Nesta tese utilizamos o Modelo de Bose-Hubbard (MBH) generalizado para duas espécies bosonicas para investigar a estabilidade dinâmica da fase superfluida de uma mistura binaria de átomos bosonicos ultra-frios confinados em uma rede optica periódica anelar com M sítios. Na primeira parte consideramos a Hamiltoniana do MBH sem a presença do tunelamento inter-especies. Deduzimos e resolvemos as equações de Gross-Pitaevskii para os estados de equilíbrio do MBH e mostramos que são misturas binarias de condensados nos quais os átomos de cada espécie ocupam um estado de quase-momento q bem definido. As excitações elementares foram determinadas resolvendo as equações de Bogoliubov-de Gennes o que foi possível graças a estrutura de acoplamento dos quase-momentos que reduziu a Hamiltoniana Efetiva a uma soma direta de um dubleto e quadrupletos. Através da analise do comportamento das energias de excitação como função dos parâmetros de controle do sistema, investigamos a estabilidade dinâmica de dois casos de misturas de condensados onde, em um caso, os átomos de cada espécie ocupam o mesmo estado de quase-momento, qA = qB e, no outro, quase-momentos opostos, qA = qB. Em ambos os casos as condições de estabilidade dependem do quase-momento q estar nos quartos centrais ou laterais da primeira zona de Brillouin. No caso qA = qB vemos que a forma do diagrama de estabilidade independe do quase-momento do condensado. Por outro lado, o mesmo não ocorre nos condensados contra-propagantes qA = qB. Esta diferença fica mais acentuada no limite termodinâmico onde os diagramas de estabilidade no centro e nas extremidades da primeira zona de Brillouin ficam idênticos nos dois casos. Já nas bordas que separam os quartos centrais e laterais o comportamento ´e diferente pois a presença de uma interação interespécies por menor que seja desestabiliza completamente a mistura com qA = qB. Em todos estes casos ficou evidente o papel desestabilizador da interação interespécies. Na segunda parte consideramos o efeito de um termo de tunelamento inter-especies. As soluções das equações de Gross-Pitaevskii revelam uma estrutura biestável de estados de equilíbrio essencial para a ocorrência de bifurcação no sistema e, portanto, a presença de catástrofe. Investigamos se a catástrofe e acessível a uma observação experimental. De acordo com nosso critério, esta observação e impossível se o plano de bifurcação for a fronteira de um domínio de instabilidade dinâmica. Através da analise da estabilidade dinâmica dos estados de equilíbrio vimos que para um sistema invariante por inversão de cor essa resposta depende apenas da razão entre as intensidades de tunelamento intra e inter-especies de modo que se JAB/J > 1 a observação e impossível e se JAB/J < 1 é possível, supondo existir uma rota adiabática ate a bifurcação. / In this thesis we used the two-component Bose-Hubbard Model (BHM) to investigate the dynamical stability of the superfluid phase of a binary mixture of ultra-cold bosonic atoms confined in a ring-shaped periodic optical lattice with M sites. In the first part we considered the BHM Hamiltonian without the presence of interspecies tunnelling. We deduced and solved the Gross-Pitaevskii equations for the equilibrium states of the BHM and showed that they are binary mixtures of condensates where the atoms of each species occupy a state of well defined quasi-momentum q. The elementary excitations were determined solving the Bogoliubov-de-Gennes equations which was possible thanks to the coupling structure of the quasi-momenta that reduced the Effective Hamiltonian to a direct sum of a doublet and quadriplets. Through the analysis of the behavior of the excitation energies as a function of the control parameters of the system, we investigated the dynamical stability of two cases of mixtures of condensates where, in one case, the atoms of each specie occupy the same state of quasi-momentum, qA = qB, and, in the other, opposite quasi-momentum, qA = qB. In both cases the stability conditions depend of the quasi-momentum q to be in the central or lateral quarters of the first Brillouin zone. In the case qA = qB, we see that the form of the stability diagram is not dependent of the quasi-momentum of the condensate. However, the same does not occur in the counter-propagating condensates qA = qB. This difference is accentuated in the thermodynamic limit where the stability diagrams in the center and in the extremities of the first Brillouin zone are identical in both cases. In the borders that separate the central and lateral quarters the behavior is different because the presence of a slightly non vanishing inter-species interaction completely destabilize the mixture with qA = qB. In all these cases it was evident the destabilizing role of the inter-species interaction. In the second part we considered the effect of a inter-species tunnelling term. The solutions of the Gross-Pitaevskii equations reveal a bi-stable structure of equilibrium states that is essential for the occurrence of the bifurcation in the system and, therefore, the presence of catastrophe. We investigated if the catastrophe is accessible to a experimental observation. According to our criteria, this observation is impossible if the bifurcation plane is the frontier of a dynamical instability domain. Through the analysis of the dynamical stability of the equilibrium states we saw that for a system invariant by color inversion this answer depends only on the ratio between the intra and inter-species tunnelling intensities in a way that if JAB/J > 1 the observation is impossible and if JAB/J < 1 it is possible, supposing that it exists an adiabatic route until the bifurcation.

O objetivo principal deste trabalho é apresentar uma exposição detalhada do Teorema de Poincaré-Andronov-Hopf para uma família de transformações do plano. Apresentaremos também uma aplicação a um sistema dinâmico que modela a evolução do preço e excesso de demanda em um mercado constituído por uma única mercadoria. / The main purpose of this work is to present a detailed exposition of the Poincaré-Andronov-Hopf Theorem for a family of transformations in the plane. We also present an application to a dynamical system modelling the evolution of the price and the excess demand in a single asset market.

The flow of blood in the human body is a very important component in un-derstanding a number of different ailments such as atherosclerosis and a falseaneurysm. In this thesis, we have utilized Poiseuille’s solution to Navier-Stokesequations with a Newtonian, incompressible fluid flowing laminar with zero ac-celeration in a pipe with non-flexible walls in order to study blood flow in anarterial tree. In order to study and simulate a larger arterial tree we have uti-lized a primitive building block, a bifurcation with one inlet and two outlets,joined together forming a tree. By prescribing an inlet flow and the pressureat every outlet at the bottom of the tree we have shown that we may solvethe system by fixed-point iteration, the Matlab functionfsolve, and Newton’smethod. This way of using primitive building blocks offers a flexible way to doanalysis as it makes it possible to easily change the shape of the tree as well asadding new building blocks such as a block that represents arteriosclerosis.

Nesse trabalho estudamos um laser de estado sólido sujeito a realimentação optica de frequência modificada de um ponto de vista da teoria de bifurcações. Fizemos uma an alise bastante ampla da dinâmica desse laser no espaço de dois parâmetros de injeção (a dessintonização de frequência e a intensidade da injeção) utilizando métodos de integração direta e continuação numérica. Enquanto o método de integração numérica nos possibilitou analisar as dinâmicas mais complexas, incluindo transições para o caos e hipercaos, o método de continuação numérica nos permitiu estudar curvas de bifurcações estáveis e instáveis. A análise foi realizada estudando os efeitos causados pela mudança dos parâmetros que representam o tempo de vida da inversão populacional e a saturação cruzada, responsável pelo acoplamento dos campos dentro do meio ativo. Mostramos que o parâmetro que descreve o tempo de vida da inversão populacional e responsável pelo surgimento de diversas instabilidades no sistema, como o fenômeno de multiestabilidade, surgimento de orbitas periódicas e quase-peri odicas, assim como rotas para o caos via dobramento de período e torus. Para o parâmetro de acoplamento dos campos, mostramos que ele possibilita a presença de hipercaos em nosso sistema, este podendo se apresentar no que denominamos de hipercaos \fraco" e \forte". Dentro da região de hipercaos \forte", mostramos transições determinísticas de dois regimes, em que num deles o laser opera no modo de Q-switching, enquanto que no outro o laser apresenta pequenas oscilações irregulares. Por m, mostramos a existência de uma estatística de eventos extremos dentro do regime hipercaótico. / In this work we studied a solid state laser subjected to frequency-shifted optical feedback from a bifurcation theory point of view. We performed a very broad analysis of the dynamics of this laser in the space of two injection parameters (frequency detuning and injection intensity) using direct integration and numerical continuation methods. While the numerical integration method allowed us to analyze the more complex dynamics, including chaos and hyperchaos transitions, the numerical continuation method allowed us to study stable and unstable bifurcation curves. The analysis was carried out by studying the e ects caused by the change of the parameters that represent the life time of the population inversion and the cross saturation, responsible for the coupling of the elds within the active medium. We show that the parameter that describes the life time of the population inversion is responsible for the appearance of several instabilities in the system, such as the multistability phenomenon, the appearance of periodic and quasi-periodic orbits, as well as routes to chaos via period doubling and torus . For the eld coupling parameter, we show that it allows the presence of hyperchaos in our system, which may present in what we call "weak"and "strong"hyperchaos. Within the "strong"hyperchaos region, we show deterministic transitions of two regimes, in which one laser operates in the Q-switching mode, while in the other the laser presents small irregular oscillations. Finally, we have shown the existence of a extreme events statistic within the hyperchaotic regime.

There is a continuous demand for new and improved methods of understanding our climate system. The work in this thesis focuses on the study of delayed feedback and critical transitions. There is much room to develop upon these concepts in their application to the climate system. We explore the two concepts independently, but also note that the two are not mutually exclusive. The thesis begins with a review of delay differential equation (DDE) theory and the use of delay models in climate, followed by a review of the literature on critical transitions and examples of critical transitions in climate. We introduce various methods of deriving delay models from more complex systems. Our main results center around the Saltzman and Maasch (1988) model for the Pleistocene climate (`Carbon cycle instability as a cause of the late Pleistocene ice age oscillations: modelling the asymmetric response.' Global biogeochemical cycles, 2(2):177-185, 1988). We observe that the model contains a chain of first-order reactions. Feedback chains of this type limits to a discrete delay for long chains. We can then approximate the chain by a delay, resulting in scalar DDE for ice mass. Through bifurcation analysis under varying the delay, we discover a previously unexplored bistable region and consider solutions in this parameter region when subjected to periodic and astronomical forcing. The astronomical forcing is highly quasiperiodic, containing many overlapping frequencies from variations in the Earth's orbit. We find that under the astronomical forcing, the model exhibits a transition in time that resembles what is seen in paleoclimate records, known as the Mid-Pleistocene Transition. This transition is a distinct feature of the quasiperiodic forcing, as confi rmed by the change in sign of the leading nite-time Lyapunov exponent. Additional results involve a box model of the Atlantic meridional overturning circulation under a future climate scenario and time-dependent freshwater forcing. We find that the model exhibits multiple types of critical transitions, as well as recovery from potential critical transitions. We conclude with an outlook on how the work presented in this thesis can be utilised for further studies of the climate system and beyond.

In this thesis, we present a dynamical systems analysis of models of movement coordination, namely the Haken-Kelso-Bunz (HKB) model and the Jirsa-Kelso excitator (JKE). The dynamical properties of the models that can describe various phenomena in discrete and rhythmic movements have been explored in the models' parameter space. The dynamics of amplitude-phase approximation of the single HKB oscillator has been investigated. Furthermore, an approximated version of the scaled JKE system has been proposed and analysed. The canard phenomena in the JKE system has been analysed. A combination of slow-fast analysis, projection onto the Poincare sphere and blow-up method has been suggested to explain the dynamical mechanisms organising the canard cycles in JKE system, which have been shown to have different properties comparing to the classical canards known for the equivalent FitzHugh-Nagumo (FHN) model. Different approaches to de fining the maximal canard periodic solution have been presented and compared. The model of two HKB oscillators coupled by a neurologically motivated function, involving the effect of time-delay and weighted self- and mutual-feedback, has been analysed. The periodic regimes of the model have been shown to capture well the frequency-induced drop of oscillation amplitude and loss of anti-phase stability that have been experimentally observed in many rhythmic movements and by which the development of the HKB model has been inspired. The model has also been demonstrated to support a dynamic regime of stationary bistability with the absence of periodic regimes that can be used to describe discrete movement behaviours.

Este trabalho é concernente a periodicidade na equação de Wright. Provaremos a existência de soluções periódicas não constantes, explorando o conceito de ejetividade de um teorema de ponto fixo. Além disso, provamos a existência de uma seqüência infinita de Bifurcação de Hopf. / This work is concerned with periodicity in the Wright's equation. We prove the existence of nonconstant periodic solutions by exploiting the ejectivity concept in a theorem of fixed point. Furthemore, we prove the existence of an infinite sequence of Hopf Bifurcations.

Neste trabalho, estudamos as Singularidades das folheações mutuamente ortogonais, numa variedade orientada M^3 de dimensão 3, cujas folhas são as curvas integrais dos campos de direções de curvatura principal associadas a uma imersão : M^3 R^4. Damos aqui continuidade às contribuições de R. Garcia referente ao estudo das singularidades genéricas das folheações principais. Apresentamos as configurações principais numa vizinhança dos pontos parcialmente umbílicos de codimensão 1, ou seja, as singularidades das folheações principais que aparecem genericamente em famílias a 1 parâmetro de hipersuperfícies imersas em R^4, e os diagramas de bifurcação pertinentes. Enfraquecendo a condição de genericidade, da maneira mais simples possível, encontramos oito tipos genéricos: D_1^ 1, D^1_ 2, D^1_ 3, D^1_, D^1_{1h,p}, D^1_{1h,n}, D^1_p e D^1_c , definidos ao longo do trabalho. Nesta tese consubstanciamos matematicamente a seguinte conclusão: As singularidades das folheações principais, que aparecem genericamente em famílias a 1 parâmetro de hipersuperfícies imersas em R^4, são os pontos parcialmente umbílicos D_1^ 1, D^1_ 2, D^1_ 3, D^1_, D^1_{1h,p}, D^1_{1h,n}, D^1_ e D^1_ , cujas definições e propriedades serão apresentados aqui. A parte central desta tese é estabelecer, analítica e geometricamente, a configuração principal destes pontos incluindo seus diagramas de bifurcação. / In this work we study the mutually ortogonal foliations, in oriented three dimensional manifolds M^3, whose leaves are the integral curves of the principal curvature direction fields associated to immersions : M^3 R^4. We focus on behavior of these foliation around singularities. Here we extend the contributions of R. Garcia concerning the study of generic singularities. To this end we establish the principal configurations in a neighborhood of partially umbilic points of codimension one. These are the singularities which appear generically in one parameter families of hypersurfaces and give their bifurcation diagrams. We express the condition of genericity by minimally weakening those given by R. Garcia and by adding instead new higher order ones. This procedure leads to the novel generic types: D^1_1, D^1_2, D^1_3, D^1_, D^1_{1h,p}, D^1_{1h,n}, D^1_p and D^1_c , studied in this work. The central part of this thesis is to establish, analitically and geometrically, the local principal configurations at these points, including their bifurcations diagrams.

abstract: A continuously and stably stratified fluid contained in a square cavity subjected to harmonic body forcing is studied numerically by solving the Navier-Stokes equations under the Boussinesq approximation. Complex dynamics are observed near the onset of instability of the basic state, which is a flow configuration that is always an exact analytical solution of the governing equations. The instability of the basic state to perturbations is first studied with linear stability analysis (Floquet analysis), revealing a multitude of intersecting synchronous and subharmonic resonance tongues in parameter space. A modal reduction method for determining the locus of basic state instability is also shown, greatly simplifying the computational overhead normally required by a Floquet study. Then, a study of the nonlinear governing equations determines the criticality of the basic state's instability, and ultimately characterizes the dynamics of the lowest order spatial mode by the three discovered codimension-two bifurcation points within the resonance tongue. The rich dynamics include a homoclinic doubling cascade that resembles the logistic map and a multitude of gluing bifurcations. The numerical techniques and methodologies are first demonstrated on a homogeneous fluid contained within a three-dimensional lid-driven cavity. The edge state technique and linear stability analysis through Arnoldi iteration are used to resolve the complex dynamics of the canonical shear-driven benchmark problem. The techniques here lead to a dynamical description of an instability mechanism, and the work serves as a basis for the remainder of the dissertation. / Dissertation/Thesis / Supplemental Materials Description File / zip file containing 10 mp4 formatted video animations, as well as a text readme and the previously submitted Supplemental Materials Description File / Doctoral Dissertation Mathematics 2019

A growing number of flavoprotein systems have been observed to bifurcate pairs of electrons. Flavin-based electron bifurcation (FBEB) results in products with greater reducing power than that of the reactants with less reducing power. Highly reducing electrons at low reduction midpoint potential are required for life processes of both aerobic and anaerobic metabolic processes. For electron bifurcation to function, the semiquinone (SQ) redox intermediate needs to be destabilized in the protein to suppress its ability to trap electrons. This dissertation examines SQ suppression across a number of flavin systems for the purpose of better understanding the nature of SQ suppression within FBEB and elucidates potential mechanistic roles of SQ. The major achievement of this work is advancing the understanding of SQ suppression and its utility in flavoproteins with the capacity to bifurcate pairs of electrons. Much of these achievements are highlighted in Chapter 6. To contextualize these mechanistic studies, we examined the kinetic and thermodynamic properties of non-bifurcating flavoproteins (Chapters 2 and 3) as well as bifurcating flavoproteins (Chapters 4 and 5). Proteins were selected as models for SQ suppression with the aim of elucidating the role of an intermediate SQ in bifurcation. The chemical reactions of flavins and those mediated by flavoproteins play critical roles in the bioenergetics of all lifeforms, both aerobic and anaerobic. We highlight our findings in the context of electron bifurcation, the recently discovered third form of biological energy conservation. Bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase I (Nfn) and the non-bifurcating flavoproteins nitroreductase, NADH oxidase, and flavodoxin were studied by transient absorption spectroscopy to compare electron transfer rates and mechanisms in the picosecond range. Different mechanisms were found to dominate SQ decay in the different proteins, producing lifetimes ranging over 3 orders of magnitude. The presence of a short-lived SQ alone was found to be insufficient to infer bifurcating activity. We established a model wherein the short SQ lifetime in Nfn results from efficient electron propagation. Such mechanisms of SQ decay may be a general feature of redox active site ensembles able to carry out bifurcation. We also investigated the proposed bifurcating electron transfer flavoprotein (Etf) from Pyrobaculum aerophilum (Pae), a hyperthermophilic archaeon. Unlike other Etfs, we observed a stable and strong charge transfer band (λmax= 724 nm) for Pae’s Etf upon reduction by NADH. Using a series of reductive titrations to probe bounds for the reduction midpoint potential of the two flavins, we argue that the heterodimer alone could participate in a bifurcation mechanism.