalition, one is certain of the outcome. The invaders will eliminate the incumbents, and stabilise at their equilibrium populations. This will occur regardless of the composition and number of incumbent species, as the ESNIS coalition forms a globally stable equilibrium point when it is at its equilibrium populations, with no other species present. The only unknown fact about the outcome in this case is the number ofgenerations that will pass before the system reaches the globally stable equilibrium consisting ofjust the ESNIS. For systems whose dynamics are not given by Lotka-Volterra equations, the existence ofa unique, globally stable ESNIS coalition has not been proved. Moreover, simulations of a non Lotka-Volterra system designed to determine the applicability ofthe proof were inconclusive, due to the ESS coalition not having unique population sizes. Whether or not the proof presented in this work can be extended to non Lotka-Volterra systems remains to be determined. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2000.

Bibliography: leaves 132-153. / viii, 153 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Spatially explicit models and computer intensive analysis were employed to explore how processes acting at the individual level scale up to population dynamics when processes are variable in space as well as the consequences of sampling spatially complex variability for drawing conclusions from limited ecological data. Dispersal and variation in marsupial mortality and development in relation to habitat selection and quality were studied, while evaluating spatially explicit models. The study of dynamics models of tick populations on sleepy lizards considered the effect of spatial and temporal variability, and demonstrated that counting ticks is a poor indicator of tick abundance. The "virtual ecologist" model is a useful method for linking the output of spatially explicit population models to reality, and will be a valuable approach for improving the design of ecological field research on spatially complex landscapes. / Thesis (Ph.D.)--University of Adelaide, Dept. of Environmental Science and Management, 1999?

Severe declines in the number of some songbirds over the last 40 years have caused heated debate amongst interested parties. Many factors have been suggested as possible causes for these declines, including an increase in the abundance and distribution of an avian predator, the Eurasian sparrowhawk Accipiter nisus. To test for evidence for a predator effect on the abundance of its prey, we analyse data on 10 species visiting garden bird feeding stations monitored by the British Trust for Ornithology in relation to the abundance of sparrowhawks. We apply Bayesian hierarchical models to data relating to averaged maximum weekly counts from a garden bird monitoring survey. These data are essentially continuous, bounded below by zero, but for many species show a marked spike at zero that many standard distributions would not be able to account for. We use the Tweedie distributions, which for certain areas of parameter space relate to continuous nonnegative distributions with a discrete probability mass at zero, and are hence able to deal with the shape of the empirical distributions of the data. The methods developed in this thesis begin by modelling single prey species independently with an avian predator as a covariate, using MCMC methods to explore parameter and model spaces. This model is then extended to a multiple-prey species model, testing for interactions between species as well as synchrony in their response to environmental factors and unobserved variation. Finally we use a relatively new methodological framework, namely the SPDE approach in the INLA framework, to fit a multi-species spatio-temporal model to the ecological data. The results from the analyses are consistent with the hypothesis that sparrowhawks are suppressing the numbers of some species of birds visiting garden feeding stations. Only the species most susceptible to sparrowhawk predation seem to be affected.

Les bioprocédés ont connu un essor considérable au cours de ces dernières années et sont promis à un bel avenir. Qu'il s'agisse de la production de vaccins, de la fermentation de levures pour l'industrie alimentaire ou encore de l'épuration biologique des eaux usées, les applications sont nombreuses et les produits sont d'un intérêt capital pour l'être humain. Étant donnés le coût et le temps de mise en oeuvre de ces procédés, il est particulièrement utile de construire des simulateurs permettant de reproduire le comportement macroscopique des cultures cellulaires utilisées. Ces simulateurs peuvent servir à déterminer des conditions optimales de fonctionnement (en fonction des critères de l'utilisateur) et à tester certains outils (régulateurs, capteurs logiciels, etc.). Par ailleurs, il est nécessaire, pour le suivi et la régulation de ces procédés, de disposer de grandeurs mesurées (concentrations cellulaires, en substrats, en le produit d'intérêt, etc.). Les problèmes liés à la mesure matérielle de ces grandeurs sont nombreux: coût des capteurs, destruction des échantillons, longues périodes d'échantillonnage, temps d'analyse élevés, etc. Il est dès lors utile de construire des observateurs d'états (ou capteurs logiciels) fournissant une estimation en temps continu de grandeurs non mesurées sur la base d'un modèle mathématique et de certaines mesures matérielles.<p><p>Les modèles mathématiques sont nécessaires pour la synthèse des deux types d'outils envisagés dans ce travail (simulateurs et capteurs logiciels). Les modèles utilisés consistent en les bilans massiques des constituants apparaissant dans le schéma réactionnel, ce dernier contenant les réactions essentielles pour la description des phénomènes à l'échelle macroscopique. Au sein de ces bilans massiques, une nouvelle structure générale de modèle cinétique est proposée, possédant un certain nombre de propriétés intéressantes, telles l'interprétation physique des paramètres cinétiques, les concentrations définies positives sous certaines conditions, la garantie de stabilité entrées bornées - états bornés, ou encore la possibilité de linéarisation en les paramètres à estimer.<p><p>Une méthodologie générale d'estimation paramétrique est proposée, afin d'identifier les coefficients pseudo-stoechiométriques, les coefficients cinétiques et certains paramètres expérimentaux (concentrations initiales des cultures). Cette méthodologie possède un caractère systématique, prend en compte les erreurs de mesure sur l'ensemble des signaux (y compris à l'instant initial), fournit à l'utilisateur la covariance des erreurs d'estimation paramétrique, prend en compte intrinsèquement les contraintes de signe sur les paramètres, fournit une estimation des erreurs de simulation, permet de réduire le nombre d'équations différentielles au sein du modèle, etc. La mise en oeuvre et l'intérêt de ces outils sont illustrés en simulation (cultures bactériennes) et dans le cas d'une application réelle (cultures de cellules animales CHO).<p><p>La première catégorie d'observateurs d'états étudiée dans ce travail est celle des observateurs utilisant pleinement le modèle cinétique. L'observation d'états basée sur l'identification des conditions initiales les plus vraisemblables est plus particulièrement analysée. Elle consiste à estimer en temps continu l'entièreté de l'état par intégration d'un modèle de simulation au départ des conditions initiales les plus vraisemblables. Ces dernières sont identifiées à chaque nouvel instant de mesure sur la base de toute l'information disponible jusqu'à cet instant. Certaines propriétés mathématiques sont étudiées (dont une comparaison avec le filtre de Kalman) et un certain nombre d'extensions de la méthode sont proposées (dont une version récurrente qui ne nécessite plus de résoudre un problème d'optimisation non linéaire à chaque nouvel instant de mesure). Ces outils sont à nouveau illustrés dans le cadre des cultures de cellules animales CHO, et se basent sur les modèles de simulation développés dans la première partie du travail.<p><p>Étant donné les risques de divergence des observateurs de cette première catégorie lorsque la qualité du modèle cinétique n'est pas suffisante, une seconde catégorie est envisagée, constituée des observateurs utilisant partiellement le modèle cinétique. Dans ce contexte, un nouvelle technique est proposée consistant en un observateur hybride entre le filtre de Kalman étendu (utilisant pleinement le modèle cinétique) et l'observateur asymptotique de Bastin et Dochain (n'utilisant pas du tout le modèle cinétique). Cette structure estime (conjointement avec l'état du système) un degré de confiance en le modèle cinétique. Elle est capable d'évoluer de façon progressive, en fonction de ce degré de confiance, entre les deux solutions extrêmes (filtre de Kalman et observateur asymptotique), tirant ainsi parti des avantages respectifs de ces deux méthodes selon les conditions opératoires et la qualité du modèle cinétique. Ces outils sont validés sur des cultures bactériennes simulées.<p><p> / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

The following thesis presents a computational framework that can capture inherently non-linear and emergent biocomplex phenomena. The main motivation behind the investigations undertaken was the absence of a suitable platform that can simulate, both the continuous features as well as the discrete, interaction-based dynamics of a given biological system, or in short, dynamic reciprocity. In order to determine the most powerful approach to achieve this, the efficacy of two modelling paradigms, transport phenomena as well as agent-based, was evaluated and eventually combined. Computational Fluid Dynamics (CFD) was utilised to investigate optimal boundary conditions, in terms of meeting cellular glucose consumption requirements and exposure to physiologically relevant shear fields, that would support mesenchymal stem cell growth in a 3-dimensional culture maintained in a commercially available bioreactor. In addition to validating the default bioreactor configuration and operational parameter ranges as suitable towards sustaining stem cell growth, the investigation underscored the effectiveness of CFD as a design tool. However, due to the homogeneity assumption, an untenable assumption for most biological systems, CFD often encounters difficulties in simulating the interaction-reliant evolution of cellular systems. Therefore, the efficacy of the agent-based approach was evaluated by simulating a morphogenetic event: development of in vitro osteogenic nodule. The novel model replicated most aspects observed in vitro, which included: spatial arrangement of relevant players inside the nodule, interaction-based development of the osteogenic nodules, and the dependence of nodule growth on its size. The model was subsequently applied to interrogate the various competing hypotheses on this process and identify the one that best captures transformation of osteoblasts into osteocytes, a subject of great conjecture. The results from this investigation annulled one of the competing hypotheses, which purported the slow-down in the rate of matrix deposition by certain osteoblasts, and also suggested the acquisition of polarity to be a non-random event. The agent-based model, however, due to being inherently computationally expensive, cannot be recommended to model bulk phenomena. Therefore, the two approaches were integrated to create a modelling platform that was utilised to capture dynamic reciprocity in a bioreactor. As a part of this investigation, an amended definition of dynamic reciprocity and its computational analogue, dynamic assimilation, were proposed. The multi-paradigm platform was validated by conducting melanoma chemotaxis under foetal bovine serum gradient. Due to its CFD and agent-based modalities, the platform can be employed as both a design optimisation as well as hypothesis testing tool.

Indiana University-Purdue University Indianapolis (IUPUI) / The black blow fly, Phormia regina (Diptera: Calliphoridae), is a widely abundant fly autochthonous to North America. Like many other Calliphorids, P. regina plays a key role in several disciplines particularly in estimating post-mortem intervals (PMI). The aim of this work was to better understand the population genetic structure of this important ecological species using microsatellites from populations collected in the U.S. during 2008 and 2013. Additionally, it sought to determine the effect of limited genetic diversity on a quantitative trait throughout immature development; larval length, a measurement used to estimate specimen age. Observed heterozygosity was lower than expected at five of the six loci and ranged from 0.529-0.880 compared to expected heterozygosity that ranged from 0.512-0.980, this is indicative of either inbreeding or the presence of null alleles. Kinship coefficients indicate that individuals within each sample are not strongly related to one another; values for the wild-caught populations ranged from 0.033-0.171 and a high proportion of the genetic variation (30%) can be found among samples within regions. The population structure of this species does not correlate well to geography; populations are different to one another resulting from a lack of gene flow irrespective of geographic distance, thus inferring temporal distance plays a greater role on the genetic variation of P. regina. Among colonized samples, flies lost much of their genetic diversity, ≥67% of alleles per locus were lost, and population samples became increasingly more related; kinship coefficient values increased from 0.036 for the wild-caught individuals to 0.261 among the F10 specimens. Colonized larvae also became shorter in length following repeated inbreeding events, with the longest recorded specimen in F1 18.75 mm in length while the longest larva measured in F11 was 1.5 mm shorter at 17.25 mm. This could have major implications in forensic entomology, as the largest specimen is often assumed to be the oldest on the corpse and is subsequently used to estimate a postmortem interval. The reduction in length ultimately resulted in a greater proportion of individuals of a similar length; the range of data became reduced. Consequently, the major reduction in genetic diversity indicates that the loss in the spread of length distributions of the larvae may have a genetic influence or control. Therefore, this data highlights the importance when undertaking either genetic or development studies, particularly of blow flies such as Phormia regina, that collections of specimens and populations take place not only from more than one geographic location, but more importantly from more than one temporal event.

Indiana University-Purdue University Indianapolis (IUPUI) / The multi-protein complex of F0F1 ATP synthase has been of great interest in the fields of microbiology and biochemistry, due to the ubiquitous use of ATP as a biological energy source. Efforts to better understand this complex have been made through structural determination of segments based on NMR and crystallographic data. Some experiments have provided useful data, while others have brought up more questions, especially when structures and functions are compared between bacteria and species with chloroplasts or mitochondria. The epsilon subunit is thought to play a signi cant role in the regulation of ATP synthesis and hydrolysis, yet the exact pathway is unknown due to the experimental difficulty in obtaining data along the transition pathway. Given starting and end point protein crystal structures, the transition pathway of the epsilon subunit was examined through computer simulation.The purpose of this investigation is to determine the likelihood of one such proposed mechanism for the involvement of the epsilon subunit in ATP regulation in bacterial species such as E. coli.