A análise de sistemas dinâmicos não lineares pode ser baseada em séries obtidas de modelos matemáticos ou de experimentos. Modelos matemáticos para respostas aeroelásticas associadas ao estol dinâmico são muito difíceis de obter. Neste caso, experimentos e ensaios em vôo parecem fornecer uma base mais apropriada para a análise da dinâmica não linear. Técnicas de sistemas dinâmicos baseadas em análise de séries temporais podem ser aplicadas para a aeroelasticidade não linear. Quando tem-se disponível apenas séries experimentais, as técnicas de reconstrução do espaço de estados têm sido extensivamente utilizadas. Além disso, os expoentes de Lyapunov fornecem uma caracterização qualitativa e quantitativa do comportamento caótico de sistemas não lineares, assim, um expoente de Lyapunov positivo é um forte indicativo de caos. Medidas de entropia também fornecem informações importantes da complexidade do sistema não linear, consequentemente sua aplicação às séries temporais aeroelásticas representam uma forma apropriada para identificar movimentos caóticos. Este trabalho apresenta a aplicação de técnicas da análise de séries temporais, tais como, reconstrução do espaço de estados, expoentes de Lyapunov e medidas de entropia para respostas aeroelásticas não lineares para prever o comportamento caótico. Um modelo de asa flexível foi construído e testado em túnel de vento de circuito fechado com velocidade do escoamento variando entre 9,0 e 17,0 m/s. O modelo foi montado sobre uma plataforma giratória que produzia variações no ângulo de incidência. Deformações estruturais foram capturadas por meio de extensômetros que forneciam informações da resposta aeroelástica. O método da defasagem é utilizado para reconstruir o espaço de estados das séries temporais obtidas no experimento. Para obter a defasagem utilizada na reconstrução foi usada a análise da função de autocorrelação. Para determinar a dimensão do atrator é calculada a integral de correlação. A evolução do espectro de frequências e do espaço de estados reconstruído é analisada com as variações da velocidade do escoamento e da frequência de oscilação da plataforma. Os expoentes de Lyapunov e a entropia de Rényi foram obtidos para identificar o comportamento caótico. Os resultados foram analisados com a variação da velocidade do escoamento e da frequência de oscilação da plataforma. As técnicas utilizadas foram eficientes para observar o aparecimento de mudanças no sistema e do comportamento caótico com uma escala de interação fluido-estrutura complexa para movimentos com altos ângulos de incidência. / The analysis of non-linear dynamical systems can be based on data from either a mathematical model or an experiment. Mathematical models for aeroelastic response associated to the dynamic stall behavior are very hard to obtain. In this case, experimental or in flight data seems to provide suitable basis for non-linear dynamical analysis. Dynamic systems techniques based on time series analysis can be adequately applied to non-linear aeroelasticity. When experimental data are available, state space reconstruction methods have been widely considered. Moreover, the Lyapunov exponents provides qualitative and quantitative characterization of nonlinear systems chaotic behavior, since positive Lyapunov exponent is a strong signature of chaos. Entropy measures also provide important information on the complexity of nonlinear system, therefore its application to aeroelastic time series represent a proper way to seek for chaotic motions. This work presents the application techniques from time series analysis, such as, state space reconstruction, Lyapunov exponents and entropy measures to nonlinear aeroelastic responses, in order to predict chaotic behavior. A flexible wing model has been constructed and tested in a closed circuit wind tunnel with freestream between 9,0 and 17,0 m/s. The wing model has been mounted on a turntable that allows variations to the wing incidence angle. Structural deformation is captured by means of strain gages, thereby providing information on the aeroelastic response. The method of delays has been used to identify an embedded attractor in the state space from experimentally acquired aeroelastic response time series. To obtain the time delay value to manipulate the time series during reconstruction, the autocorrelation function analysis has been used. For the attractor embeeding dimension calculation the correlation integral approach has been considered. The evolution of frequency spectra and the reconstrueted state space is analyzed for variations of the freestream and the frequency of oscilIation of the turntable. Lyapunov exponents and Rényi entropy have been achieved in order to seek for chaotic behavior. The results were analyzed with the variation of the freestream and the frequency of oscillation of the turntable. The used techniques had been efficient to observe the occurence of changes and chaotic behavior withim a range of complex fluid-structure interaction at higher angle of incidence motions.

Vertebrate evolution has resulted in a diversity of feeding mechanisms. Cetaceans are secondarily derived tetrapods that have returned to a marine habitat. As a result, they display feeding modes that have converged with more basal aquatic vertebrates, but display a diversity of new solutions and adaptations. To begin to explore the diversity of feeding adaptations among odontocetes, kinematics of feeding modes and feeding adaptations for belugas (Delphinapterus leucas), Pacific white-sided dolphins (Lagenorhynchus obliquidens), and long-finned pilot whales (Globicephala melas) were characterized. In addition, direct measurements of intraoral pressure were collected to determine maximum suction performance. Characters from these analyses were combined with data for other odontocetes, and were mapped onto a phylogeny of Odontoceti to begin to explore where changes in feeding modes took place. Feeding modes were diverse in belugas, Pacific white-sided dolphins, and pilot whales and included suction, ram, and a combination of both. In general, four phases were observed: (I) preparatory, (II) jaw opening, (III) gular depression, and (IV) jaw closing. Suction was a large component of the prey capture method in belugas and subambient pressures in excess of 100 kPa were generated. Belugas were also capable of lateral lip gape occlusion and anterior lip pursing to form a small anterior aperture. Pacific whitesided dolphins relied on ram to capture prey. However, some degree of pursing and resultant subambient pressure was observed that was likely used to compensate for high ram speeds or for prey manipulation and transport to the esophagus. Pilot whales were more similar to belugas in kinematics, but maintained high approach velocities and did not generate significant suction pressures; suction and ram were used in combination. Belugas and pilot whales appeared to employ hyolingual depression as a primary suction generation mechanism, whereas Pacific white-sided dolphins relied on fast jaw opening. Ancestral state reconstructions indicated that suction feeding capability evolved independently at least six times within Odontoceti. These results indicate the diversity of feeding behaviors in odontocetes and provide directives for future studies on the diversity of feeding in secondarily aquatic mammals.

A análise de sistemas dinâmicos não lineares pode ser baseada em séries obtidas de modelos matemáticos ou de experimentos. Modelos matemáticos para respostas aeroelásticas associadas ao estol dinâmico são muito difíceis de obter. Neste caso, experimentos e ensaios em vôo parecem fornecer uma base mais apropriada para a análise da dinâmica não linear. Técnicas de sistemas dinâmicos baseadas em análise de séries temporais podem ser aplicadas para a aeroelasticidade não linear. Quando tem-se disponível apenas séries experimentais, as técnicas de reconstrução do espaço de estados têm sido extensivamente utilizadas. Além disso, os expoentes de Lyapunov fornecem uma caracterização qualitativa e quantitativa do comportamento caótico de sistemas não lineares, assim, um expoente de Lyapunov positivo é um forte indicativo de caos. Medidas de entropia também fornecem informações importantes da complexidade do sistema não linear, consequentemente sua aplicação às séries temporais aeroelásticas representam uma forma apropriada para identificar movimentos caóticos. Este trabalho apresenta a aplicação de técnicas da análise de séries temporais, tais como, reconstrução do espaço de estados, expoentes de Lyapunov e medidas de entropia para respostas aeroelásticas não lineares para prever o comportamento caótico. Um modelo de asa flexível foi construído e testado em túnel de vento de circuito fechado com velocidade do escoamento variando entre 9,0 e 17,0 m/s. O modelo foi montado sobre uma plataforma giratória que produzia variações no ângulo de incidência. Deformações estruturais foram capturadas por meio de extensômetros que forneciam informações da resposta aeroelástica. O método da defasagem é utilizado para reconstruir o espaço de estados das séries temporais obtidas no experimento. Para obter a defasagem utilizada na reconstrução foi usada a análise da função de autocorrelação. Para determinar a dimensão do atrator é calculada a integral de correlação. A evolução do espectro de frequências e do espaço de estados reconstruído é analisada com as variações da velocidade do escoamento e da frequência de oscilação da plataforma. Os expoentes de Lyapunov e a entropia de Rényi foram obtidos para identificar o comportamento caótico. Os resultados foram analisados com a variação da velocidade do escoamento e da frequência de oscilação da plataforma. As técnicas utilizadas foram eficientes para observar o aparecimento de mudanças no sistema e do comportamento caótico com uma escala de interação fluido-estrutura complexa para movimentos com altos ângulos de incidência. / The analysis of non-linear dynamical systems can be based on data from either a mathematical model or an experiment. Mathematical models for aeroelastic response associated to the dynamic stall behavior are very hard to obtain. In this case, experimental or in flight data seems to provide suitable basis for non-linear dynamical analysis. Dynamic systems techniques based on time series analysis can be adequately applied to non-linear aeroelasticity. When experimental data are available, state space reconstruction methods have been widely considered. Moreover, the Lyapunov exponents provides qualitative and quantitative characterization of nonlinear systems chaotic behavior, since positive Lyapunov exponent is a strong signature of chaos. Entropy measures also provide important information on the complexity of nonlinear system, therefore its application to aeroelastic time series represent a proper way to seek for chaotic motions. This work presents the application techniques from time series analysis, such as, state space reconstruction, Lyapunov exponents and entropy measures to nonlinear aeroelastic responses, in order to predict chaotic behavior. A flexible wing model has been constructed and tested in a closed circuit wind tunnel with freestream between 9,0 and 17,0 m/s. The wing model has been mounted on a turntable that allows variations to the wing incidence angle. Structural deformation is captured by means of strain gages, thereby providing information on the aeroelastic response. The method of delays has been used to identify an embedded attractor in the state space from experimentally acquired aeroelastic response time series. To obtain the time delay value to manipulate the time series during reconstruction, the autocorrelation function analysis has been used. For the attractor embeeding dimension calculation the correlation integral approach has been considered. The evolution of frequency spectra and the reconstrueted state space is analyzed for variations of the freestream and the frequency of oscilIation of the turntable. Lyapunov exponents and Rényi entropy have been achieved in order to seek for chaotic behavior. The results were analyzed with the variation of the freestream and the frequency of oscillation of the turntable. The used techniques had been efficient to observe the occurence of changes and chaotic behavior withim a range of complex fluid-structure interaction at higher angle of incidence motions.

No description available.

Les Angiospermes sont le clade le plus diversifié des plantes actuelles et sont exceptionnellement riches en espèces dans les régions tropicales. Dans cette thèse, j’ai étudié l’évolution des systèmes sexuels et l’histoire biogéographique de la famille des Moraceae, clade modèle utilisé pour comprendre l’origine et l’évolution de la diversité chez les Angiospermes. Dans le Chapitre I, j’ai reconstruit et calibré un nouvel arbre phylogénétique daté pour les Moraceae. J’ai ensuite utilisé cet arbre pour reconstruire les états ancestraux des systèmes sexuels chez les Moraceae et Ficus. Les âges des groupes-couronne des Moraceae et du genre Ficus sont estimés au Crétacé et à l’Eocène, respectivement. La dioécie est inférée comme l’état ancestral des systèmes sexuels chez les Moraceae, avec plusieurs transitions ultérieures vers la monoécie, y compris chez Ficus. Ce résultat suggère que la dioécie ne représente pas nécessairement un cul-de-sac évolutif. Dans le Chapitre II, j’ai reconstruit un arbre phylogénétique daté pour la tribu des Dorstenieae, distribuée principalement dans les régions tropicales, à partir d’un nouveau jeu de données génomiques nucléaires produit avec une approche Hyb-Seq. L’histoire biogéographique du groupe a ensuite été reconstruite en utilisant les modèles de dispersion-extinction-cladogenèse. Les âges des groupes-couronne des Dorstenieae et du genre Dorstenia sont estimés au Crétacé et dans la période du Crétacé au Paléocène, respectivement. Deux évènements de dispersion à longue distance depuis l’Afrique continentale vers l’Amérique du Sud ont eu lieu au Cénozoïque (Dorstenia et Brosimum s.l.). Dans le Chapitre III, j’ai testé les différences de niche climatique (température et précipitation) entre les deux systèmes sexuels (monoécie et gynodioécie) chez Ficus avec un nouveau jeu de données fiables d’occurrences spatiales et de systèmes sexuels chez 183 espèces. À cette fin, j’ai utilisé deux approches comparatives : équations d’estimation généralisées (GEE) et modèles linéaires généralisés (GLM). Une relation positive entre précipitation et gynodioécie est soutenue par les analyses GLM, et aucune méthode ne soutient une relation entre température et système sexuel. Une meilleure capacité à se disperser et le potentiel d’autopollinisation sont deux explications possibles pour la colonisation et la survie des espèces monoïques dans des environnements plus secs. Cette thèse démontre le potentiel des méthodes phylogénétiques comparatives et des données phylogénomiques pour répondre aux questions d’évolution des systèmes sexuels et de biogéographie chez les Moraceae et ouvre plusieurs nouvelles perspectives importantes méritant d’être approfondies chez d’autres clades de plantes, telles que la relation entre système sexuel et niche climatique. / Angiosperms are the most diversified clade of extant plants and are exceptionally species-rich in tropical regions. In this thesis, I investigated breeding system evolution and biogeographic history in the family Moraceae, which I used as a model clade to understand the origin and evolution of diversity of angiosperms. In Chapter I, I reconstructed and calibrated a new dated phylogenetic tree for Moraceae as a whole. I then used this tree to reconstruct ancestral states of breeding systems in Moraceae and Ficus. The crown group ages of Moraceae and Ficus were estimated in the Cretaceous and in the Eocene, respectively. Dioecy was inferred as the ancestral breeding systems of Moraceae, with several subsequent transitions to monoecy, including in Ficus. This result suggests that dioecy is not necessarily an evolutionary dead end. In Chapter II, I reconstructed a dated phylogenetic tree for tribe Dorstenieae, mainly distributed in tropical regions, with a new data set of nuclear genomic data generated with a Hyb-Seq approach. Biogeographic history was then reconstructed using dispersal-extinction-cladogenesis models. The crown group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous and in the Cretaceous/Paleocene period, respectively. Two long-distance dispersal events from continental Africa to South America occurred in the Cenozoic (Dorstenia and Brosimum s.l.). In Chapter III, I tested the climatic niche difference (temperature and precipitation) between the two breeding systems (monoecy and gynodioecy) in Ficus using a new dataset of cleaned spatial occurrence records and breeding systems for 183 species. I used two comparative approaches: generalized estimating equations (GEE) and generalized linear models (GLM). A positive relationship between precipitation and gynodioecy was supported by GLM, but not GEE analyses, and no relationship between temperature and breeding systems was supported by either method. Higher dispersal ability and the potential for self-fertilization may explain why monoecious species of Ficus have been able to colonize and survive in drier environments. This thesis highlights the potential of phylogenetic comparative methods and phylogenomic data to address questions of breeding system evolution and biogeography in Moraceae, and opens up several important new perspectives worth investigating in other plant clades, such as a relationship between breeding system and climatic niche.

Microorganisms play crucial roles in aquatic environments in determining ecosystemstability and driving the turnover of elements essential to life. Understanding thedistribution and evolution of aquatic microorganisms will help us predict how aquaticecosystems will respond to Global Change, and such understanding can be gained bystudying these processes of the past. In this project, we investigate the evolutionaryrelationship between brackish water bacteria from the Baltic Sea and Caspian Seawith freshwater and marine bacteria, with the goal of understanding how brackishwater bacteria have evolved. 11,276 bacterial metagenome-assembled genomes(MAGs) from seven metagenomic datasets were used to conduct a comparativeanalysis of freshwater, brackish and marine bacteria. When clustering the genomes bypairwise average nucleotide identity (ANI) at the approximate species level (96.5%ANI), the Baltic Sea genomes were more likely to form clusters with the Caspian Seagenomes than with Swedish lakes genomes, even though geographic distancesbetween Swedish lakes and the Baltic Sea are much smaller. Phylogenomic analysisand ancestral state reconstruction showed that approximately half of the brackishMAGs had freshwater ancestors and half had marine ancestors. Phylogeneticdistances were on average shorter to freshwater ancestors, but when subsampling thetree to the same number of freshwater and marine MAG clusters, the distances werenot significantly different. Brackish genomes belonging to Acidimicrobiia,Actinobacteria and Cyanobacteriia tended to originate from freshwater bacteria, whilethose of Alphaproteobacteria and Bacteroidia mainly had evolved from marinebacteria. / Mikroorganismer spelar avgörande roller i akvatiska ekosystem där de driverkretsloppen av näringsämnen. En ökad förståelse för hur mikroorganismer anpassarsig till miljöförändringar är viktigt för att förutsäga hur akvatiska ekosystem kommeratt förändras som en konsekvens av global uppvärmning, och sådan förståelse kanuppnås genom att studera tidigare skeenden i evolutionen. I detta projekt undersökervi det evolutionära förhållandet mellan brackvatten-bakterier från Östersjön ochKaspiska havet med sötvattens- och marina bakterier, med målet att förstå hurbrackvatten-bakterier har utvecklats. 11,276 bakteriella arvsmassor somrekonstruerats med metagenomik från sju data-set användes för att utföra enjämförande analys av bakterie-genom från söt-, brack och havsvatten. Klustring avgenomen baserat på parvis genomsnittlig nukleotididentitet (ANI) på ungefärligartnivå (96,5% ANI), grupperade Östersjöns bakterier tillsammans med Kaspiskahavets bakterier mer än med bakterier från svenska sjöar, trots att det geografiskaavståndet mellan svenska sjöar och Östersjön är mycket mindre. Fylogenetisk analysvisade att ungefär hälften av brackvatten arterna hade anfäder från sötvatten ochhälften från havsvatten. De fylogenetiska avstånden var i genomsnitt kortare tillanfaderna i sötvatten, men när man reducerade trädet till att ha samma antal sötvattenoch marina arter var avstånden inte längre signifikant olika. Brackvatten-arter somtillhörde Acidimicrobiia, Actinobacteria och Cyanobacteriia tenderade att härstammafrån sötvattenbakterier, medan de från Alphaproteobacteria och Bacteroidia främsthärstammade från marina bakterier.

Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that today's highly virulent P. syringae crop pathogens with narrow host range might have evolved after the advent of agriculture from ancestral P. syringae strains with wide host range that were adapted to mixed plant communities. The model tomato and Arabidopsis pathogen P. syringae pv. tomato (Pto) DC3000 and its close relatives isolated from crop plants were thus selected to unravel basic principles of host range evolution by applying molecular evolutionary analysis and comparative genomics approaches. Phylogenetic analysis was combined with host range tests to reconstruct the host range of the most recent common ancestor of all analyzed strains isolated from crop plants. Even though reconstruction of host range of the most recent common ancestor of all analyzed strains was not conclusive, support for this hypothesis was found in some sub-groups of strains. The focus of my studies then turned to Pto T1, which was found to represent the most common P. syringae lineage causing bacterial speck disease on tomato world-wide. Five genomes were sequenced and compared to each other. Identical genotypes were found in North America and Europe suggesting frequent pathogen movement between these continents. Moreover, the type III-secreted effector gene hopM1 was found to be under strong selection for loss of function and non-synonymous mutations in the fliC gene allowed to identify a region that triggers plant immunity. Finally, Pto T1 was compared to closely related bacteria isolated from snow pack and surface water in the French Alps. Recombination between alpine strains and crop strains was inferred and virulence gene repertoires of alpine strains and crop strains were found to overlap. Alpine strains cause disease on tomato and have relatively wider host ranges than Pto T1. The conclusion from these studies is that Pto T1 and other crop pathogens may have evolved from ancestors similar to the characterized environmental strains isolated in the French Alps by adapting their effector repertoire to individual crops becoming more virulent on these crops but losing virulence on other plants. / Ph. D.

The design and evaluation of computer systems rely heavily upon simulation. Simulation is also a major bottleneck in the iterative design process. Applications that may be executed natively on physical systems in a matter of minutes may take weeks or months to simulate. As designs incorporate increasingly higher numbers of processor cores, it is expected the times required to simulate future systems will become an even greater issue. Simulation exhibits a tradeoff between speed and accuracy. By basing experimental procedures upon known statistical methods, the simulation of systems may be dramatically accelerated while retaining reliable methods to estimate error. This thesis focuses on the acceleration of simulation through statistical processes. The first two techniques discussed in this thesis focus on accelerating single-threaded simulation via cluster sampling. Cluster sampling extracts multiple groups of contiguous population elements to form a sample. This thesis introduces techniques to reduce sampling and non-sampling bias components, which must be reduced for sample measurements to be reliable. Non-sampling bias is reduced through the Reverse State Reconstruction algorithm, which removes ineffectual instructions from the skipped instruction stream between simulated clusters. Sampling bias is reduced via the Single Pass Sampling Regimen Design Process, which guides the user towards selected representative sampling regimens. Unfortunately, the extension of cluster sampling to include multi-threaded architectures is non-trivial and raises many interesting challenges. Overcoming these challenges will be discussed. This thesis also introduces thread skew, a useful metric that quantitatively measures the non-sampling bias associated with divergent thread progressions at the beginning of a sampling unit. Finally, the Barrier Interval Simulation method is discussed as a technique to dramatically decrease the simulation times of certain classes of multi-threaded programs. It segments a program into discrete intervals, separated by barriers, which are leveraged to avoid many of the challenges that prevent multi-threaded sampling.

No description available.

We investigate two different coupling schemes between a nano-scale mechanical resonator and one-electron atoms. In these schemes, classical electromagnetic radiation mediates a mutual communication between the mechanical resonator and the atoms. In the process it generates atomic coherences, quantum superpositions of excited electronic levels of the atoms. An atomic coherence is highly responsive to subtle variations in the relative frequencies of the levels participating in such superposition state. By exposing the atoms to electromagnetic radiation modulated by the motion of the mechanical resonator, we show how the response of an atomic coherence can, under appropriate conditions, be used to affect on demand the dynamical state of the mechanical resonator. The first scheme realizes a long range interface between a mechanical resonator and an ensemble of three-level atoms. Here, mechanically modulated electromagnetic radiation comes from a laser beam reflected off an oscillating mirror, the mechanical resonator. This light beam drives the transition between an excited level and a hyperfine sublevel of the atoms with a certain detuning. A weaker light beam resonantly couples to the transition between the excited level and another hyperfine sublevel. On full resonance, the atoms evolve into a stationary coherence of the above (non-absorbing) hyperfine sublevels only. The atoms then become transparent to the weaker light beam, in a phenomenon called electromagnetically induced transparency. Off resonance, we find that this transparency is modulated at the mirror frequency with some phase shift, which allows the weaker beam to cause resonant backaction onto the moving mirror. The strength of this backaction is enhanced near atomic resonances and its character can be switched between amplification or damping of mirror vibrations by adjusting the detuning. In contrast, the second scheme accomplishes a closer range interface between a torsion pendulum and guided two level Rydberg atoms. Attaching a point electric dipole to the torsion pendulum allows electromagnetic coupling to two Rydberg levels of a passing atom. This coupling modifies the eigenfrequencies of the Rydberg levels such that they become dependent on the phonon number of the torsion pendulum. Via Ramsey interferometry, we may readout this effect and thus measure the phonon number. We show that, by subjecting several atoms, one by one, to a Ramsey measurement, a quantum non-demolition detection of the phonon number is feasible. Likewise, we show coherent oscillator displacements possible, by driving the atoms with external fields while they interact with the torsion pendulum. We propose a protocol to reconstruct the quantum state of motion of the torsion pendulum, combining these two techniques, Ramsey measurements and oscillator displacements. Our interfaces between a mechanical resonator and atoms provide alternative routes for the control of the state of motion, ultimately quantum mechanical, of a mechanical resonator, in which the latter is not restricted to be part of a cavity. We will thus ease quantum dynamical manipulations of mechanical resonators of sub micron scales, for which an efficient design of cavity opto- and electro-mechanical systems is hard.