A dynamical systems analysis of vortex pinch-off

Vortex rings constitute the main structure in the wakes of a wide class of swimming and flying animals, as well as in cardiac flows and in the jets generated by some moss and fungi. However, there is a physical limit, determined by an energy maximization principle called the Kelvin-Benjamin principle, to the size that axisymmetric vortex rings can achieve. The existence of this limit is known to lead to the separation of a growing vortex ring from the shear layer feeding it, a process known as `vortex pinch-off', and characterized by the dimensionless vortex formation number. The goal of this thesis is to improve our understanding of vortex pinch-off as it relates to biological propulsion, and to provide future researchers with tools to assist in identifying and predicting pinch-off in biological flows.

To this end, we introduce a method for identifying pinch-off in starting jets using the Lagrangian coherent structures in the flow, and apply this criterion to an experimentally generated starting jet. Since most naturally occurring vortex rings are not circular, we extend the definition of the vortex formation number to include non-axisymmetric vortex rings, and find that the formation number for moderately non-axisymmetric vortices is similar to that of circular vortex rings. This suggests that naturally occurring vortex rings may be modeled as axisymmetric vortex rings. Therefore, we consider the perturbation response of the Norbury family of axisymmetric vortex rings. This family is chosen to model vortex rings of increasing thickness and circulation, and their response to prolate shape perturbations is simulated using contour dynamics. Finally, the response of more realistic models for vortex rings, constructed from experimental data using nested contours, to perturbations which resemble those encountered by forming vortices more closely, is simulated using contour dynamics. In both families of models, a change in response analogous to pinch-off is found as members of the family with progressively thicker cores are considered. We posit that this analogy may be exploited to understand and predict pinch-off in complex biological flows, where current methods are not applicable in practice, and criteria based on the properties of vortex rings alone are necessary.

Validation of a method for estimating realized annual fecundity in a multiple spawner, the long-snouted seahorse (Hippocampus guttulatus), using underwater visual census

The long-snouted seahorse (Hippocampus guttulatus) (Cuvier, 1829), was used to validate the pre-dictive accuracy of three progressively realistic models for estimating the realized annual fecundity of asyn-chronous, indeterminate, multiple spawners. Underwater surveys and catch data were used to estimate the duration of the reproductive season, female spawning frequency, male brooding frequency, and batch fecun-dity. The most realistic model, a generalization of the spawning fraction method, produced unbiased estimates of male brooding frequency (mean ±standard deviation [SD]=4.2 ±1.6 broods/year). Mean batch fecundity and realized annual fecundity were 213.9 (±110.9) and 903.6 (±522.4), respectively. However, females prepared significantly more clutches than the number of broods produced by males. Thus, methods that infer spawning frequency from patterns in female egg production may lead to significant overestimates of realized annual fecundity. The spawning fraction method is broadly applicable to many taxa that exhibit parental care and can be applied nondestructively to species for which conservation is a concern.

Analysis of micro-failure behaviors in hybrid fiber model composites

Micro-failure modes and statistical fragment lengths in the hybrid fiber and non-hybrid reference composites in the uniaxial tension were investigated. Similiar to the reference experiments, fibers in hybrid strong interface/medium interface fiber composites display a decrease in aspect ratio and an increase in interfacial shear stress (IFSS) with the increase of inter-fiber spacing. While for the fibers with weak interfaces in the hybrid strong interface/weak interface fiber composites, the aspect ratio increases and IFSS decreases with enlargement of inter-fiber spacing, which is contrary to other systems. Finite element numerical analysis was used to interpret the special phenomena.

Accelerating Internet Streaming Media Delivery Using Network-Aware Partial Caching

Internet streaming applications are adversely affected by network conditions such as high packet loss rates and long delays. This paper aims at mitigating such effects by leveraging the availability of client-side caching proxies. We present a novel caching architecture (and associated cache management algorithms) that turn edge caches into accelerators of streaming media delivery. A salient feature of our caching algorithms is that they allow partial caching of streaming media objects and joint delivery of content from caches and origin servers. The caching algorithms we propose are both network-aware and stream-aware; they take into account the popularity of streaming media objects, their bit-rate requirements, and the available bandwidth between clients and servers. Using realistic models of Internet bandwidth (derived from proxy cache logs and measured over real Internet paths), we have conducted extensive simulations to evaluate the performance of various cache management alternatives. Our experiments demonstrate that network-aware caching algorithms can significantly reduce service delay and improve overall stream quality. Also, our experiments show that partial caching is particularly effective when bandwidth variability is not very high.

Multi-scale modelling of atomic layer deposition

High-permittivity ("high-k") dielectric materials are used in the transistor gate stack in integrated circuits. As the thickness of silicon oxide dielectric reduces below 2 nm with continued downscaling, the leakage current because of tunnelling increases, leading to high power consumption and reduced device reliability. Hence, research concentrates on finding materials with high dielectric constant that can be easily integrated into a manufacturing process and show the desired properties as a thin film. Atomic layer deposition (ALD) is used practically to deposit high-k materials like HfO2, ZrO2, and Al2O3 as gate oxides. ALD is a technique for producing conformal layers of material with nanometer-scale thickness, used commercially in non-planar electronics and increasingly in other areas of science and technology. ALD is a type of chemical vapor deposition that depends on self-limiting surface chemistry. In ALD, gaseous precursors are allowed individually into the reactor chamber in alternating pulses. Between each pulse, inert gas is admitted to prevent gas phase reactions. This thesis provides a profound understanding of the ALD of oxides such as HfO2, showing how the chemistry affects the properties of the deposited film. Using multi-scale modelling of ALD, the kinetics of reactions at the growing surface is connected to experimental data. In this thesis, we use density functional theory (DFT) method to simulate more realistic models for the growth of HfO2 from Hf(N(CH3)2)4/H2O and HfCl4/H2O and for Al2O3 from Al(CH3)3/H2O.Three major breakthroughs are discovered. First, a new reaction pathway, ’multiple proton diffusion’, is proposed for the growth of HfO2 from Hf(N(CH3)2)4/H2O.1 As a second major breakthrough, a ’cooperative’ action between adsorbed precursors is shown to play an important role in ALD. By this we mean that previously-inert fragments can become reactive once sufficient molecules adsorb in their neighbourhood during either precursor pulse. As a third breakthrough, the ALD of HfO2 from Hf(N(CH3)2)4 and H2O is implemented for the first time into 3D on-lattice kinetic Monte-Carlo (KMC).2 In this integrated approach (DFT+KMC), retaining the accuracy of the atomistic model in the higher-scale model leads to remarkable breakthroughs in our understanding. The resulting atomistic model allows direct comparison with experimental techniques such as X-ray photoelectron spectroscopy and quartz crystal microbalance.

DEVELOPING AN INTELLIGENT DIGITAL MOCK UP TO INTEGRATE DESIGN AND MANUFACTURING DISCIPLINES

This paper presents an approach to develop an intelligent digital mock-up (DMU) through integration of design and manufacturing disciplines to enable a better understanding of assembly related issues during design evolution. The intelligent DMU will contain tolerance information related to manufacturing capabilities so it can be used as a source for assembly simulations of realistic models to support the manufacturing decision making process within the design domain related to tolerance build ups. A literature review of the contributing research areas is presented, from which identification of the need for an intelligent DMU has been developed. The proposed methodology including the applications of cellular modelling and potential features of the intelligent DMU are presented and explained. Finally a conclusion examines the work to date and the future work to achieve an intelligent DMU.

New methodologies for directed functional connectivity applied to brain neuroimaging research

Tese de doutoramento, Engenharia Biomédica e Biofísica, Universidade de Lisboa, Faculdade de Ciências, 2015

Estimation des longueurs de branche et artefact sur la datation moléculaire

La phylogénie moléculaire fournit un outil complémentaire aux études paléontologiques et géologiques en permettant la construction des relations phylogénétiques entre espèces ainsi que l’estimation du temps de leur divergence. Cependant lorsqu’un arbre phylogénétique est inféré, les chercheurs se focalisent surtout sur la topologie, c'est-à-dire l’ordre de branchement relatif des différents nœuds. Les longueurs des branches de cette phylogénie sont souvent considérées comme des sous-produits, des paramètres de nuisances apportant peu d’information. Elles constituent cependant l’information primaire pour réaliser des datations moléculaires. Or la saturation, la présence de substitutions multiples à une même position, est un artefact qui conduit à une sous-estimation systématique des longueurs de branche. Nous avons décidé d’estimer l‘influence de la saturation et son impact sur l’estimation de l’âge de divergence. Nous avons choisi d’étudier le génome mitochondrial des mammifères qui est supposé avoir un niveau élevé de saturation et qui est disponible pour de nombreuses espèces. De plus, les relations phylogénétiques des mammifères sont connues, ce qui nous a permis de fixer la topologie, contrôlant ainsi un des paramètres influant la longueur des branches. Nous avons utilisé principalement deux méthodes pour améliorer la détection des substitutions multiples : (i) l’augmentation du nombre d’espèces afin de briser les plus longues branches de l’arbre et (ii) des modèles d’évolution des séquences plus ou moins réalistes. Les résultats montrèrent que la sous-estimation des longueurs de branche était très importante (jusqu'à un facteur de 3) et que l’utilisation d'un grand nombre d’espèces est un facteur qui influence beaucoup plus la détection de substitutions multiples que l’amélioration des modèles d’évolutions de séquences. Cela suggère que même les modèles d’évolution les plus complexes disponibles actuellement, (exemple: modèle CAT+Covarion, qui prend en compte l’hétérogénéité des processus de substitution entre positions et des vitesses d’évolution au cours du temps) sont encore loin de capter toute la complexité des processus biologiques. Malgré l’importance de la sous-estimation des longueurs de branche, l’impact sur les datations est apparu être relativement faible, car la sous-estimation est plus ou moins homothétique. Cela est particulièrement vrai pour les modèles d’évolution. Cependant, comme les substitutions multiples sont le plus efficacement détectées en brisant les branches en fragments les plus courts possibles via l’ajout d’espèces, se pose le problème du biais dans l’échantillonnage taxonomique, biais dû à l‘extinction pendant l’histoire de la vie sur terre. Comme ce biais entraine une sous-estimation non-homothétique, nous considérons qu’il est indispensable d’améliorer les modèles d’évolution des séquences et proposons que le protocole élaboré dans ce travail permettra d’évaluer leur efficacité vis-à-vis de la saturation.

Modélisation de la diffraction des ondes de cisaillement en élastographie dynamique ultrasonore

L'élastographie ultrasonore est une technique d'imagerie émergente destinée à cartographier les paramètres mécaniques des tissus biologiques, permettant ainsi d’obtenir des informations diagnostiques additionnelles pertinentes. La méthode peut ainsi être perçue comme une extension quantitative et objective de l'examen palpatoire. Diverses techniques élastographiques ont ainsi été proposées pour l'étude d'organes tels que le foie, le sein et la prostate et. L'ensemble des méthodes proposées ont en commun une succession de trois étapes bien définies: l'excitation mécanique (statique ou dynamique) de l'organe, la mesure des déplacements induits (réponse au stimulus), puis enfin, l'étape dite d'inversion, qui permet la quantification des paramètres mécaniques, via un modèle théorique préétabli. Parallèlement à la diversification des champs d'applications accessibles à l'élastographie, de nombreux efforts sont faits afin d'améliorer la précision ainsi que la robustesse des méthodes dites d'inversion. Cette thèse regroupe un ensemble de travaux théoriques et expérimentaux destinés à la validation de nouvelles méthodes d'inversion dédiées à l'étude de milieux mécaniquement inhomogènes. Ainsi, dans le contexte du diagnostic du cancer du sein, une tumeur peut être perçue comme une hétérogénéité mécanique confinée, ou inclusion, affectant la propagation d'ondes de cisaillement (stimulus dynamique). Le premier objectif de cette thèse consiste à formuler un modèle théorique capable de prédire l'interaction des ondes de cisaillement induites avec une tumeur, dont la géométrie est modélisée par une ellipse. Après validation du modèle proposé, un problème inverse est formulé permettant la quantification des paramètres viscoélastiques de l'inclusion elliptique. Dans la continuité de cet objectif, l'approche a été étendue au cas d'une hétérogénéité mécanique tridimensionnelle et sphérique avec, comme objectifs additionnels, l'applicabilité aux mesures ultrasonores par force de radiation, mais aussi à l'estimation du comportement rhéologique de l'inclusion (i.e., la variation des paramètres mécaniques avec la fréquence d'excitation). Enfin, dans le cadre de l'étude des propriétés mécaniques du sang lors de la coagulation, une approche spécifique découlant de précédents travaux réalisés au sein de notre laboratoire est proposée. Celle-ci consiste à estimer la viscoélasticité du caillot sanguin via le phénomène de résonance mécanique, ici induit par force de radiation ultrasonore. La méthode, dénommée ARFIRE (''Acoustic Radiation Force Induced Resonance Elastography'') est appliquée à l'étude de la coagulation de sang humain complet chez des sujets sains et sa reproductibilité est évaluée.

Delta(1232) isobar excitations in nuclear many-body systems from varios NN interactions.

Delta isobar components in the nuclear many-body wave function are investigated for the deuteron, light nuclei (16O), and infinite nuclear matter within the framework of the coupled-cluster theory. The predictions derived for various realistic models of the baryon-baryon interaction are compared to each other. These include local (V28) and nonlocal meson exchange potentials (Bonn2000) but also a model recently derived by the Salamanca group accounting for quark degrees of freedom. The characteristic differences which are obtained for the NDelta and Delta Delta correlation functions are related to the approximation made in deriving the matrix elements for the baryon-baryon interaction.

An empirical study of process-related attributes in segmented software cost-estimation relationships

Parametric software effort estimation models consisting on a single mathematical relationship suffer from poor adjustment and predictive characteristics in cases in which the historical database considered contains data coming from projects of a heterogeneous nature. The segmentation of the input domain according to clusters obtained from the database of historical projects serves as a tool for more realistic models that use several local estimation relationships. Nonetheless, it may be hypothesized that using clustering algorithms without previous consideration of the influence of well-known project attributes misses the opportunity to obtain more realistic segments. In this paper, we describe the results of an empirical study using the ISBSG-8 database and the EM clustering algorithm that studies the influence of the consideration of two process-related attributes as drivers of the clustering process: the use of engineering methodologies and the use of CASE tools. The results provide evidence that such consideration conditions significantly the final model obtained, even though the resulting predictive quality is of a similar magnitude.

A hybrid data assimilation scheme for model parameter estimation: application to morphodynamic modelling

We present a novel algorithm for joint state-parameter estimation using sequential three dimensional variational data assimilation (3D Var) and demonstrate its application in the context of morphodynamic modelling using an idealised two parameter 1D sediment transport model. The new scheme combines a static representation of the state background error covariances with a flow dependent approximation of the state-parameter cross-covariances. For the case presented here, this involves calculating a local finite difference approximation of the gradient of the model with respect to the parameters. The new method is easy to implement and computationally inexpensive to run. Experimental results are positive with the scheme able to recover the model parameters to a high level of accuracy. We expect that there is potential for successful application of this new methodology to larger, more realistic models with more complex parameterisations.

A complete atomistic model of molten polyethylene from neutron scattering data: a new methodology for polymer structure

A new approach to the study of the local organization in amorphous polymer materials is presented. The method couples neutron diffraction experiments that explore the structure on the spatial scale 1–20 Å with the reverse Monte Carlo fitting procedure to predict structures that accurately represent the experimental scattering results over the whole momentum transfer range explored. Molecular mechanics and molecular dynamics techniques are also used to produce atomistic models independently from any experimental input, thereby providing a test of the viability of the reverse Monte Carlo method in generating realistic models for amorphous polymeric systems. An analysis of the obtained models in terms of single chain properties and of orientational correlations between chain segments is presented. We show the viability of the method with data from molten polyethylene. The analysis derives a model with average C-C and C-H bond lengths of 1.55 Å and 1.1 Å respectively, average backbone valence angle of 112, a torsional angle distribution characterized by a fraction of trans conformers of 0.67 and, finally, a weak interchain orientational correlation at around 4 Å.

Response of El Niño sea surface temperature variability to greenhouse warming

The destructive environmental and socio-economic impacts of the El Niño/Southern Oscillation1, 2 (ENSO) demand an improved understanding of how ENSO will change under future greenhouse warming. Robust projected changes in certain aspects of ENSO have been recently established3, 4, 5. However, there is as yet no consensus on the change in the magnitude of the associated sea surface temperature (SST) variability6, 7, 8, commonly used to represent ENSO amplitude1, 6, despite its strong effects on marine ecosystems and rainfall worldwide1, 2, 3, 4, 9. Here we show that the response of ENSO SST amplitude is time-varying, with an increasing trend in ENSO amplitude before 2040, followed by a decreasing trend thereafter. We attribute the previous lack of consensus to an expectation that the trend in ENSO amplitude over the entire twenty-first century is unidirectional, and to unrealistic model dynamics of tropical Pacific SST variability. We examine these complex processes across 22 models in the Coupled Model Intercomparison Project phase 5 (CMIP5) database10, forced under historical and greenhouse warming conditions. The nine most realistic models identified show a strong consensus on the time-varying response and reveal that the non-unidirectional behaviour is linked to a longitudinal difference in the surface warming rate across the Indo-Pacific basin. Our results carry important implications for climate projections and climate adaptation pathways.

An accelerating cosmology without dark energy

The negative pressure accompanying gravitationally-induced particle creation can lead to a cold dark matter (CDM) dominated, accelerating Universe (Lima et al. 1996 [1]) without requiring the presence of dark energy or a cosmological constant. In a recent study, Lima et al. 2008 [2] (LSS) demonstrated that particle creation driven cosmological models are capable of accounting for the SNIa observations [3] of the recent transition from a decelerating to an accelerating Universe, without the need for Dark Energy. Here we consider a class of such models where the particle creation rate is assumed to be of the form Gamma = beta H + gamma H(0), where H is the Hubble parameter and H(0) is its present value. The evolution of such models is tested at low redshift by the latest SNe Ia data provided by the Union compilation [4] and at high redshift using the value of z(eq), the redshift of the epoch of matter - radiation equality, inferred from the WMAP constraints on the early Integrated Sachs-Wolfe (ISW) effect [5]. Since the contributions of baryons and radiation were ignored in the work of LSS, we include them in our study of this class of models. The parameters of these more realistic models with continuous creation of CDM are constrained at widely-separated epochs (z(eq) approximate to 3000 and z approximate to 0) in the evolution of the Universe. The comparison of the parameter values, {beta, gamma}, determined at these different epochs reveals a tension between the values favored by the high redshift CMB constraint on z(eq) from the ISW and those which follow from the low redshift SNIa data, posing a potential challenge to this class of models. While for beta = 0 this conflict is only at less than or similar to 2 sigma, it worsens as beta increases from zero.