An increasing number of contemporary studies in aquatic ecology emphasize the im- portance of highly unsaturated fatty acids (HUFAs) at the plant-animal interface. Studies have demonstrated a wide range of fatty acid profiles in primary producers, forcing her- bivorous zooplankton to differentially retain fatty acids to meet somatic requirements. Herbivores also vary in their somatic fatty acid profiles; cladocerans collect Eicosapen- taenoic Acid (EPA), copepods prefer Docosahexaenoic Acid (DHA). Fatty acid internal reserves can be broken down to meet structural needs (i.e. phospholipid synthesis), fuel reproduction and may play a role in cold weather adaptation. Several authors have noted increases in HUFA concentration with lowering ambient temperatures. Cladoceran membranes form a gel at lower temperatures, while copepod membranes remain fluid and allow active overwintering. Both fish and crustaceans accumulate high concentrations of HUFAs during periods of rapid growth, but colimitation with elemental resources may exist. Recent modeling results suggest food webs with high quality (nutritional and biochemical) primary producers can attain inverted biomass distributions with efficient energy transfer between trophic levels. The adoption rate for this material into man- agement studies remains low, and while other sectors of the scientific community thrive on the potential of HUFAs, planktonic food-web studies are choosing traditional view points over forward thinking. Bearing in mind the emerging hypotheses on the critical factors that drive the energy flow in the plant-animal interface, my dissertation will at- tempt to address the following general questions: What are the distinct signatures of food quality and food quantity on planktonic food web dynamics? How do nutritional and biochemical factors affect the flow of energy at the plant-animal interface? What is our current understanding of the role of highly unsaturated fatty acids (HUFAs) in aquatic food webs? To what extent can the current generation of plankton models reproduce the lower food web patterns when explicitly accounting for HUFAs? Is the integration of the HUFA role into water quality management models feasible? Explicitly accounting for HUFAs requires integrating factors of animal physiology with macro-ecology: what are the ramifications? Finally, what are the evolutionary aspects of animals coping with food quality?

Das Phänomen der Rissmusterentstehung stellt ein anschauliches und numerisch nachvollziehbares Beispiel für Strukturbildung dar. Im Rahmen der vorliegenden Arbeit gelang es, einfache dreidimensionale Rissmuster zu berechnen, die durch Zugspannungen infolge inhomogener Schrumpfung durch Wärme- oder Stofftransport wachsen. Aufgrund wechselseitiger Entlastung bleiben Risse oder Teile einer Rissfront zurück. Für idealisierte periodische Rissanordnungen wurden durch bruchmechanische Verzweigungsanalyse kritische Last- und Geometrieparameter berechnet, für die sich neben der Grundlösung eine weitere Lösung finden lässt. Dadurch konnte die Frage beantwortet werden, warum verschiedene Typen von Rissmustern entstehen. Untersucht wurden Rissmuster in trocknender Stärke und Basalt sowie Tunnelrisse zwischen Glasplatten. Dafür war es nötig, die Risskontur numerisch zu bestimmen, wofür ein neues iteratives Verfahren entwickelt wurde. Für Säulen bildende Rissmuster in Basalt und trocknender Stärke mit konstanten Säulendurchmessern, welche stationär getrieben wachsen, wurde gezeigt, dass entgegen der Annahme in der Literatur eine Verzweigungslösung für zusammenhängende dreidimensionale Rissmuster existiert. Die berechneten kritischen Rissabstände unterscheiden sich nur unwesentlich von denjenigen zweidimensionaler Rissmodelle. Zum Verständnis der Herausbildung der Basaltsäulen wurde ein neuer Mechanismus gefunden, für den die Wechselwirkung zwischen Riss- und Erstarrungsfront der flüssigen Lava eine wesentliche Rolle spielt. Mittels eines iterativen Verfahrens wurde dafür die Erstarrungsfront berechnet. Die Ergebnisse zeigen gute Übereinstimmung mit den experimentellen Werten. Die Durchmesser von Stärkesäulen und Basaltsäulen nehmen nach dem gleichen Potenzgesetz mit zunehmender Wachstumsgeschwindigkeit ab. Für Tunnelrisse sind die Rissabstände nahezu konstant, obwohl entgegen ursprünglicher Annahmen gezeigt werden konnte, dass diese instationär getrieben wachsen. Als Ursache dafür wurde die durch die Rissgeometrie stark reduzierte Wechselwirkung zwischen den Tunnelrissen erkannt. Der Rissabstand nimmt potenzartig mit Dicke der trocknenden Schicht zu. Mittels einer Skalenanalyse konnte gute Übereinstimmung mit den Experimenten gefunden werden. / Crack patterns are a remarkable example of pattern formation. In this work simple three-dimensional crack patterns where analysed that are driven by inhomogeneous shrinkage caused from heat or mass transport. Caused by mutual unloading, parts of the crack front stop to grow. For idealised periodically repeatable crack configurations through fracture mechanics bifurcation analysis critical loading or geometry parameters where calculated for which beside the basic solution (growth of all cracks) another solution is possible. Analysed were crack patterns in drying starch and basalt and tunnelling cracks between glass plates. For this it was necessary to calculate the crack contour numerically, for this a new iteration method was developed. For the connected crack patterns in starch and basalt that form columns, driven stationary, it could be shown that there exists a bifurcation solution. Agreement with experimental data was found by including the solidification front ahead the crack tips. For the tunnelling cracks the crack spacing is nearly constant also they are unsteadily driven. The crack spacing scales with a power law of the thickness of the drying layer. With a scaling analysis good agreement with experimental data was found.

A bactéria Zymomonas mobilis atraiu considerável interesse nas últimas décadas devido ao seu metabolismo único e eficientes características fermentativas na produção de etanol a partir de açúcares simples. No entanto, apesar das aparentes vantagens na conversão e taxas específicas quando comparada com as leveduras, estas ainda dominam o mercado produtivo de etanol. Dentre os diversos modelos encontrados na literatura para representar o processo fermentativo de glicose através de Z. mobilis, o modelo proposto por Jöbses et al. (1986) aparenta ser bem estruturado e ideal para a criação de estratégias de controle e otimização de processos fermentativos com este microrganismo, viabilizando sua utilização em escala industrial. Fermentações de Z. mobilis em regime contínuo apresentam comportamento oscilatório para baixas taxas de diluição, fenômeno este comprovado experimentalmente. Experimentos laboratoriais foram utilizados para a estimação de parâmetros do modelo de Jöbses, através da técnica de minimização da derivada do erro da função objetivo. O novo modelo ajustado apresenta dinâmica equivalente ao modelo original de Jöbses, fato este comprovado através da construção dos diagramas de bifurcação. Os diagramas de fase dos modelos apresentam algumas diferenças estruturais entre si, entretanto, a ocorrência de multiplicidade de estados estacionários em baixos valores de taxa de diluição está presente em todos. Em bioprocessos, a obtenção de informações sobre o sistema é um tanto complexa, devido a estes meios serem muito suscetíveis a distúrbios, contaminações, além de que medidas de concentrações são relativamente dispendiosas, associadas com um alto tempo morto, o que impossibilita, muitas vezes, a implementação de sistemas de controle eficientes. Para contribuir com a resolução deste problema foi desenvolvida uma nova inferência das variáveis de estado através da informação de consumo de hidróxido de sódio, utilizado no controle de pH do meio. Inferidores de variáveis de estado que utilizam a variação no consumo de hidróxido de sódio foram ajustados e apresentaram resultados promissores, mostrando a viabilidade do desenvolvimento de metodologias para este tipo de análise, tornando a caracterização de sistemas fermentativos mais rápida e acessível, não apenas em nível acadêmico, que a desenvolvida atualmente, principalmente devido ao baixo custo associado, e a dinâmica rápida deste tipo de sensor. / The bacterium Zymomonas mobilis has attracted considerable interest in recent decades due to their unique metabolism and efficient characteristics in the production of ethanol by simple sugars. However, despite the apparent advantages in the conversion and specific rates, when compared with yeast, there is no industrial-scale fermentations with these bacteria. Among the various models found in literature to represent glucose fermentation with Z. mobilis, the model proposed by Jöbses et al. (1986) appears to be well structured and ideal for the creation of control strategies and optimization methods for increase productions. Fermentation in continuous mode with this organism exhibit oscillatory behavior at low dilution rates, phenomenon showed or demonstrated by experiments performed on laboratory scale. A laboratorial experiment also was used for estimation of new parameters group of Jöbses models, using the technique of minimization of error derivative for objective function. The new adjusted model set presents dynamics similar to the original model, fact confirmed by bifurcation analyses of both models. The diagram for these models show structural differences, but both presents steady states multiplicity and Hopf bifurcations. The obtained of fermentation characteristics is very complex, due to these reactive means being very susceptible to disturbances, contamination, among others, and concentrations measures are relatively expensive and whit a high dead time associated, which often prevents the implementation of control tools. The proposed inference of state variables by consumption rate of hydroxide sodium, used for maintenance pH medium, was tested and confirmed. Virtual sensors using the information of consumption rate of hydroxide were adjusted and have shown promising results, demonstrating the feasibility of developing methods of analysis based on this methodology, making the characterization of fermentative systems faster and cheaper them currently developed, mainly due to low cost associated, and the dynamics of this fast type of sensor.

A bactéria Zymomonas mobilis atraiu considerável interesse nas últimas décadas devido ao seu metabolismo único e eficientes características fermentativas na produção de etanol a partir de açúcares simples. No entanto, apesar das aparentes vantagens na conversão e taxas específicas quando comparada com as leveduras, estas ainda dominam o mercado produtivo de etanol. Dentre os diversos modelos encontrados na literatura para representar o processo fermentativo de glicose através de Z. mobilis, o modelo proposto por Jöbses et al. (1986) aparenta ser bem estruturado e ideal para a criação de estratégias de controle e otimização de processos fermentativos com este microrganismo, viabilizando sua utilização em escala industrial. Fermentações de Z. mobilis em regime contínuo apresentam comportamento oscilatório para baixas taxas de diluição, fenômeno este comprovado experimentalmente. Experimentos laboratoriais foram utilizados para a estimação de parâmetros do modelo de Jöbses, através da técnica de minimização da derivada do erro da função objetivo. O novo modelo ajustado apresenta dinâmica equivalente ao modelo original de Jöbses, fato este comprovado através da construção dos diagramas de bifurcação. Os diagramas de fase dos modelos apresentam algumas diferenças estruturais entre si, entretanto, a ocorrência de multiplicidade de estados estacionários em baixos valores de taxa de diluição está presente em todos. Em bioprocessos, a obtenção de informações sobre o sistema é um tanto complexa, devido a estes meios serem muito suscetíveis a distúrbios, contaminações, além de que medidas de concentrações são relativamente dispendiosas, associadas com um alto tempo morto, o que impossibilita, muitas vezes, a implementação de sistemas de controle eficientes. Para contribuir com a resolução deste problema foi desenvolvida uma nova inferência das variáveis de estado através da informação de consumo de hidróxido de sódio, utilizado no controle de pH do meio. Inferidores de variáveis de estado que utilizam a variação no consumo de hidróxido de sódio foram ajustados e apresentaram resultados promissores, mostrando a viabilidade do desenvolvimento de metodologias para este tipo de análise, tornando a caracterização de sistemas fermentativos mais rápida e acessível, não apenas em nível acadêmico, que a desenvolvida atualmente, principalmente devido ao baixo custo associado, e a dinâmica rápida deste tipo de sensor. / The bacterium Zymomonas mobilis has attracted considerable interest in recent decades due to their unique metabolism and efficient characteristics in the production of ethanol by simple sugars. However, despite the apparent advantages in the conversion and specific rates, when compared with yeast, there is no industrial-scale fermentations with these bacteria. Among the various models found in literature to represent glucose fermentation with Z. mobilis, the model proposed by Jöbses et al. (1986) appears to be well structured and ideal for the creation of control strategies and optimization methods for increase productions. Fermentation in continuous mode with this organism exhibit oscillatory behavior at low dilution rates, phenomenon showed or demonstrated by experiments performed on laboratory scale. A laboratorial experiment also was used for estimation of new parameters group of Jöbses models, using the technique of minimization of error derivative for objective function. The new adjusted model set presents dynamics similar to the original model, fact confirmed by bifurcation analyses of both models. The diagram for these models show structural differences, but both presents steady states multiplicity and Hopf bifurcations. The obtained of fermentation characteristics is very complex, due to these reactive means being very susceptible to disturbances, contamination, among others, and concentrations measures are relatively expensive and whit a high dead time associated, which often prevents the implementation of control tools. The proposed inference of state variables by consumption rate of hydroxide sodium, used for maintenance pH medium, was tested and confirmed. Virtual sensors using the information of consumption rate of hydroxide were adjusted and have shown promising results, demonstrating the feasibility of developing methods of analysis based on this methodology, making the characterization of fermentative systems faster and cheaper them currently developed, mainly due to low cost associated, and the dynamics of this fast type of sensor.

Nous présentons dans cette étude le développement de la convection à partir de différentes perturbations de l'état conductif d'une couche fluide confinée dans une cavité cylindrique, chauffée par le bas et avec une surface supérieure libre. La discrétisation spatiale du domaine repose sur la méthode des éléments spectraux et les itérations temporelles sont assurées par une méthode splitting.Au déclenchement de la convection, les structures convectives correspondent à des modes de Fourier, et les seuils critiques dépendent du rapport de forme de la cavité, et des nombres de Biotet de Marangoni qui caractérisent la surface libre. Les transitions d'écoulements au-delà du seuil primaire sont caractérisées quantitativement en fonction du nombre de Rayleigh pour différentes valeurs du nombre de Biot et Ma = 0. Les résultats présentés sont obtenus en résolvant l'ensemble des équations non-linéaires de conservation à travers une méthode de continuation. Lorsque la convection se déclenche sous la forme d'un mode axisymétrique m = 0, l'évolution non-linéaire montre la coexistence de différentes structures convectives, des structures axisymétriques avec écoulement montant ou descendant au centre de la cavité et des structures correspondant à des combinaisons de modes qui apparaissent sur des branches secondaires sous-critiques.L'action d'un champ magnétique constant est ensuite étudiée pour des fluides conducteurs dans une même configuration comprenant une surface supérieure libre. Nous montrons l'effet stabilisateur du champ magnétique sur les seuils primaires ainsi que son action sélective sur les différents modes de convection. Nous analysons l'évolution des structures convectives au delà de ces seuils et montrons comment le champ magnétique modifie les transitions entre ces structures.En soumettant le bain fondu à un champ magnétique tournant, le mouvement de rotation du fluide se superpose aux mouvements de convection thermique et on observe une diminution des fluctuations de température et un retard du déclenchement de l'instabilité de Rayleigh-Bénard(lorsque les deux parois haut/bas du bain sont rigides). La rotation influe sur ce déclenchement qui de stationnaire devient oscillatoire, à l'exception du mode m = 0 de Fourier, pour qui la transition reste stationnaire jusqu'à une certaine valeur critique du nombre de Taylor magnétique.La dynamique de l'écoulement axisymétrique de part et d'autre de cette valeur critique sera étudiée en détail. / The growth of thermal convection out of different perturbations of the conductive base state is investigated using a spectral element time-stepping code. The fluid is subject to a vertical heat transfer in a cylindrical cavity with an upper free surface corresponding to the so-called Rayleigh-Bénard-Marangoni situation and the heat exchange through the free surface is evaluated via the Biot number. The results of the stability diagrams show that the evolution of the primary thresholds are largely influenced by the Biot number, the Marangoni number, and the aspect ratio of the cavity. Flow transitions are elucidated in quantitative detail as a function of the Rayleigh number for different Biot numbers in the tension free limit Ma = 0. The results shown are obtained by solving the full nonlinear field equations numerically among a continuation method. When an axisymmetric m = 0 Fourier mode is obtained at onset, the non-linear evolution shows the coexistence of different convective structures, the axisymmetric structures with up-ow or down-ow at the center and mixed-mode structures which appear on secondary subcritical branches. The action of a constant magnetic field is then considered for melts in the same type of configuration with an upper free surface. We show the global stabilizing effect of the magnetic field on the primary bifurcation thresholds and the selective effect on the different instability modes. We also analyze the evolution of the convective structures above the thresholds and show how the magnetic field modifies the transitions between these structures. When applying a magnetic body forcing in the azimuthal direction (RMF), one can damp the unavoidable thermal fluctuations inside the melt and delay the transition to the Rayleigh-Bénard instability (for rigid-rigid circular plates at top and bottom). The rotation effect also changes the transitions from steady to oscillatory, except for the m = 0 Fourier mode where the transitionis first steady until a critical Taylor number and then becomes oscillatory. The dynamics of the transitions to the axisymmetric flow, below and above this value of critical magnetic Taylor number, is particularly interesting and will be described.

Philosophiae Doctor - PhD / The global impact of the converging dual epidemics of tuberculosis (TB) and human immunodeficiency virus (HIV) is one of the major public health challenges of our time, because in many countries, human immunodeficiency virus (HIV) and mycobacterium tuberculosis (TB) are among the leading causes of morbidity and mortality. It is found that infection with HIV increases the risk of reactivating latent TB infection, and HIV-infected individuals who acquire new TB infections have high rates of disease progression. Research has shown that these two diseases are enormous public health burden, and unfortunately, not much has been done in terms of modeling the dynamics of HIV-TB co-infection at a population level. In this thesis, we study these models and design and analyze robust numerical methods to solve them. To proceed in this direction, first we study the sub-models and then the full model. The first sub-model describes the transmission dynamics of HIV that accounts for behavior change. The impact of HIV educational campaigns is also studied. Further, we explore the effects of behavior change and different responses of individuals to educational campaigns in a situation where individuals may not react immediately to these campaigns. This is done by considering a distributed time delay in the HIV sub-model. This leads to Hopf bifurcations around the endemic equilibria of the model. These bifurcations correspond to the existence of periodic solutions that oscillate around the equilibria at given thresholds. Further, we show how the delay can result in more HIV infections causing more increase in the HIV prevalence. Part of this study is then extended to study a co-infection model of HIV-TB. A thorough bifurcation analysis is carried out for this model. Robust numerical methods are then designed and analyzed for these models. Comparative numerical results are also provided for each model. / South Africa

Les neurones sont des cellules excitables capables de coder et transmettre l’information sous forme d’oscillations du potentiel membranaire. Cette activité électrique est produite par une modification des flux ioniques transmembranaires. Les neurones constituent un exemple d’oscillateur cellulaire dont la dynamique non linéaire permet l’apparition d’une activité électrique complexe. Dans ce système, les ions calciques sont des messagers intracellulaires importants. Ils servent de médiateur entre un signal électrique et un signal chimique, par une modulation de l’activité enzymatique de certaines protéines. Ils interviennent dans de nombreuses fonctions neuronales, dont l’excitabilité électrique. Un des mécanismes mis en place par les neurones pour contrôler l’homéostasie du calcium intracellulaire provient de protéines cytoplasmiques capables de lier les ions calciques. Ces protéines jouent un rôle de « tampon » du calcium. Cependant, toutes leurs fonctions n’ont pas encore été mises en évidence. C’est l’objectif de notre travail. Nous avons voulu comprendre le rôle joué par une protéine « tampon » particulière, la calrétinine, sur le mode de décharge électrique d’un neurone où elle est exprimée en abondance, le grain cérébelleux. Pour cela, nous avons utilisé une approche théorique et expérimentale. Au niveau théorique, nous avons élaboré un modèle mathématique de l’activité électrique du grain cérébelleux, prenant en compte la chélation du calcium intracellulaire. Il permet de clarifier le rôle de la chélation du calcium intracellulaire sur les oscillations du potentiel membranaire. La modélisation de l’activité électrique du grain cérébelleux repose sur le formalisme développé par Hodgkin et Huxley pour l’axone géant de calmar. Dans ce contexte, l’application de la conservation de la charge au circuit équivalent de la membrane cellulaire fournit un système d’équations différentielles ordinaires, non linéaires. Dès lors, notre modèle nous a permis d’étudier l’impact des variations de la concentration de chélateur calcique sur les oscillations du potentiel membranaire. Nous avons ainsi pu constater qu’une diminution de la concentration en chélateur calcique induisait une augmentation de l’excitabilité électrique du grain cérébelleux, sans altérer le régime d’oscillations. Par contre, en augmentant fortement la concentration en chélateur calcique, nous avons montré que le grain cérébelleux changeait de dynamique oscillatoire, montrant des transitions d’un mode de décharge périodique régulier vers des oscillations en salve du potentiel membranaire. Au niveau expérimental, nous avons vérifié les résultats prévus par le modèle théorique. Nous avons ainsi montré que des grains de souris transgéniques déficientes en calrétinine présentaient une excitabilité électrique accrue par rapport aux grains contrôles. Puis, en restaurant un niveau de chélation calcique normal dans ces grains, par perfusion intracellulaire de chélateur calcique, nous montrons qu’ils retrouvent un niveau d’excitabilité normal. Ensuite, nous avons introduit dans des grains cérébelleux de souris sauvages, une forte concentration en chélateur calcique exogène. Conformément aux résultats théoriques, nous avons pu observer des transitions vers des oscillations en salve du potentiel membranaire. Enfin, nous avons montré que l’absence de calrétinine affecte les paramètres morphologiques du grain cérébelleux des souris transgéniques déficientes en calrétinine. En conclusion, ces résultats suggèrent que le mode de décharge des cellules excitables peut être modulé d’une façon importante par les protéines liant le calcium. De ce fait, des changements dans le niveau d’expression et/ou dans la localisation subcellulaire des protéines liant le calcium pourraient aussi jouer un rôle critique dans la régulation de processus physiologiques contrôlés par l’excitabilité membranaire. De plus, les mécanismes que nous avons mis en évidence pourraient être à l’origine d’un nouveau principe de régulation de la signalisation dans les circuits neuronaux et pourraient jouer un rôle fonctionnel dans le contrôle du codage de l’information et de son stockage dans le système nerveux central.

Dynamische Effekte in Halbleiterlasern aufgrund aktiver optischer Rückkopplung werden untersucht. Basierend auf Laserstrukturen mit verteilter Rückkopplung wird ein neuer Lasertyp entwickelt. Durch Experimente und ergänzende Simulationen wird ein umfassender Überblick der Dynamik dieses neuen Lasertyps gegeben. Zuerst werden die grundsätzlichen Veränderungen der Laserdynamik durch verzögerte optische Rückkopplung diskutiert. Es zeigen sich Hysterese- und Pulsationsphänomene. Ursprung der Pulsationen sind entdämpfte Relaxationsoszillationen und Modenschwebungen. Die Pulsationsphänomene werden anhand von integrierten Mehrsektionslasern mit passiver und aktiver optischer Rückkopplung untersucht. Es zeigt sich, daß nur Laser mit aktiver Rückkopplung die vollständige Kontrolle von Rückkoppelphase und -stärke erlauben, und damit den Zugang zum gesamten Spektrum der Laserdynamik mit sehr kurzer Verzögerungszeit bieten. Anhand des Lasertyps mit aktiver Rückkopplung wird eine umfassende Bifurkationsanalyse durchgeführt. Die Ergebnisse einer numerischen Untersuchung werden durch umfangreiche Experimente verifiziert. Sattel-Knoten-, Hopf- und Torus-Bifurkationen organisieren das Bauelementverhalten. Die Koexistenz von entdämpften Relaxationsoszillationen und Schwebungspulsationen erlaubt die Untersuchung von internen Synchronisationsphänomenen, Resonanzen und chaotischer Dynamik. Der Einfluß spontaner Emission auf die Laserdynamik zeigt sich am Beispiel rauschinduzierter Vorläufer einzelner Bifurkationen sowie am Übergang zwischen den beiden Pulsationsphänomenen. Abschließend wird die Anwendung des Lasers mit integriert-aktiver Rückkopplung als optischer Taktregenerator bei einer Datenrate von 40 Gbit/s demonstriert. Arbeitspunkte mit koexistierenden Oszillatoren und ganzzahligem Frequenzverhältnis eignen sich darüber hinaus zur rein optischen Frequenzteilung im GHz-Bereich. / Dynamical effects in semiconductor lasers due to active optical feedback are investigated. A novel laser type based on distributed feedback structures is developed and realized. Experiments as well as simulations give a comprehensive overview on the nonlinear dynamics of this laser type. First, the fundamental modifications of the solitary laser dynamics due to delayed optical feedback in the very short feedback cavity regime are discussed. Hysteresis effects and pulsation phenomena due to undamped relaxation oscillations and mode beating are identified. These oscillation types are experimentally confirmed by multi-section lasers with integrated passive and active feedback. It turns out that only the active feedback laser (AFL) allows for the full control of feedback phase and strength, enabling the access to the whole spectrum of laser dynamics in the very short delay limit. A complete bifurcation analysis for the AFL is presented. Results obtained in a numerical path-following study are verified by extensive experiments. Saddle-node, Hopf and torus bifurcations are identified to organize the device behavior. The coexistence of undamped relaxation oscillations and mode beating in the strong feedback regime allows for the experimental investigation of resonances, mutual locking and chaotic behavior. The modification of the laser dynamics by spontaneous emission noise is shown with the example of noisy precursors and irregular dynamics at the transition between the two oscillation types. Finally, the applicability of the AFL for optical clock recovery is demonstrated at a data rate of 40 Gbit/s. Operation points with coexisting oscillations and rational frequencies are shown to be suited for all-optical frequency division in the GHz range.

Macrophages are the largest cells in the immune system and they regulate inflammatory signalling and inform cell fate decisions. Many signals, including those mediated by Tumor Necrosis Factor alpha (TNFα) converge on a few key intracellular signalling pathways, including the Nuclear Factor kappa B (NFκB) network. The NFκB signalling pathway plays a vital role in the regulation of many different cellular responses, including the production of TNFα itself, which is required to sustain and propagate immune responses to, for example, infection or tissue damage. In this thesis we report on studies-both experimental and theoretical-of the NFκB signalling pathway in macrophages. Our collaborators stimulated these cells with various doses of Lipopolysaccharide (LPS), a molecule that forms the major component of the outer membrane of Gram-negative bacteria: in these experiments it serves as a proxy for bacterial infection. The macrophages, studied in vitro, respond as they are believed to do in tissues, by secreting certain signalling molecules called cytokines: the level of secretion proved to depend on the strength of the LPS stimulus. Further, heterogeneity of macrophage signalling was observed in response to a range of LPS doses. Within individual macrophages LPS stimulation results in oscillatory behaviour of NFκB localisation-NFκB shuttles in and out of the nucleus-with an amplitude (peak nuclear concentration) that also depends on the LPS dose. Heterogeneity was also observed in cells that were stimulated with the same dose intensity. This raises an important question about how immune cells coordinate inflammatory activity in the presence of this variability. In this thesis we aim to achieve an understanding of the system through the qualitative analysis of mathematical models of it. This work explores both the parametric sensitivity and bifurcation analyses for two mathematical models of NFκB in macrophages. Parametric sensitivity analysis is used to investigate the role of parameters on the model's output, especially on certain features of the signal-peak amplitudes, inter-peak intervals and areas beneath curves-that are commonly measured in single-cell experiments. Local bifurcation analysis is conducted in order to show all the possible behaviours produced when varying parameters.

Uncertainties are pervasive in the Earth System modelling. This is not just due to a lack of knowledge about physical processes but has its seeds in intrinsic, i.e. inevitable and irreducible, uncertainties concerning the process of modelling as well. Therefore, it is indispensable to quantify uncertainty in order to determine, which are robust results under this inherent uncertainty. The central goal of this thesis is to explore how uncertainties map on the properties of interest such as phase space topology and qualitative dynamics of the system. We will address several types of uncertainty and apply methods of dynamical systems theory on a trendsetting field of climate research, i.e. the Indian monsoon.<br><br> For the systematic analysis concerning the different facets of uncertainty, a box model of the Indian monsoon is investigated, which shows a saddle node bifurcation against those parameters that influence the heat budget of the system and that goes along with a regime shift from a wet to a dry summer monsoon. As some of these parameters are crucially influenced by anthropogenic perturbations, the question is whether the occurrence of this bifurcation is robust against uncertainties in parameters and in the number of considered processes and secondly, whether the bifurcation can be reached under climate change. Results indicate, for example, the robustness of the bifurcation point against all considered parameter uncertainties. The possibility of reaching the critical point under climate change seems rather improbable. <br><br> A novel method is applied for the analysis of the occurrence and the position of the bifurcation point in the monsoon model against parameter uncertainties. This method combines two standard approaches: a bifurcation analysis with multi-parameter ensemble simulations. As a model-independent and therefore universal procedure, this method allows investigating the uncertainty referring to a bifurcation in a high dimensional parameter space in many other models. <br><br> With the monsoon model the uncertainty about the external influence of El Niño / Southern Oscillation (ENSO) is determined. There is evidence that ENSO influences the variability of the Indian monsoon, but the underlying physical mechanism is discussed controversially. As a contribution to the debate three different hypotheses are tested of how ENSO and the Indian summer monsoon are linked. In this thesis the coupling through the trade winds is identified as key in linking these two key climate constituents. On the basis of this physical mechanism the observed monsoon rainfall data can be reproduced to a great extent. Moreover, this mechanism can be identified in two general circulation models (GCMs) for the present day situation and for future projections under climate change. <br><br> Furthermore, uncertainties in the process of coupling models are investigated, where the focus is on a comparison of forced dynamics as opposed to fully coupled dynamics. The former describes a particular type of coupling, where the dynamics from one sub-module is substituted by data. Intrinsic uncertainties and constraints are identified that prevent the consistency of a forced model with its fully coupled counterpart. Qualitative discrepancies between the two modelling approaches are highlighted, which lead to an overestimation of predictability and produce artificial predictability in the forced system. The results suggest that bistability and intermittent predictability, when found in a forced model set-up, should always be cross-validated with alternative coupling designs before being taken for granted. <br><br> All in this, this thesis contributes to the fundamental issue of dealing with uncertainties the climate modelling community is confronted with. Although some uncertainties allow for including them in the interpretation of the model results, intrinsic uncertainties could be identified, which are inevitable within a certain modelling paradigm and are provoked by the specific modelling approach. / Die vorliegende Arbeit untersucht, auf welche Weise Unsicherheiten, wie sie in der integrierten Klima(folgen)forschung allgegenwärtig sind, die Stabilität und die Struktur dynamischer Systeme beeinflussen. <br> Im Rahmen der Erdsystemmodellierung wird der Unsicherheitsanalyse zunehmend eine zentrale Bedeutung beigemessen. Einerseits können mit ihrer Hilfe disziplinäre Qualitäts-standards verbessert werden, andererseits ergibt sich die Chance, im Zuge von "Integrated Assessment" robuste entscheidungsrelevante Aussagen abzuleiten. <br><br> Zur systematischen Untersuchung verschiedener Arten von Unsicherheit wird ein konzeptionelles Modell des Indischen Monsuns eingesetzt, das einen übergang von einem feuchten in ein trockenes Regime aufgrund einer Sattel-Knoten-Bifurkation in Abhängigkeit derjenigen Parameter zeigt, die die Wärmebilanz des Systems beeinflussen. Da einige dieser Parameter anthropogenen Einflüssen und Veränderungen unterworfen sind, werden zwei zentrale Punkte untersucht: zum einen, ob der Bifurkationspunkt robust gegenüber Unsicherheiten in Parametern und in Bezug auf die Anzahl und die Art der im Modell implementierten Prozesse ist und zum anderen, ob durch anthropogenen Einfluss der Bifurkationspunkt erreicht werden kann. Es zeigt sich unter anderem, dass das Auftreten der Bifurkation überaus robust, die Lage des Bifurkationspunktes im Phasenraum ist hingegen sehr sensitiv gegenüber Parameterunsicherheiten ist. <br><br> Für diese Untersuchung wird eine neuartige Methode zur Untersuchung des Auftretens und der Lage einer Bifurkation gegenüber Unsicherheiten im hochdimensionalen Parameterraum entwickelt, die auf der Kombination einer Bifurkationsanalyse mit einer multi parametrischen Ensemble Simulation basiert. <br><br> Mit dem Monsunmodell wird des weiteren die Unsicherheit bezüglich des externen Einflusses von El Niño / Southern Oscillation (ENSO) untersucht. Es ist bekannt, dass durch ENSO die Variabilität des Indischen Monsun beeinflußt wird, wohingegen der zu Grunde liegende Mechanismus kontrovers diskutiert wird. In dieser Arbeit werden drei verschiedene Hypothesen zur Kopplung zwischen diesen beiden Phänomenen untersucht. Es kann gezeigt werden, dass die Passat Winde einen Schlüsselmechanismus für den Einfluß von ENSO auf den Indischen Monsun darstellen.<br> Mit Hilfe dieses Mechanismus können die beobachteten Niederschlagsdaten des Monsuns zu einem großen Anteil reproduziert werden. Zudem kann dieser Mechanismus kann auch in zwei globalen Zirkulationsmodellen (GCMs) für den heutigen Zustand und für ein Emissionsszenario unter Klimawandel identifiziert werden. <br><br> Im weiteren Teil der Arbeit werden intrinsische Unsicherheiten identifiziert, die den Unterschied zwischen der Kopplung von Teilmodulen und dem Vorschreiben von einzelnen dieser Module durch Daten betreffen. Untersucht werden dazu ein getriebenes GCM-Ensemble und ein konzeptionelles Ozean-Atmosphären-Modell, das eine strukturierte Analyse anhand von Methoden der Theorie dynamischer Systeme ermöglicht.<br> In den meisten Fällen kann die getriebene Version, in der ein Teil der Dynamik als externer Antrieb vorschrieben wird, das voll gekoppelte Pendant nachbilden. Es wird gezeigt, dass es jedoch auch Regionen im Phasen- und Parameterraum gibt, in dem sich die zwei Modellierungsansätze signifikant unterscheiden und unter anderem zu einer überschätzung der Vorhersagbarkeit und zu künstlichen Zuständen im getriebenen System führen. Die Ergebnisse legen den Schluss nahe, dass immer auch alternative Kopplungsmechanismen getestet werden müssen bevor das getriebene System als adäquate Beschreibung des gekoppelten Gesamtsystems betrachtet werden kann. <br><br> Anhand der verschiedenen Anwendungen der Unsicherheitsanalyse macht die Arbeit deutlich, dass zum einen Unsicherheiten intrinsisch durch bestimmte Arten der Modellierung entstehen und somit unvermeidbar innerhalb eines Modellierungsansatzes sind, dass es zum anderen aber auch geeignete Methoden gibt, Unsicherheiten in die Modellierung und in die Bewertung von Modellergebnissen einzubeziehen.