Synthesis of FPGA-based accelerators implementing recursive algorithms

O desenvolvimento de sistemas computacionais é um processo complexo, com múltiplas etapas, que requer uma análise profunda do problema, levando em consideração as limitações e os requisitos aplicáveis. Tal tarefa envolve a exploração de técnicas alternativas e de algoritmos computacionais para optimizar o sistema e satisfazer os requisitos estabelecidos. Neste contexto, uma das mais importantes etapas é a análise e implementação de algoritmos computacionais. Enormes avanços tecnológicos no âmbito das FPGAs (Field-Programmable Gate Arrays) tornaram possível o desenvolvimento de sistemas de engenharia extremamente complexos. Contudo, o número de transístores disponíveis por chip está a crescer mais rapidamente do que a capacidade que temos para desenvolver sistemas que tirem proveito desse crescimento. Esta limitação já bem conhecida, antes de se revelar com FPGAs, já se verificava com ASICs (Application-Specific Integrated Circuits) e tem vindo a aumentar continuamente. O desenvolvimento de sistemas com base em FPGAs de alta capacidade envolve uma grande variedade de ferramentas, incluindo métodos para a implementação eficiente de algoritmos computacionais. Esta tese pretende proporcionar uma contribuição nesta área, tirando partido da reutilização, do aumento do nível de abstracção e de especificações algorítmicas mais automatizadas e claras. Mais especificamente, é apresentado um estudo que foi levado a cabo no sentido de obter critérios relativos à implementação em hardware de algoritmos recursivos versus iterativos. Depois de serem apresentadas algumas das estratégias para implementar recursividade em hardware mais significativas, descreve-se, em pormenor, um conjunto de algoritmos para resolver problemas de pesquisa combinatória (considerados enquanto exemplos de aplicação). Versões recursivas e iterativas destes algoritmos foram implementados e testados em FPGA. Com base nos resultados obtidos, é feita uma cuidada análise comparativa. Novas ferramentas e técnicas de investigação que foram desenvolvidas no âmbito desta tese são também discutidas e demonstradas.

Flexible management of bandwidth and redundancy in fieldbuses

Os sistemas distribuídos embarcados (Distributed Embedded Systems – DES) têm sido usados ao longo dos últimos anos em muitos domínios de aplicação, da robótica, ao controlo de processos industriais passando pela aviónica e pelas aplicações veiculares, esperando-se que esta tendência continue nos próximos anos. A confiança no funcionamento é uma propriedade importante nestes domínios de aplicação, visto que os serviços têm de ser executados em tempo útil e de forma previsível, caso contrário, podem ocorrer danos económicos ou a vida de seres humanos poderá ser posta em causa. Na fase de projecto destes sistemas é impossível prever todos os cenários de falhas devido ao não determinismo do ambiente envolvente, sendo necessária a inclusão de mecanismos de tolerância a falhas. Adicionalmente, algumas destas aplicações requerem muita largura de banda, que também poderá ser usada para a evolução dos sistemas, adicionandolhes novas funcionalidades. A flexibilidade de um sistema é uma propriedade importante, pois permite a sua adaptação às condições e requisitos envolventes, contribuindo também para a simplicidade de manutenção e reparação. Adicionalmente, nos sistemas embarcados, a flexibilidade também é importante por potenciar uma melhor utilização dos, muitas vezes escassos, recursos existentes. Uma forma evidente de aumentar a largura de banda e a tolerância a falhas dos sistemas embarcados distribuídos é a replicação dos barramentos do sistema. Algumas soluções existentes, quer comerciais quer académicas, propõem a replicação dos barramentos para aumento da largura de banda ou para aumento da tolerância a falhas. No entanto e quase invariavelmente, o propósito é apenas um, sendo raras as soluções que disponibilizam uma maior largura de banda e um aumento da tolerância a falhas. Um destes raros exemplos é o FlexRay, com a limitação de apenas ser permitido o uso de dois barramentos. Esta tese apresentada e discute uma proposta para usar a replicação de barramentos de uma forma flexível com o objectivo duplo de aumentar a largura de banda e a tolerância a falhas. A flexibilidade dos protocolos propostos também permite a gestão dinâmica da topologia da rede, sendo o número de barramentos apenas limitado pelo hardware/software. As propostas desta tese foram validadas recorrendo ao barramento de campo CAN – Controller Area Network, escolhido devido à sua grande implantação no mercado. Mais especificamente, as soluções propostas foram implementadas e validadas usando um paradigma que combina flexibilidade com comunicações event-triggered e time-triggered: o FTT – Flexible Time- Triggered. No entanto, uma generalização para CAN nativo é também apresentada e discutida. A inclusão de mecanismos de replicação do barramento impõe a alteração dos antigos protocolos de replicação e substituição do nó mestre, bem como a definição de novos protocolos para esta finalidade. Este trabalho tira partido da arquitectura centralizada e da replicação do nó mestre para suportar de forma eficiente e flexível a replicação de barramentos. Em caso de ocorrência de uma falta num barramento (ou barramentos) que poderia provocar uma falha no sistema, os protocolos e componentes propostos nesta tese fazem com que o sistema reaja, mudando para um modo de funcionamento degradado. As mensagens que estavam a ser transmitidas nos barramentos onde ocorreu a falta são reencaminhadas para os outros barramentos. A replicação do nó mestre baseia-se numa estratégia líder-seguidores (leaderfollowers), onde o líder (leader) controla todo o sistema enquanto os seguidores (followers) servem como nós de reserva. Se um erro ocorrer no nó líder, um dos nós seguidores passará a controlar o sistema de uma forma transparente e mantendo as mesmas funcionalidades. As propostas desta tese foram também generalizadas para CAN nativo, tendo sido para tal propostos dois componentes adicionais. É, desta forma possível ter as mesmas capacidades de tolerância a falhas ao nível dos barramentos juntamente com a gestão dinâmica da topologia de rede. Todas as propostas desta tese foram implementadas e avaliadas. Uma implementação inicial, apenas com um barramento foi avaliada recorrendo a uma aplicação real, uma equipa de futebol robótico onde o protocolo FTT-CAN foi usado no controlo de movimento e da odometria. A avaliação do sistema com múltiplos barramentos foi feita numa plataforma de teste em laboratório. Para tal foi desenvolvido um sistema de injecção de faltas que permite impor faltas nos barramentos e nos nós mestre, e um sistema de medida de atrasos destinado a medir o tempo de resposta após a ocorrência de uma falta.

Study of multiferroic materials

The present PhD work aims the research and development of materials that exhibit multiferroic properties, in particular having a significant interaction between ferromagnetism and ferroelectricity; either directly within an intrinsic single phase or by combining extrinsic materials, achieving the coupling of properties through mechanic phenomena of the respective magnetostriction and piezoelectricity. These hybrid properties will allow the cross modification of magnetic and electric polarization states by the application of cross external magnetic and/or electric fields, giving way to a vast area for scientific investigation and potential technological applications in a new generation of electronic devices, such as computer memories, signal processing, transducers, sensors, etc. Initial experimental work consisted in chemical synthesis of nano powders oxides by urea pyrolysis method: A series of ceramic bulk composites with potential multiferroic properties comprised: of LuMnO3 with La0.7Sr0.3MnO3 and BaTiO3 with La0.7Ba0.3MnO3; and a series based on the intrinsic multiferroic LuMn1-zO3 phase modified with of Manganese vacancies. The acquisition of a new magnetron RF sputtering deposition system, in the Physics Department of Aveiro University, contributed to the proposal of an analogous experimental study in multiferroic thin films and multilayer samples. Besides the operational debut of this equipment several technical upgrades were completed like: the design and construction of the heater electrical contacts; specific shutters and supports for the magnetrons and for the substrate holder and; the addition of mass flow controllers, which allowed the introduction of N2 or O2 active atmosphere in the chamber; and the addition of a second RF generator, enabling co-deposition of different targets. Base study of the deposition conditions and resulting thin films characteristics in different substrates was made from an extensive list of targets. Particular attention was given to thin film deposition of magnetic phases La1-xSrxMnO3, La1-xBaxMnO3 and Ni2+x-yMn1-xGa1+y alloy, from the respective targets: La0.7Sr0.3MnO3, La0.7Ba0.3MnO3; and NiGa with NiMn. Main structural characterization of samples was performed by conventional and high resolution X-Ray Diffraction (XRD); chemical composition was determined by Electron Dispersion Spectroscopy (EDS); magnetization measurements recur to a Vibrating Sample Magnetometer (VSM) prototype; and surface probing (SPM) using Magnetic-Force (MFM) and Piezo-Response (PFM) Microscopy. Results clearly show that the composite bulk samples (LuM+LSM and BTO+LBM) feat the intended quality objectives in terms of phase composition and purity, having spurious contents below 0.5 %. SEM images confirm compact grain packaging and size distribution around the 50 nm scale. Electric conductivity, magnetization intensity and magneto impedance spreading response are coherent with the relative amount of magnetic phase in the sample. The existence of coupling between the functional phases is confirmed by the Magnetoelectric effect measurements of the sample “78%LuM+22%LSM” reaching 300% of electric response for 1 T at 100 kHz; while in the “78%BTO+22%LBM” sample the structural transitions of the magnetic phase at ~350 K result in a inversion of ME coefficient the behavior. A functional Magneto-Resistance measurement system was assembled from the concept stage until the, development and operational status; it enabled to test samples from 77 to 350 K, under an applied magnetic field up to 1 Tesla with 360º horizontal rotation; this system was also designed to measure Hall effect and has the potential to be further upgraded. Under collaboration protocols established with national and international institutions, complementary courses and sample characterization studies were performed using Magneto-Resistance (MR), Magneto-Impedance (MZ) and Magneto-Electric (ME) measurements; Raman and X-ray Photoelectron Spectroscopy (XPS); SQUID and VSM magnetization; Scanning Electron Microscopy (SEM) and Rutherford Back Scattering (RBS); Scan Probe Microscopy (SPM) with Band Excitation Probe Spectroscopy (BEPS); Neutron Powder Diffraction (NPD) and Perturbed Angular Correlations (PAC). Additional collaboration in research projects outside the scope of multiferroic materials provided further experience in sample preparation and characterization techniques, namely VSM and XPS measurements were performed in cubane molecular complex compounds and enable to identify the oxidation state of the integrating cluster of Ru ions; also, XRD and EDS/SEM analysis of the acquired targets and substrates implied the devolution of some items not in conformity with the specifications. Direct cooperation with parallel research projects regarding multiferroic materials, enable the assess to supplementary samples, namely a preliminary series of nanopowder Y1-x-yCaxØyMn1O3 and of Eu0.8Y0.2MnO3, a series of micropowder composites of LuMnO3 with La0.625Sr0.375MnO3 and of BaTiO3 with hexagonal ferrites; mono and polycrystalline samples of Pr1-xCaxMnO3, La1-xSrxMnO3 and La1-xCaxMnO3.

Accidental release of hazardous gases: modelling and assessing risk

The renewed concern in assessing risks and consequences from technological hazards in industrial and urban areas continues emphasizing the development of local-scale consequence analysis (CA) modelling tools able to predict shortterm pollution episodes and exposure effects on humans and the environment in case of accident with hazardous gases (hazmat). In this context, the main objective of this thesis is the development and validation of the EFfects of Released Hazardous gAses (EFRHA) model. This modelling tool is designed to simulate the outflow and atmospheric dispersion of heavy and passive hazmat gases in complex and build-up areas, and to estimate the exposure consequences of short-term pollution episodes in accordance to regulatory/safety threshold limits. Five main modules comprising up-to-date methods constitute the model: meteorological, terrain, source term, dispersion, and effects modules. Different initial physical states accident scenarios can be examined. Considered the main core of the developed tool, the dispersion module comprises a shallow layer modelling approach capable to account the main influence of obstacles during the hazmat gas dispersion phenomena. Model validation includes qualitative and quantitative analyses of main outputs by the comparison of modelled results against measurements and/or modelled databases. The preliminary analysis of meteorological and source term modules against modelled outputs from extensively validated models shows the consistent description of ambient conditions and the variation of the hazmat gas release. Dispersion is compared against measurements observations in obstructed and unobstructed areas for different release and dispersion scenarios. From the performance validation exercise, acceptable agreement was obtained, showing the reasonable numerical representation of measured features. In general, quality metrics are within or close to the acceptance limits recommended for ‘non-CFD models’, demonstrating its capability to reasonably predict hazmat gases accidental release and atmospheric dispersion in industrial and urban areas. EFRHA model was also applied to a particular case study, the Estarreja Chemical Complex (ECC), for a set of accidental release scenarios within a CA scope. The results show the magnitude of potential effects on the surrounding populated area and influence of the type of accident and the environment on the main outputs. Overall the present thesis shows that EFRHA model can be used as a straightforward tool to support CA studies in the scope of training and planning, but also, to support decision and emergency response in case of hazmat gases accidental release in industrial and built-up areas.

Interactions of cetaceans with Spanish and Portuguese fisheries in Atlantic waters : costs, benefits and implications for management

With the aim to provide new insights into operational cetacean-fishery interactions in Atlantic waters, this thesis assesses interactions of cetaceans with Spanish and Portuguese fishing vessels operating in Iberian and South West Atlantic waters. Different opportunistic research methodologies were applied, including an interview survey with fishers (mainly skippers) and onboard observations by fisheries observers and skippers, to describe different types of interactions and to identify potential hotspots for cetacean-fishery interactions and the cetacean species most involved, and to quantify the extent and the consequences of these interactions in terms of benefits and costs for cetaceans and fisheries. In addition, the suitability of different mitigation strategies was evaluated and discussed. The results of this work indicate that cetaceans interact frequently with Spanish and Portuguese fishing vessels, sometimes in a beneficial way (e.g. cetaceans indicate fish schools in purse seine fisheries), but mostly with negative consequences (depredation on catch, gear damage and cetacean bycatch). Significant economic loss and high bycatch rates are, however, only reported for certain fisheries and associated with particular cetacean species. In Galician fisheries, substantial economic loss was reported as a result of bottlenose dolphins damaging artisanal coastal gillnets, while high catch loss may arise from common dolphins scattering fish in purse seine fisheries. High cetacean bycatch mortality arises in trawl fisheries, mainly of common dolphin and particularly during trawling in water depths below 350 m, and in coastal set gillnet fisheries (mainly common and bottlenose dolphins). In large-scale bottom-set longline fisheries in South West Atlantic waters, sperm whales may significantly reduce catch rates through depredation on catch. The high diversity of cetacean-fishery interactions observed in the study area indicates that case-specific management strategies are needed to reduce negative impacts on fisheries and cetaceans. Acoustic deterrent devices (pingers) may be used to prevent small cetaceans from approaching and getting entangled in purse seines and set gillnets, although possible problems include cetacean habituation to the pinger sounds, as well as negative side effects on non-target cetaceans (habitat exclusion) and fisheries target species (reduced catch rates). For sardine and horse mackerel, target species of Iberian Atlantic fisheries, no aversive reaction to pinger sounds was detected during tank experiments conducted in the scope of this thesis. Bycatch in trawls may be reduced by the implementation of time/area restrictions of fishing activity. In addition, the avoidance of fishing areas with high cetacean abundance combined with the minimization of fishery-specific sound cues that possibly attract cetaceans, may also help to decrease interactions. In large-scale bottom-set longline fisheries, cetacean depredation on catch may be reduced by covering hooked fish with net sleeves ("umbrellas") provided that catch rates are not negatively affected by this gear modification. Trap fishing, as an alternative fishing method to bottom-set gillnetting and longlining, also has the potential to reduce cetacean bycatch and depredation, given that fish catch rates are similar to the rates obtained by bottom-set gillnets and longlines, whereas cetacean by-catch is unlikely. Economic incentives, such as the eco-certification of dolphin-safe fishing methods, should be promoted in order to create an additional source of income for fishers negatively affected by interactions with cetaceans, which, in turn, may also increase fishers’ willingness to accept and adopt mitigation measures. Although the opportunistic sampling methods applied in this work have certain restrictions concerning their reliability and precision, the results are consistent with previous studies in the same area. Moreover, they allow for the active participation of fishers that can provide important complementary ecological and technical knowledge required for cetacean management and conservation.

Seamless integration of heterogeneous networks in multicast environments

Nowadays, communication environments are already characterized by a myriad of competing and complementary technologies that aim to provide an ubiquitous connectivity service. Next Generation Networks need to hide this heterogeneity by providing a new abstraction level, while simultaneously be aware of the underlying technologies to deliver richer service experiences to the end-user. Moreover, the increasing interest for group-based multimedia services followed by their ever growing resource demands and network dynamics, has been boosting the research towards more scalable and exible network control approaches. The work developed in this Thesis enables such abstraction and exploits the prevailing heterogeneity in favor of a context-aware network management and adaptation. In this scope, we introduce a novel hierarchical control framework with self-management capabilities that enables the concept of Abstract Multiparty Trees (AMTs) to ease the control of multiparty content distribution throughout heterogeneous networks. A thorough evaluation of the proposed multiparty transport control framework was performed in the scope of this Thesis, assessing its bene ts in terms of network selection, delivery tree recon guration and resource savings. Moreover, we developed an analytical study to highlight the scalability of the AMT concept as well as its exibility in large scale networks and group sizes. To prove the feasibility and easy deployment characteristic of the proposed control framework, we implemented a proof-of-concept demonstrator that comprehends the main control procedures conceptually introduced. Its outcomes highlight a good performance of the multiparty content distribution tree control, including its local and global recon guration. In order to endow the AMT concept with the ability to guarantee the best service experience by the end-user, we integrate in the control framework two additional QoE enhancement approaches. The rst employs the concept of Network Coding to improve the robustness of the multiparty content delivery, aiming at mitigating the impact of possible packet losses in the end-user service perception. The second approach relies on a machine learning scheme to autonomously determine at each node the expected QoE towards a certain destination. This knowledge is then used by di erent QoE-aware network management schemes that, jointly, maximize the overall users' QoE. The performance and scalability of the control procedures developed, aided by the context and QoE-aware mechanisms, show the advantages of the AMT concept and the proposed hierarchical control strategy for the multiparty content distribution with enhanced service experience. Moreover we also prove the feasibility of the solution in a practical environment, and provide future research directions that bene t the evolved control framework and make it commercially feasible.

Evaluation of the matabolic response of osteosarcoma cells to conventional and new anticancer drugs by NMR metabolomics

The main scope of this work was to evaluate the metabolic effects of anticancer agents (three conventional and one new) in osteosarcoma (OS) cells and osteoblasts, by measuring alterations in the metabolic profile of cells by nuclear magnetic resonance (NMR) spectroscopy metabolomics. Chapter 1 gives a theoretical framework of this work, beginning with the main metabolic characteristics that globally describe cancer as well as the families and mechanisms of action of drugs used in chemotherapy. The drugs used nowadays to treat OS are also presented, together with the Palladium(II) complex with spermine, Pd2Spm, potentially active against cancer. Then, the global strategy for cell metabolomics is explained and the state of the art of metabolomic studies that analyze the effect of anticancer agents in cells is presented. In Chapter 2, the fundamentals of the analytical techniques used in this work, namely for biological assays, NMR spectroscopy and multivariate and statistical analysis of the results are described. A detailed description of the experimental procedures adopted throughout this work is given in Chapter 3. The biological and analytical reproducibility of the metabolic profile of MG-63 cells by high resolution magic angle spinning (HRMAS) NMR is evaluated in Chapter 4. The metabolic impact of several factors (cellular integrity, spinning rate, temperature, time and acquisition parameters) on the 1H HRMAS NMR spectral profile and quality is analysed, enabling the definition of the best acquisition parameters for further experiments. The metabolic consequences of increasing number of passages in MG-63 cells as well as the duration of storage are also investigated. Chapter 5 describes the metabolic impact of drugs conventionally used in OS chemotherapy, through NMR metabolomics studies of lysed cells and aqueous extracts analysis. The results show that MG-63 cells treated with cisplatin (cDDP) undergo a strong up-regulation of lipid contents, alterations in phospholipid constituents (choline compounds) and biomarkers of DNA degradation, all associated with cell death by apoptosis. Cells exposed to doxorubicin (DOX) or methotrexate (MTX) showed much slighter metabolic changes, without any relevant alteration in lipid contents. However, metabolic changes associated with altered Krebs cycle, oxidative stress and nucleotides metabolism were detected and were tentatively interpreted at the light of the known mechanisms of action of these drugs. The metabolic impact of the exposure of MG-63 cells and osteoblasts to cDDP and the Pd2Spm complex is described in Chapter 6. Results show that, despite the ability of the two agents to bind DNA, the metabolic consequences that arise from exposure to them are distinct, namely in what concerns to variation in lipid contents (absent for Pd2Spm). Apoptosis detection assays showed that, differently from what was seen for MG-63 cells treated with cDDP, the decreased number of living cells upon exposure to Pd2Spm was not due to cell death by apoptosis or necrosis. Moreover, the latter agent induces more marked alterations in osteoblasts than in cancer cells, while the opposite seemed to occur upon cDDP exposure. Nevertheless, the results from MG-63 cells exposure to combination regimens with cDDP- or Pd2Spm-based cocktails, described in Chapter 7, revealed that, in combination, the two agents induce similar metabolic responses, arising from synergy mechanisms between the tested drugs. Finally, the main conclusions of this thesis are summarized in Chapter 8, and future perspectives in the light of this work are presented.