Development of a Coupling Model for Fluid-Structure Interaction using the Mesh-free Finite Element Method and the Lattice Boltzmann Method

In the presented thesis work, the meshfree method with distance fields was coupled with the lattice Boltzmann method to obtain solutions of fluid-structure interaction problems. The thesis work involved development and implementation of numerical algorithms, data structure, and software. Numerical and computational properties of the coupling algorithm combining the meshfree method with distance fields and the lattice Boltzmann method were investigated. Convergence and accuracy of the methodology was validated by analytical solutions. The research was focused on fluid-structure interaction solutions in complex, mesh-resistant domains as both the lattice Boltzmann method and the meshfree method with distance fields are particularly adept in these situations. Furthermore, the fluid solution provided by the lattice Boltzmann method is massively scalable, allowing extensive use of cutting edge parallel computing resources to accelerate this phase of the solution process. The meshfree method with distance fields allows for exact satisfaction of boundary conditions making it possible to exactly capture the effects of the fluid field on the solid structure.

New evidence for the zoom lens model using the RSVP technique

A main prediction from the zoom lens model for visual attention is that performance is an inverse function of the size of the attended area. The "attention shift paradigm" developed by Sperling and Reeves (1980) was adapted here to study predictions from the zoom lens model. In two experiments two lists of items were simultaneously presented using the rapid serial visual presentation technique. Subjects were to report the first item he/she was able to identify in the series that did not include the target (the letter T) after he/she saw the target. In one condition, subjects knew in which list the target would appear, in another condition, they did not have this knowledge, having to attend to both positions in order to detect the target. The zoom lens model predicts an interaction between this variable and the distance separating the two positions where the lists are presented. In both experiments, this interaction was observed. The results are also discussed as a solution to the apparently contradictory results with regard to the analog movement model.

An application of two techniques for the analysis of short, multivariate non-stationary time-series of Mauritanian trawl survey data

Min/max autocorrelation factor analysis (MAFA) and dynamic factor analysis (DFA) are complementary techniques for analysing short (> 15-25 y), non-stationary, multivariate data sets. We illustrate the two techniques using catch rate (cpue) time-series (1982-2001) for 17 species caught during trawl surveys off Mauritania, with the NAO index, an upwelling index, sea surface temperature, and an index of fishing effort as explanatory variables. Both techniques gave coherent results, the most important common trend being a decrease in cpue during the latter half of the time-series, and the next important being an increase during the first half. A DFA model with SST and UPW as explanatory variables and two common trends gave good fits to most of the cpue time-series. (c) 2004 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.

A multi-model approach to evaluate the role of environmental variability and fishing pressure in sardine fisheries

Understanding the fluctuations in population abundance is a central question in fisheries. Sardine fisheries is of great importance to Portugal and is data-rich and of primary concern to fisheries managers. In Portugal, sub-stocks of Sardina pilchardus (sardine) are found in different regions: the Northwest (IXaCN), Southwest (IXaCS) and the South coast (IXaS-Algarve). Each of these sardine sub-stocks is affected differently by a unique set of climate and ocean conditions, mainly during larval development and recruitment, which will consequently affect sardine fisheries in the short term. Taking this hypothesis into consideration we examined the effects of hydrographic (river discharge), sea surface temperature, wind driven phenomena, upwelling, climatic (North Atlantic Oscillation) and fisheries variables (fishing effort) on S. pilchardus catch rates (landings per unit effort, LPUE, as a proxy for sardine biomass). A 20-year time series (1989-2009) was used, for the different subdivisions of the Portuguese coast (sardine sub-stocks). For the purpose of this analysis a multi-model approach was used, applying different time series models for data fitting (Dynamic Factor Analysis, Generalised Least Squares), forecasting (Autoregressive Integrated Moving Average), as well as Surplus Production stock assessment models. The different models were evaluated, compared and the most important variables explaining changes in LPUE were identified. The type of relationship between catch rates of sardine and environmental variables varied across regional scales due to region-specific recruitment responses. Seasonality plays an important role in sardine variability within the three study regions. In IXaCN autumn (season with minimum spawning activity, larvae and egg concentrations) SST, northerly wind and wind magnitude were negatively related with LPUE. In IXaCS none of the explanatory variables tested was clearly related with LPUE. In IXaS-Algarve (South Portugal) both spring (period when large abundances of larvae are found) northerly wind and wind magnitude were negatively related with LPUE, revealing that environmental effects match with the regional peak in spawning time. Overall, results suggest that management of small, short-lived pelagic species, such as sardine quotas/sustainable yields, should be adapted to a regional scale because of regional environmental variability.

Single diode model parameters analysis of photovoltaic cell

In this paper it is proposed to obtain enhanced and more efficient parameters model from generalized five parameters (single diode) model of PV cells. The paper also introduces, describes and implements a seven parameter model for photovoltaic cell (PV cell) which includes two internal parameters and five external parameters. To obtain the model the mathematical equations and an equivalent circuit consisting of a photo generated current source, a series resistor, a shunt resistor and a diode is used. The fundamental equation of PV cell is used to analyse and best fit the observation data. Especially bisection iteration method is used to obtain the expected result and to understand the deviation of changes in different parameters situation at various conditions respectively. The produced model can be used of measuring and understanding the actions of photovoltaic cells for certain changes and parameters extraction. The effect is also studied with I-V and P-V characteristics of PV cells though it is a challenge to optimize the output with real time simulation. The working procedure is also discussed and an experiment presented to get the closure and insight about the produced model and to decide upon the model validity. At the end, we observed that the result of the simulation is very close to the produced model.

Dynamics of undeactuated cable-driven parallel robots

This thesis focuses on the dynamics of underactuated cable-driven parallel robots (UACDPRs), including various aspects of robotic theory and practice, such as workspace computation, parameter identification, and trajectory planning. After a brief introduction to CDPRs, UACDPR kinematic and dynamic models are analyzed, under the relevant assumption of inextensible cables. The free oscillatory motion of the end-effector (EE), which is a unique feature of underactuated mechanisms, is studied in detail, from both a kinematic and a dynamic perspective. The free (small) oscillations of the EE around equilibria are proved to be harmonic and the corresponding natural oscillation frequencies are analytically computed. UACDPR workspace computation and analysis are then performed. A new performance index is proposed for the analysis of the influence of actuator errors on cable tensions around equilibrium configurations, and a new type of workspace, called tension-error-insensitive, is defined as the set of poses that a UACDPR EE can statically attain even in presence of actuation errors, while preserving tensions between assigned (positive) bounds. EE free oscillations are then employed to conceive a novel procedure aimed at identifying the EE inertial parameters. This approach does not require the use of force or torque measurements. Moreover, a self-calibration procedure for the experimental determination of UACDPR initial cable lengths is developed, which consequently enables the robot to automatically infer the EE initial pose at machine start-up. Lastly, trajectory planning of UACDPRs is investigated. Two alternative methods are proposed, which aim at (i) reducing EE oscillations even when model parameters are uncertain or (ii) eliminate EE oscillations in case model parameters are perfectly known. EE oscillations are reduced in real-time by dynamically scaling a nominal trajectory and filtering it with an input shaper, whereas they can be eliminated if an off-line trajectory is computed that accounts for the system internal dynamics.

Geometrico-static modelling of continuum parallel robots

In this thesis, we explore three methods for the geometrico-static modelling of continuum parallel robots. Inspired by biological trunks, tentacles and snakes, continuum robot designs can reach confined spaces, manipulate objects in complex environments and conform to curvilinear paths in space. In addition, parallel continuum manipulators have the potential to inherit some of the compactness and compliance of continuum robots while retaining some of the precision, stability and strength of rigid-links parallel robots. Subsequently, the foundation of our work is performed on slender beam by applying the Cosserat rod theory, appropriate to model continuum robots. After that, three different approaches are developed on a case study of a planar parallel continuum robot constituted of two connected flexible links. We solve the forward and inverse geometrico-static problem namely by using (a) shooting methods to obtain a numerical solution, (b) an elliptic method to find a quasi-analytical solution, and (c) the Corde model to perform further model analysis. The performances of each of the studied methods are evaluated and their limits are highlighted. This thesis is divided as follows. Chapter one gives the introduction on the field of the continuum robotics and introduce the parallel continuum robots that is studied in this work. Chapter two describe the geometrico-static problem and gives the mathematical description of this problem. Chapter three explains the numerical approach with the shooting method and chapter four introduce the quasi-analytical solution. Then, Chapter five introduce the analytic method inspired by the Corde model and chapter six gives the conclusions of this work.

Variational and learning models for image and time series inverse problems

Inverse problems are at the core of many challenging applications. Variational and learning models provide estimated solutions of inverse problems as the outcome of specific reconstruction maps. In the variational approach, the result of the reconstruction map is the solution of a regularized minimization problem encoding information on the acquisition process and prior knowledge on the solution. In the learning approach, the reconstruction map is a parametric function whose parameters are identified by solving a minimization problem depending on a large set of data. In this thesis, we go beyond this apparent dichotomy between variational and learning models and we show they can be harmoniously merged in unified hybrid frameworks preserving their main advantages. We develop several highly efficient methods based on both these model-driven and data-driven strategies, for which we provide a detailed convergence analysis. The arising algorithms are applied to solve inverse problems involving images and time series. For each task, we show the proposed schemes improve the performances of many other existing methods in terms of both computational burden and quality of the solution. In the first part, we focus on gradient-based regularized variational models which are shown to be effective for segmentation purposes and thermal and medical image enhancement. We consider gradient sparsity-promoting regularized models for which we develop different strategies to estimate the regularization strength. Furthermore, we introduce a novel gradient-based Plug-and-Play convergent scheme considering a deep learning based denoiser trained on the gradient domain. In the second part, we address the tasks of natural image deblurring, image and video super resolution microscopy and positioning time series prediction, through deep learning based methods. We boost the performances of supervised, such as trained convolutional and recurrent networks, and unsupervised deep learning strategies, such as Deep Image Prior, by penalizing the losses with handcrafted regularization terms.

Interpretable Convolutional Neural Networks for Decoding and Analyzing Neural Time Series Data

Machine learning is widely adopted to decode multi-variate neural time series, including electroencephalographic (EEG) and single-cell recordings. Recent solutions based on deep learning (DL) outperformed traditional decoders by automatically extracting relevant discriminative features from raw or minimally pre-processed signals. Convolutional Neural Networks (CNNs) have been successfully applied to EEG and are the most common DL-based EEG decoders in the state-of-the-art (SOA). However, the current research is affected by some limitations. SOA CNNs for EEG decoding usually exploit deep and heavy structures with the risk of overfitting small datasets, and architectures are often defined empirically. Furthermore, CNNs are mainly validated by designing within-subject decoders. Crucially, the automatically learned features mainly remain unexplored; conversely, interpreting these features may be of great value to use decoders also as analysis tools, highlighting neural signatures underlying the different decoded brain or behavioral states in a data-driven way. Lastly, SOA DL-based algorithms used to decode single-cell recordings rely on more complex, slower to train and less interpretable networks than CNNs, and the use of CNNs with these signals has not been investigated. This PhD research addresses the previous limitations, with reference to P300 and motor decoding from EEG, and motor decoding from single-neuron activity. CNNs were designed light, compact, and interpretable. Moreover, multiple training strategies were adopted, including transfer learning, which could reduce training times promoting the application of CNNs in practice. Furthermore, CNN-based EEG analyses were proposed to study neural features in the spatial, temporal and frequency domains, and proved to better highlight and enhance relevant neural features related to P300 and motor states than canonical EEG analyses. Remarkably, these analyses could be used, in perspective, to design novel EEG biomarkers for neurological or neurodevelopmental disorders. Lastly, CNNs were developed to decode single-neuron activity, providing a better compromise between performance and model complexity.

Vocabulary Transfer and Knowledge Distillation for Language Model Compression

Natural Language Processing (NLP) has seen tremendous improvements over the last few years. Transformer architectures achieved impressive results in almost any NLP task, such as Text Classification, Machine Translation, and Language Generation. As time went by, transformers continued to improve thanks to larger corpora and bigger networks, reaching hundreds of billions of parameters. Training and deploying such large models has become prohibitively expensive, such that only big high tech companies can afford to train those models. Therefore, a lot of research has been dedicated to reducing a model’s size. In this thesis, we investigate the effects of Vocabulary Transfer and Knowledge Distillation for compressing large Language Models. The goal is to combine these two methodologies to further compress models without significant loss of performance. In particular, we designed different combination strategies and conducted a series of experiments on different vertical domains (medical, legal, news) and downstream tasks (Text Classification and Named Entity Recognition). Four different methods involving Vocabulary Transfer (VIPI) with and without a Masked Language Modelling (MLM) step and with and without Knowledge Distillation are compared against a baseline that assigns random vectors to new elements of the vocabulary. Results indicate that VIPI effectively transfers information of the original vocabulary and that MLM is beneficial. It is also noted that both vocabulary transfer and knowledge distillation are orthogonal to one another and may be applied jointly. The application of knowledge distillation first before subsequently applying vocabulary transfer is recommended. Finally, model performance due to vocabulary transfer does not always show a consistent trend as the vocabulary size is reduced. Hence, the choice of vocabulary size should be empirically selected by evaluation on the downstream task similar to hyperparameter tuning.

Feedback control of underactuated cable-driven parallel robots

In this work an Underactuated Cable-Driven Parallel Robot (UACDPR) that operates in the three dimensional Euclidean space is considered. The End-Effector has 6 degrees of freedom and is actuated by 4 cables, therefore from a mechanical point of view the robot is defined underconstrained. However, considering only three controlled pose variables, the degree of redundancy for the control theory can be considered one. The aim of this thesis is to design a feedback controller for a point-to-point motion that satisfies the transient requirements, and is capable of reducing oscillations that derive from the reduced number of constraints. A force control is chosen for the positioning of the End-Effector, and error with respect to the reference is computed through data measure of several sensors (load cells, encoders and inclinometers) such as cable lengths, tension and orientation of the platform. In order to express the relation between pose and cable tension, the inverse model is derived from the kinematic and dynamic model of the parallel robot. The intrinsic non-linear nature of UACDPRs systems introduces an additional level of complexity in the development of the controller, as a result the control law is composed by a partial feedback linearization, and damping injection to reduce orientation instability. The fourth cable allows to satisfy a further tension distribution constraint, ensuring positive tension during all the instants of motion. Then simulations with different initial conditions are presented in order to optimize control parameters, and lastly an experimental validation of the model is carried out, the results are analysed and limits of the presented approach are defined.

Integrated Proteomics Identified Up-regulated Focal Adhesion-mediated Proteins In Human Squamous Cell Carcinoma In An Orthotopic Murine Model.

Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.

The Soluble Guanylyl Cyclase Activator Bay 60-2770 Potently Relaxes The Pulmonary Artery On Congenital Diaphragmatic Hernia Rabbit Model.

Congenital diaphragmatic hernia (CDH) is associated with pulmonary hypertension which is often difficult to manage, and a significant cause of morbidity and mortality. In this study, we have used a rabbit model of CDH to evaluate the effects of BAY 60-2770 on the in vitro reactivity of left pulmonary artery. CDH was performed in New Zealand rabbit fetuses (n = 10 per group) and compared to controls. Measurements of body, total and left lung weights (BW, TLW, LLW) were done. Pulmonary artery rings were pre-contracted with phenylephrine (10 μM), after which cumulative concentration-response curves to glyceryl trinitrate (GTN; NO donor), tadalafil (PDE5 inhibitor) and BAY 60-2770 (sGC activator) were obtained as well as the levels of NO (NO3/NO2). LLW, TLW and LBR were decreased in CDH (p < 0.05). In left pulmonary artery, the potency (pEC50) for GTN was markedly lower in CDH (8.25 ± 0.02 versus 9.27 ± 0.03; p < 0.01). In contrast, the potency for BAY 60-2770 was markedly greater in CDH (11.7 ± 0.03 versus 10.5 ± 0.06; p < 0.01). The NO2/NO3 levels were 62 % higher in CDH (p < 0.05). BAY 60-2770 exhibits a greater potency to relax the pulmonary artery in CDH, indicating a potential use for pulmonary hypertension in this disease.

Chemical Immobilization Of Crosslinked Polymeric Ionic Liquids On Nitinol Wires Produces Highly Robust Sorbent Coatings For Solid-phase Microextraction.

Super elastic nitinol (NiTi) wires were exploited as highly robust supports for three distinct crosslinked polymeric ionic liquid (PIL)-based coatings in solid-phase microextraction (SPME). The oxidation of NiTi wires in a boiling (30%w/w) H2O2 solution and subsequent derivatization in vinyltrimethoxysilane (VTMS) allowed for vinyl moieties to be appended to the surface of the support. UV-initiated on-fiber copolymerization of the vinyl-substituted NiTi support with monocationic ionic liquid (IL) monomers and dicationic IL crosslinkers produced a crosslinked PIL-based network that was covalently attached to the NiTi wire. This alteration alleviated receding of the coating from the support, which was observed for an analogous crosslinked PIL applied on unmodified NiTi wires. A series of demanding extraction conditions, including extreme pH, pre-exposure to pure organic solvents, and high temperatures, were applied to investigate the versatility and robustness of the fibers. Acceptable precision of the model analytes was obtained for all fibers under these conditions. Method validation by examining the relative recovery of a homologous group of phthalate esters (PAEs) was performed in drip-brewed coffee (maintained at 60 °C) by direct immersion SPME. Acceptable recoveries were obtained for most PAEs in the part-per-billion level, even in this exceedingly harsh and complex matrix.