Monte Carlo studies of phase transitions and adsorption : application to n-6 Lennard-Jones, C60 and zeolite systems

The solid-fluid transition properties of the n - 6 Lennard-Jones system are studied by means of extensive free energy calculations. Different values of the parameter n which regulates the steepness of the short-range repulsive interaction are investigated. Furthermore, the free energies of the n < 12 systems are calculated using the n = 12 system as a reference. The method relies on a generalization of the multiple histogram method that combines independent canonical ensemble simulations performed with different Hamiltonians and computes the free energy difference between them. The phase behavior of the fullerene C60 solid is studied by performing NPT simulations using atomistic models which treat each carbon in the molecule as a separate interaction site with additional bond charges. In particular, the transition from an orientationally frozen phase at low temperatures to one where the molecules are freely rotating at higher temperatures is studied as a function of applied pressure. The adsorption of molecular hydrogen in the zeolite NaA is investigated by means of grand-canonical Monte Carlo, in a wide range of temperatures and imposed gas pressures, and results are compared with available experimental data. A potential model is used that comprises three main interactions: van der Waals, Coulomb and induced polarization by the permanent electric field in the zeolite.

Decentralizing IP mobility management in future networks

The massive adoption of sophisticated mobile devices and applications led to the increase of mobile data in the last decade, which it is expected to continue. This increase of mobile data negatively impacts the network planning and dimension, since core networks are heavy centralized. Mobile operators are investigating atten network architectures that distribute the responsibility of providing connectivity and mobility, in order to improve the network scalability and performance. Moreover, service providers are moving the content servers closer to the user, in order to ensure high availability and performance of content delivery. Besides the e orts to overcome the explosion of mobile data, current mobility management models are heavy centralized to ensure reachability and session continuity to the users connected to the network. Nowadays, deployed architectures have a small number of centralized mobility anchors managing the mobile data and the mobility context of millions of users, which introduces issues related to performance and scalability that require costly network mechanisms. The mobility management needs to be rethought out-of-the box to cope with atten network architectures and distributed content servers closer to the user, which is the purpose of the work developed in this Thesis. The Thesis starts with a characterization of mobility management into well-de ned functional blocks, their interaction and potential grouping. The decentralized mobility management is studied through analytical models and simulations, in which di erent mobility approaches distinctly distribute the mobility management functionalities through the network. The outcome of this study showed that decentralized mobility management brings advantages. Hence, it was proposed a novel distributed and dynamic mobility management approach, which is exhaustively evaluated through analytical models, simulations and testbed experiments. The proposed approach is also integrated with seamless horizontal handover mechanisms, as well as evaluated in vehicular environments. The mobility mechanisms are also speci ed for multihomed scenarios, in order to provide data o oading with IP mobility from cellular to other access networks. In the pursuing of the optimized mobile routing path, a novel network-based strategy for localized mobility is addressed, in which a replication binding system is deployed in the mobility anchors distributed through the access routers and gateways. Finally, we go further in the mobility anchoring subject, presenting a context-aware adaptive IP mobility anchoring model that dynamically assigns the mobility anchors that provide the optimized routing path to a session, based on the user and network context. The integration of dynamic and distributed concepts in the mobility management, such as context-aware adaptive mobility anchoring and dynamic mobility support, allow the optimization of network resources and the improvement of user experience. The overall outcome demonstrates that decentralized mobility management is a promising direction, hence, its ideas should be taken into account by mobile operators in the deployment of future networks.

Codon ambiguities as a mechanism to alter the genetic code in Saccharomyces cerevisiae

Although the genetic code is generally viewed as immutable, alterations to its standard form occur in the three domains of life. A remarkable alteration to the standard genetic code occurs in many fungi of the Saccharomycotina CTG clade where the Leucine CUG codon has been reassigned to Serine by a novel transfer RNA (Ser-tRNACAG). The host laboratory made a major breakthrough by reversing this atypical genetic code alteration in the human pathogen Candida albicans using a combination of tRNA engineering, gene recombination and forced evolution. These results raised the hypothesis that synthetic codon ambiguities combined with experimental evolution may release codons from their frozen state. In this thesis we tested this hypothesis using S. cerevisiae as a model system. We generated ambiguity at specific codons in a two-step approach, involving deletion of tRNA genes followed by expression of non-cognate tRNAs that are able to compensate the deleted tRNA. Driven by the notion that rare codons are more susceptible to reassignment than those that are frequently used, we used two deletion strains where there is no cognate tRNA to decode the rare CUC-Leu codon and AGG-Arg codon. We exploited the vulnerability of the latter by engineering mutant tRNAs that misincorporate Ser at these sites. These recombinant strains were evolved over time using experimental evolution. Although there was a strong negative impact on the growth rate of strains expressing mutant tRNAs at high level, such expression at low level had little effect on cell fitness. We found that not only codon ambiguity, but also destabilization of the endogenous tRNA pool has a strong negative impact in growth rate. After evolution, strains expressing the mutant tRNA at high level recovered significantly in several growth parameters, showing that these strains adapt and exhibit higher tolerance to codon ambiguity. A fluorescent reporter system allowing the monitoring of Ser misincorporation showed that serine was indeed incorporated and possibly codon reassignment was achieved. Beside the overall negative consequences of codon ambiguity, we demonstrated that codons that tolerate the loss of their cognate tRNA can also tolerate high Ser misincorporation. This raises the hypothesis that these codons can be reassigned to standard and eventually to new amino acids for the production of proteins with novel properties, contributing to the field of synthetic biology and biotechnology.

Controle activo de estruturas adaptativas com sensores e actuadores piezoeléctricos

Nos últimos anos o estudo de estruturas inteligentes tem atraído vários investigadores devido às suas potenciais vantagens numa larga gama de aplicações, tais como controle de forma, supressão de vibrações, atenuação de ruído e detecção de dano. O uso de materiais “inteligentes” tal como os materiais piezoeléctricos na forma de lâminas ou “patches”, embebidas ou coladas na superfície de estruturas construídas de materiais compósitos, permite assim obter estruturas que por um lado são adaptativas e por outro revelam excelentes propriedades mecânicas, aumentando assim bastante o desempenho e a fiabilidade de sistemas estruturais. Os materiais piezoeléctricos têm a propriedade de gerar uma carga eléctrica sob a acção duma carga mecânica e o reverso, isto é, aplicando um campo eléctrico nos elementos piezoeléctricos da estrutura, esta deforma-se. Neste trabalho, é apresentado um modelo de elementos finitos, baseado na teoria clássica de placas, desenvolvido para a análise do controle activo em estática e dinâmica lineares de estruturas integrando sensores e actuadores piezoeléctrico na forma de lâminas, os quais introduzem um grau de liberdade referente ao potencial eléctrico, por cada camada piezoeléctrica do elemento finito. É utilizado método de Newmark para a solução iterativa das equações de equilíbrio. Apresentam-se os resultados obtidos em três exemplos ilustrativos.

Population model of the recent subtidal invasion of Sargassum muticum in southern Portugal

Dissertação de Mestrado, Biologia Marinha, Especialização em Ecologia e Conservação, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2007

Development of the sustainability of coastal activities through ICZM process

Dissertação de Mestrado, Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2008

Análise e caracterização da expressão e papel funcional dos potenciais genes da família 2 GPCRs no protostómio Caenorhabditis elegans

Dissertação de Mestrado, Biotecnologia, Faculdade de Engenharia de Recursos Naturais, Universidade do Algarve, 2009

Trance psicadélico no Algarve: um estudo sobre as práticas culturais de um movimento marginal

Dissertação de mest., Comunicação, Cultura e Artes (Estudos Culturais), Faculdade de Ciências Humanas e Sociais, Univ. do Algarve, 2011

Cartografia solar: estimativa do potencial solar no município de Albufeira

A dependência energética dos combustíveis fósseis é, reconhecidamente, uma das principiais inquietações das economias mundiais. Questões como a concentração de gases de efeito de estufa, poluição atmosférica e o facto de estes combustíveis serem esgotáveis estão cada vez mais no centro das atenções globais, ao que se associa um aumento significativo da população mundial e por conseguinte, dos consumos. Contudo, começa a ser notório um empenho na procura de soluções viáveis que possam contornar esta dependência, nomeadamente no desenvolvimento de tecnologia que permita o aproveitamento de fontes de energias renováveis. Neste sentido, Portugal encontra-se numa posição privilegiada sendo, dos países da europa, o que apresenta índices mais elevados de radiação solar por unidade de superfície, em média cerca de 1500kWh/m2/ano. O sucesso do aproveitamento de fontes de energia renováveis vai depender, em muito, da análise e compreensão do potencial determinado pelas realidades locais, pelos dados meteorológicos, pelas tecnologias existentes e por fatores económicos. (WITTMAN et al., 1997). O processo para estimativa o potencial não é simples e implica uma interação disciplinar; no entanto tendem a aparecer modelos que, a montante do processo, simplificam a análise espacial da energia solar. Neste campo, o contributo dos Sistemas de Informação Geográfica tem sido fundamental, oferecendo um conjunto de ferramentas de processamento de dados bastantes úteis para a modelação solar. A presente dissertação combina a utilização dos SIG com a análise do potencial solar, apresentando como objetivos principais: i) a estimativa do potencial solar no Município de Albufeira e ii) a criação de uma aplicação que disponibilize os resultados através da web, facilitando a consulta e análise espacial dos mesmos.

Molecular structure and functional analysis of runx3 in zebrafish

Tese de doutoramento, Ciências Biomédicas, Universidade do Algarve, Departamento de Ciências Biomédicas e Medicina, 2014

Um modelo para a melhoria da qualidade dos recursos humanos das autarquias locais

Dissertação de Mestrado, Gestão Empresarial, Faculdade de Economia, Universidade do Algarve, 2004

Identification and molecular characterization of bone-related micrornas: functional implications

Tese de doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2014

Modeling the suitable habitat of a structural red gorgonian species in the Mediterranean/east Atlantic regions predicts a wider distribution than previously known

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Univerdade do Algarve, 2015

Limites de distribuição vertical da espécie Patella depressa: padrões e processos

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015