Classical Continuous System Simulation (CSS) is restricted to modelling continuous flows, and therefore, cannot correctly realise a conceptual model with discrete objects. The development of Full Potential CSS solves this problem by (1) handling discrete quantities as discrete and continuous matter as continuous, (2) preserving the sojourn time distribution of a stage, (3) implementing attributes correctly, and (4) describing different types of uncertainties in a proper way. In order to apply Full Potential CSS a new software, StochSD, has been developed. This thesis evaluates StochSD's ability to model Full Potential CSS, where the points 1-4 above are included. As a test model a well-defined conceptual epidemic model, which includes all aspects of Full Potential CSS, was chosen. The study was performed by starting with a classical SIR model and then stepwise add the different aspects of the Conceptual Model. The effects of each step were demonstrated in terms of size and duration of the epidemic. Finally, the conceptual model was also realised as an Agent Based Model (ABM). The results from 10 000 replications each of the CSS and ABM models were compared and no statistical differences could be confirmed. The conclusion is that StochSD passed the evaluation.

[pt] Este trabalho analisa a propagação de uma doença epidemiológica com uma abordagem estocástica. Na análise, o número de indivíduos que cada membro infectado da população pode infectar é modelado como uma variável aleatória e o número de indivíduos infectados ao longo do tempo é modelado como um processo estocástico de ramificação. O foco do trabalho é caracterizar a influência do modelo probabilístico da variável aleatória que modela o contágio entre indivíduos na disseminação da doença e na probabilidade de extinção, e analisar a influência de uma vacinação em massa no controle da propagação da doença. A comparação é feita com base em histogramas e estatísticas amostrais do número de indivíduos infectados ao longo do tempo, como média e variância. Os modelos estatísticos referentes à parte que trata de uma população não vacinada são calculados usando simulações de Monte Carlo para 3 diferentes famílias de variáveis aleatórias: binomial, geométrica-1 e geométrica-0. Para cada família, 21 distribuições diferentes foram selecionadas e, para cada distribuição, 4000 simulações do processo de ramificação foram computadas. Os modelos estatísticos referentes a uma população parcialmente vacinada foram calculados usando simulações de Monte Carlo para a família de variável aleatória binomial. Para essa família, 21 distribuições diferentes foram selecionadas e, para cada uma delas foram escolhidas 6 diferentes percentagens de população vacinada. Para cada percentagem, foram analisadas vacinas com 4 diferentes eficácias. No total, foram realizadas 2.2 milhões de simulações, caracterizando o problema como big data. / [en] This work analyzes the spread of an epidemiological disease with a stochastic approach. In the analysis, the number of individuals that each infected member of the population can infect is modeled as a random variable and the number of infected individuals over time is modeled as a stochastic branching process. The focus of the work is to characterize the influence of the probabilistic model of the random variable that models contagion between individuals on the spread of the disease and the probability of extinction, and to analyze the influence of mass vaccination in controlling the spread of a disease. The comparison is based on histograms and sample statistics of the number of infected individuals over time, such as mean and variance. Statistical models for the chapter dealing with a vaccine free population are calculated using Monte Carlo simulations for 3 different families of random variables: binomial, geometric-1 and geometric-0. For each of the 3 families, 21 different distributions were selected and, for each distribution, 4000 simulations of the branching process were computed. Statistical models for a partially vaccinated population were calculated using Monte Carlo simulations for one family of random variable: the binomial. For it, 21 different distributions were selected and, for each of them, 6 different percentages of the vaccinated population were chosen. For each of them, 4 different vaccine efficacy were stipulated. In total, 2.2 million simulations were performed, featuring a big data problem.

[pt] O objetivo principal desta dissertação é o de buscar formas de modelar e controlar, adequadamente, condicionadores de ar de janela, pois tratam-se de máquinas que possuem um elevado consumo de energia, perdendo somente para o chuveiro elétrico. A contribuição do mesmo para a demanda do setor doméstico é da ordem de 7 %. As pesquisas de posse de eletrodomésticos mostram que somente 6 % dos domicílios têm instalada tal tipo de máquina, o que representa um expressivo potencial de crescimento para os próximos anos na aquisição deste produto. É oportuno observar que em edifí­cios comerciais, 48 % da energia é consumida com refrigeração, o que implica na necessidade de novos projetos em que centrais de grande porte sejam implantadas, visando um gasto comparativamente menor ao somatório de aparelhos individuais. / [en] This work involves the modeling of window air conditioners, with the purpose to obtain the electrical potential consume by itself, related to the medium external temperature. To obtain such goal, it was necessary the study of all features which involve their several components, aiming the conduct fitted from the parts, due to the result expected. It was made a public research with the users from these equipments. From this result, it was developed a stochastic model to be used in energy demand from a specific region, considering that the equipment / machine in use shows similar qualifications. After that, it was added to the system of machine a direct load control, which delay the compressor, obtaining an efficient working from it (saving demand), without affecting deeply normal using conditions. Finally, comparing two examples mentioned above, it was concluded that in the less powerful equipment (air conditioner) the thermal control with changed features, had good results, while more powerful equipments are more economic with direct load control. / [es] Esta disertación tiene como objetivo principal buscar formas de modelar y controlar adecuadamente, equipos de aire acondicionado de tipo ventana, por tratarse de equipos que poseen un alto consumo de energía, superado tan solo por la ducha eléctrica. La contribución de éste para la demanda del sector doméstico es del orden de 7 %. Las investigaciones sobre la pose de electrodomésticos muestran que sólo el 6 % de los domicilios tiene instalada tal tipo de máquina, lo que representa um expresivo potencial de crescimiento en la adquisición de este producto para los próximos años. Es oportuno observar que en edificios comerciales, 48 % de la energia consumida se refiere a refrigeración, lo que nos lleva a la necesidad de nuevos proyectos donde, centrales de grande porte seam implantadas, para conseguir un gasto comparativamente menor a la suma de equipos individuales.

La décroissance de la consommation électrique des dispositifs électroniques leur a permis une croissance sans précédent. Néanmoins, les éléments de stockage d’énergie (piles et batteries), bien qu’ayant initialement promus ce développement, sont devenus un frein à la prolifération des microsystèmes électroniques, de part leur durée de vie limitée ainsi que des considérations environnementales (recyclage). Pour palier à ce problème, la possibilité d’exploiter l’énergie de l’environnement immédiat du dispositif a été proposée et a fait l’objet de nombreuses recherches au cours des dernières années. En particulier, la récupération d’énergie mécanique exploitant l’effet piézoélectrique est l’une des pistes les plus étudiées actuellement pour la conception de microgénérateurs autonomes capables d’alimenter les dispositifs électroniques. Par ailleurs, dans ce domaine, il a été démontré qu’un traitement non-linéaire de la tension de sortie de l’élément actif permet d’améliorer les capacités de récupération de l’énergie vibratoire. L’une de ces approches, nommée «Synchronized Switch Harvesting on Inductor» (récupération par commutation synchronisée sur inductance) et consistant en une inversion de la tension de manière synchrone avec le déplacement, s’est montrée particulièrement efficace, pouvant augmenter la quantité d’énergie récupérée par un facteur supérieur à 10. Cette dernière conduit à un processus cumulatif qui augmente artificiellement la tension de sortie de l’élément piézoélectrique ainsi qu’à une réduction du déphasage entre tension et vitesse de déplacement ; ces deux effets conduisant à l’augmentation importante des capacités de conversion. Néanmoins, l’étude des microgénérateurs d’énergie s’est quasiment toujours faite en considérant une excitation sinusoïdale, ce qui correspond rarement à la réalité. Peu de travaux expérimentaux, et encore moins théoriques, ont été menés en considérant une excitation large bande ; ceci étant d’autant plus vrai pour les dispositifs incluant un élément non-linéaire. Ainsi l’objectif de cette thèse est d’étudier le comportement des récupérateurs d’énergie piézoélectriques interfacés de manière non-linéaire. Pour ce faire, différentes approches seront envisagées, en considérant le processus de commutation comme un « auto-échantillonnage » du signal, ou en appliquant des théories d’analyse stochastique pour quantifier les performances du dispositif. Ainsi, plusieurs formes d’excitation appliquée au système pourront être analysées, permettant d’étudier la réponse du système sous des conditions plus réalistes. Toujours dans l’optique d’une implémentation réaliste, un autre objectif de cette thèse consistera à évaluer l’impact de la récupération d’énergie par couplage sismique sur la structure hôte, démontrant la nécessité d’envisager le système dans sa globalité afin de disposer de systèmes performants capables de convertir efficacement l’énergie vibratoire sous forme électrique pour un usage ultérieur. / A nonlinear interface consisting in a switching device has been proved to improve the piezoelectric harvester performance. Although existing works are usually done under single frequency excitation. practical cases are more likely broadband and random. In addition, the coupling effect due to the harvesting process is also an interesting issue to discuss. In terms of energy conversion process in seismic piezoelectric harvesters, mechanical interactions between host structure and harvester is an essential issue as well. The purpose of this work is to analysis seismic type piezoelectric harvesters from a practical perspective and to provide an optimal design of the latter. The broadband modeling based on the concepts of self-sampling and self-aliasing is described under broadband excitations for the nonlinear interface called "Periodic Switching Harvesting on Inductor" (PSHI). For this technique, the switching device is considered to be turned on at a fixed switching frequency. Then stochastic modeling is applied to have mathematical expressions that can describe broadband performance of the harvester with power spectral density (PSD) function of signals. As the switch is turned on at a given frequency, the modeling can be derived using cyclostationary theory. The effectiveness of stochastic modeling is validated with experimental measurements and time-domain iterative calculations, and the harvester performance under a band-limited noise excitation is discussed under bell-curved spectra excitations. An optimal switching frequency slightly less than twice the harvester resonant frequency is proved to have the optimal power output under the optimal resistive load. This switching frequency is however dependent on the electromechanical coupling factor of the harvester. Another part of this work discusses the interaction between the host structure and the harvester. The analysis is conducted with a Two-Degree-of-Freedom (TDOF) model. An energy conversion loop is therefore formed between the host structure and the harvester, within the harvester and the resistive load. The TDOF model is verified with Finite Element model and experimental work. An optimal mass ratio is proved to provide the maximal power output. The modeling is further applied to a practical self-powered Structural Health Monitoring system providing the best design of the harvester. A practical consideration of the broadband excitation is also introduced showing the effect of frequency detuning between the host structure and the harvester. Compared to constant force factor case, the harvester performance with a constant electromechanical coupling factor is surprisingly with very little decreases due to the mismatching of harvester and host structure resonant.

In spite of remarkable progress in molecular biology, our understanding of the dynamics and functions of intra- and inter-cellular biological networks has been hampered by their complexity. Kinetics modelling, an important type of mathematical modelling, provides a rigorous and reliable way to reveal the complexity of biological networks. In this thesis, two genetic regulatory networks have been investigated via kinetic models. In the first part of the study, a model is developed to represent the transcriptional regulatory network essential for the circadian rhythms in Drosophila. The model incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not used to describe the regulation of genes, instead the explicit reactions of binding and unbinding processes of transcription factors to promoters are modelled. The model is described by a set of ordinary differential equations and the parameters are estimated from the in vitro experimental data of the clocks’ components. The simulation results show that the model reproduces sustained circadian oscillations in mRNA and protein concentrations that are in agreement with experimental observations. It also simulates the entrainment by light-dark cycles, the disappearance of the rhythmicity in constant light and the shape of phase response curves resembling that of experimental results. The model is robust over a wide range of parameter variations. In addition, the simulated E-box mutation, perS and perL mutants are similar to that observed in the experiments. The deficiency between the simulated mRNA levels and experimental observations in per01, tim01 and clkJrk mutants suggests some differences in the model from reality. Finally, a possible function of VRI/PDP1 loops is proposed to increase the robustness of the clock. In the second part of the study, the sources of intrinsic noise and the influence of extrinsic noise are investigated on an intracellular viral infection system. The contribution of the intrinsic noise from each reaction is measured by means of a special form of stochastic differential equation, the chemical Langevin equation. The intrinsic noise of the system is the linear sum of the noise in each of the reactions. The intrinsic noise arises mainly from the degradation of mRNA and the transcription processes. Then, the effects of extrinsic noise are studied by means of a general form of stochastic differential equation. It is found that the noise of the viral components grows logarithmically with increasing noise intensities. The system is most susceptible to noise in the virus assembly process. A high level of noise in this process can even inhibit the replication of the viruses. In summary, the success of this thesis demonstrates the usefulness of models for interpreting experimental data, developing hypotheses, as well as for understanding the design principles of genetic regulatory networks.

Living cells are made up of networks of interacting genes, proteins and other bio-molecules. Simple interactions between network components in forms of feedback regulations can lead to complex collective dynamics. A key task in cell biology is to gain a thorough understanding of the dynamics of intracellular systems and processes. In this thesis, a combined approach of mathematical modelling, computational simulation and analytical techniques, has been used to obtain a deeper insight into the dynamical aspects of a variety of feedback systems commonly encountered in cells. These systems range from model system with detailed available molecular knowledge to general regulatory motifs with varying network structures. Deterministic as well as stochastic modelling techniques have been employed, depending primarily on the specific questions asked. The first part of the thesis focuses on dissecting the principles behind the regulatory design of the Tryptophan Operon system in Escherichia coli. It has evolved three negative feedback loops, namely repression, attenuation and enzyme inhibition, as core regulator mechanisms to control the intracellular level of tryptophan amino acid, which is taken up for protein synthesis. Despite extensive experimental knowledge, the roles of these seemingly redundant loops remain unclear from a dynamical point of view. We aim to understand why three loops, rather than one, have evolved. Using a large-scale perturbation/response analysis through modelling and simulations and novel metrics for transient dynamics quantification, it has been revealed that the multiple negative feedback loops employed by the tryptophan operon are not redundant. In fact, they have evolved to concertedly give rise to a much more efficient, adaptive and stable system, than any single mechanism would provide. Since even the full topology of feedback interactions within a network is insufficient to determine its behavioural dynamics, other factors underlying feedback loops must be characterised to better predict system dynamics. In the second part of the thesis, we aim to derive these factors and explore how they shape system dynamics. We develop an analytical approach for stability and bifurcation analysis and apply it to class of feedback systems commonly encountered in cells. Our analysis showed that the strength and the Hill coefficient of a feedback loop play key role in determining the dynamics of the system carrying the loop. Not only that, the position of the loop was also found to be crucial in this decision. The analytical method we developed also facilitates parameter sensitivity analysis in which we investigate how the production and degradation rates affect system dynamics. We find that these rates are quite different in the way they shape up system behaviour, with the degradation rates exhibiting a more intricate manner. We demonstrated that coupled-loop systems display greater complexity and a richer repertoire of behaviours in comparison with single-loop ones. Different combinations of the feedback strengths of individual loops give rise to different dynamical regimes. The final part of the thesis aims to understand the effects of molecular noise on dynamics of specific systems, in this case the Tryptophan Operon. We developed two stochastic models for the system and compared their predictions to those given by the deterministic model. By means of simulations, we have shown that noise can induce oscillatory behaviour. On the other hand, incorporating noise in an oscillatory system can alter the characteristics of oscillation by shifting the bifurcation point of certain parameters by a substantial amount. Measurement of fluctuations reveals that that noise at the transcript level is most significant while noise at the enzyme level is smallest. This study highlights that noise should not be neglected if we want to obtain a complete understanding of the dynamic behaviour of cells.

The management and administration of legally defined marine boundaries in Australia is subject to a variety of political, legal and technical challenges. The purpose of this thesis is to address three of the technical challenges faced in the implementation of marine boundaries which cannot be dealt with by applying conventional land cadastre and land administration principles. The three challenges that are identified and addressed are (i) marine boundary delimitation and positioning uncertainty, (ii) the construction and maintenance of four dimensional marine parcels, and (iii) the modelling and management of marine boundary uncertainty metadata.

Les astrocytes sont des cellules gliales du système nerveux central, essentielles à la formation des synapses, à la barrière hémato-encéphalique ainsi qu’au maintien de l'homéostasie. Récemment, les astrocytes ont été identifiés comme éléments clés du traitement de l'information dans le système nerveux central. Les astrocytes peuvent communiquer avec les neurones au niveau des synapses et moduler la communication neuronale en libérant des gliotransmetteurs et en absorbant des neurotransmetteurs. L’utilisation de nouvelles techniques comme la microscopie à super-résolution et les indicateurs calciques encodés génétiquement a permis de révéler une grande diversité spatio-temporelle des signaux calciques astrocytaires. La majorité de ces signaux sont observés au sein de leurs prolongements cellulaires, qui sont le site de communication entre neurones et astrocytes. Ces prolongements sont trop fins pour être observés en microscopie optique conventionnelle, de sorte que la microscopie à super-résolution et la modélisation informatique sont les seules méthodes adaptées à leur étude. Les travaux présentés dans cette thèse ont pour but d’étudier l'effet des propriétés spatiales (telles que la géométrie cellulaire, les distributions moléculaires et la diffusion) sur les signaux calciques dans les prolongements astrocytaires. Historiquement, les signaux calciques ont été modélisés à l'aide d'approches déterministes non spatiales. Ces modèles ont permis l'étude des signaux calciques à l’échelle de la cellule entière voire à l’échelle du réseau de cellules. Ces méthodes ne prennent cependant pas en compte la stochasticité inhérente aux interactions moléculaires ainsi que les effets de diffusion, qui jouent un rôle important dans les petits volumes. Cette thèse présente un modèle stochastique et spatial qui a été développé dans le but d’étudier les signaux calciques dans les prolongements fins astrocytaires. Ce travail a été réalisé en collaboration avec des expérimentateurs, qui nous ont fourni des données de microscopie électronique et à super-résolution. Ces données ont permis de valider le modèle. Les simulations du modèle suggèrent que (1) la diffusion moléculaire, fortement influencée par la concentration et la cinétique des buffers calciques endogènes et exogènes, (2) l'organisation spatiale intracellulaire des molécules, notamment le co-clustering des canaux calciques, (3) la géométrie du reticulum endoplasmique et sa localisation dans la cellule, (4) la géométrie cellulaire influencent fortement les signaux calciques et pourraient être responsables de leur grande diversité spatio-temporelle. Ces travaux contribuent à une meilleure compréhension du traitement de l’information par les astrocytes, un prérequis pour une meilleure compréhension de la communication entre les neurones et les astrocytes ainsi que de son influence sur le fonctionnement du cerveau. / Astrocytes are predominant glial cells in the central nervous system, which are essential for the formation of synapses, participate to the blood-brain barrier and maintain the metabolic, ionic and neurotransmitter homeostasis. Recently, astrocytes have emerged as key elements of information processing in the central nervous system. Astrocytes can contact neurons at synapses and modulate neuronal communication via the release of gliotransmitters and the uptake of neurotransmitters. The use of super-resolution microscopy and highly sensitive genetically encoded Ca2+ indicators (GECIs) has revealed a striking spatiotemporal diversity of Ca2+ signals in astrocytes. Most astrocytic signals occur in processes, which are the sites of neuron-astrocyte communication. Those processes are too fine to be resolved by conventional light microscopy so that super-resolution microscopy and computational modeling remain the only methodologies to study those compartments. The work presented in this thesis aims at investigating the effect of spatial properties (as e.g cellular geometry, molecular distributions and diffusion) on Ca2+ signals in those processes, which are deemed essential in such small volumes. Historically, Ca2+ signals were modeled with deterministic well-mixed approaches, which enabled the study of Ca2+ signals in astrocytic networks or whole-cell events. Those methods however ignore the stochasticity inherent to molecular interactions as well as diffusion effects, which both play important roles in small volumes. In this thesis, we present the spatially-extended stochastic model that we have developed in order to investigate Ca2+ signals in fine astrocytic processes. This work was performed in collaboration with experimentalists that performed electron as well as super-resolution microscopy. The model was validated against experimental data. Simulations of the model suggest that (1) molecular diffusion, strongly influenced by the concentration and kinetics of endogenous and exogenous buffers, (2) intracellular spatial organization of molecules, notably the co-clustering of Ca2+ channels, (3) ER geometry and localization within the cell, (4) cellular geometry strongly influence Ca2+ dynamics and can be responsible for the striking diversity of astrocytic Ca2+ signals. This work contributes to a better understanding of astrocyte Ca2+ signals, a prerequisite for understanding neuron-astrocyte communication and its influence on brain function.

Subject of the dissertation is a probability analysis on creation of embankment subsoil filtration deformations. Out of the broad topic of filtration deformations, the dissertation is focused at initiation of the process. At this phase, the overlying layers downstream of levee get uplifted, and eventually get breached. The process of downstream subsoil failure probability estimation is formulated using mathematical and statistical modelling. Within the scope of parametrical study the suggested method is applied onto a test environment. Results of the probability estimation are compared with results obtained using Limit state design method. The results of stochastic modelling can be used for improvement of Limit state design method precision.

Uganda is using a strategy called treatment as prevention where as many individuals as possible that are infected with HIV receive treatment. As a result, the number of newly infected individuals has decreased significantly. However, there is a discussion about a potential problem regarding transmitted drug resistance. This work aims to investigate if this in fact will be a problem in the future, and to estimate the costs for different scenarios. Through developing a population-based mathematical model that describes transmission dynamics of HIV in Uganda, stochastic simulations are made for different conditions. Through analysing our simulations, we can see that Uganda may have to change their approach to HIV treatment. / För att minska smittoriskerna av HIV nyttjar Uganda en strategi som syftar till att behandla så många smittade personer som möjligt. Detta har lett till en signifikant minskning av antalet smittade personer. Det har dock uppstått en diskussion angående om läkemedels-resistent smitta kan komma att utgöra ett problem. Detta arbete syftar till att undersöka om detta kan utgöra ett problem i framtiden samt till att uppskatta de kostnader som kan uppstå i olika typer av scenarion. Under olika förutsättningar genomförs stokastiska simuleringar med hjälp av en matematisk populationsmodell framtagen för att beskriva spridningen av HIV i Uganda. Genom att analysera resultaten från olika simuleringar dras slutsatsen att Uganda kan behöva omvärdera sitt tillvägagångssätt gällande behandling av HIV.