Characterization of novel heme-containing sensor proteins from Geobacter sulfurreducens

The focus of this Thesis was the study of the sensor domains of two heme-containing methyl-accepting chemotaxis proteins (MCP) from Geobacter sulfurreducens: GSU0582 and GSU0935. These domains contain one c-type heme, form swapped dimers with a PAS-like fold and are the first examples of a new class of heme sensors. NMR spectroscopy was used to assign the heme and polypeptide signals in both sensors, as a first step to probe conformational changes in the vicinity of the hemes. However, the presence of two conformations in solution impaired the confident assignment of the polypeptide signals. To understand how conformational changes and swapped dimerization mechanism can effectively modulate the function of the two sensor domains and their signal transduction process, the sensor domains folding and stability were studied by circular dichroism and UV-visible spectroscopy. The results showed differences in the thermodynamic stability of the sensors, with GSU0582 displaying higher structural stability. These studies also demonstrated that the heme moiety undergoes conformational changes matching those occurring at the global protein structure and that the content of intrinsically disordered segments within these proteins (25% for GSU0935; 13% for GSU0582) correlates with the stability differences observed. The thermodynamic and kinetic properties of the sensor domains were determined at different pH and ionic strength by visible spectroscopy and stopped-flow techniques. Despite the remarkably similar spectroscopic and structural features of the two sensor domains, the results showed that their properties are quite distinct. Sensor domain GSU0935 displayed more negative reduction potentials and smaller reduction rate constants, which were more affected by pH and ionic strength. The available structures were used to rationalize these differences. Overall, the results described in this Thesis indicate that the two G. sulfurreducens MCP sensor domains are designed to function in different working potential ranges, allowing this bacterium to trigger an adequate cellular response in distinct anoxic subsurface environments.

A piezoelectric based energy harvester interface for a CMOS wireless sensor IC

In this thesis a piezoelectric energy harvesting system, responsible for regulating the power output of a piezoelectric transducer subjected to ambient vibration, is designed to power an RF receiver with a 6 mW power consump-tion. The electrical characterisation of the chosen piezoelectric transducer is the starting point of the design, which subsequently presents a full-bridge cross-coupled rectifier that rectifies the AC output of the transducer and a low-dropout regulator responsible for delivering a constant voltage system output of 0.6 V, with low voltage ripple, which represents the receiver’s required sup-ply voltage. The circuit is designed using CMOS 130 nm UMC technology, and the system presents an inductorless architecture, with reduced area and cost. The electrical simulations run for the complete circuit lead to the conclusion that the proposed piezoelectric energy harvesting system is a plausible solution to power the RF receiver, provided that the chosen transducer is subjected to moderate levels of vibration.

A systematic methodology to analyse the performance and design configurations of business interoperability in cooperative industrial networks

This thesis proposes a methodology for modelling business interoperability in a context of cooperative industrial networks. The purpose is to develop a methodology that enables the design of cooperative industrial network platforms that are able to deliver business interoperability and the analysis of its impact on the performance of these platforms. To achieve the proposed objective, two modelling tools have been employed: the Axiomatic Design Theory for the design of interoperable platforms; and Agent-Based Simulation for the analysis of the impact of business interoperability. The sequence of the application of the two modelling tools depends on the scenario under analysis, i.e. whether the cooperative industrial network platform exists or not. If the cooperative industrial network platform does not exist, the methodology suggests first the application of the Axiomatic Design Theory to design different configurations of interoperable cooperative industrial network platforms, and then the use of Agent-Based Simulation to analyse or predict the business interoperability and operational performance of the designed configurations. Otherwise, one should start by analysing the performance of the existing platform and based on the achieved results, decide whether it is necessary to redesign it or not. If the redesign is needed, simulation is once again used to predict the performance of the redesigned platform. To explain how those two modelling tools can be applied in practice, a theoretical modelling framework, a theoretical Axiomatic Design model and a theoretical Agent-Based Simulation model are proposed. To demonstrate the applicability of the proposed methodology and/or to validate the proposed theoretical models, a case study regarding a Portuguese Reverse Logistics cooperative network (Valorpneu network) and a case study regarding a Portuguese construction project (Dam Baixo Sabor network) are presented. The findings of the application of the proposed methodology to these two case studies suggest that indeed the Axiomatic Design Theory can effectively contribute in the design of interoperable cooperative industrial network platforms and that Agent-Based Simulation provides an effective set of tools for analysing the impact of business interoperability on the performance of those platforms. However, these conclusions cannot be generalised as only two case studies have been carried out. In terms of relevance to theory, this is the first time that the network effect is addressed in the analysis of the impact of business interoperability on the performance of networked companies and also the first time that a holistic approach is proposed to design interoperable cooperative industrial network platforms. Regarding the practical implications, the proposed methodology is intended to provide industrial managers a management tool that can guide them easily, and in practical and systematic way, in the design of configurations of interoperable cooperative industrial network platforms and/or in the analysis of the impact of business interoperability on the performance of their companies and the networks where their companies operate.

An automated framework for the management of P2P traffic in ISP infrastructures

Peer-to-Peer (P2P) is nowadays a widely used paradigm underpinning the deployment of several Internet services and applications. However, the management of P2P traffic aggregates is not an easy task for Internet Service Providers (ISPs). In this perspective, and considering an expectable proliferation in the use of such ap- plications, future networks require the development of smart mechanisms fostering an easier coexistence between P2P applications and ISP infrastructures. This paper aims to contribute for such research efforts presenting a framework incorporating useful mechanisms to be activated by network administrators, being also able to operate as an automated management tool dealing with P2P traffic aggregates.

Nonlinear behavior of gelatin networks reveals a hierarchical structure

We investigate the strain hardening behavior of various gelatin networks-namely physical gelatin gel, chemically cross-linked gelatin gel, and a hybrid gel made of a combination of the former two-under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillations shear protocols. Further, the internal structures of physical gelatin gels and chemically cross-linked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically cross-linked network whereas, in the physical gelatin gels, a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as the correlation length (ξ), the cross-sectional polymer chain radius (Rc) and the fractal dimension (df) of the gel networks. The fractal dimension df obtained from the SANS data of the physical and chemically cross-linked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized nonlinear elastic theory that has been used to fit the stress-strain curves. The chemical cross-linking that generates coils and aggregates hinders the free stretching of the triple helix bundles in the physical gels.

Label Space Reduction in All-Optical Label Switchiing Networks

Report for the scientific sojourn at the Department of Information Technology (INTEC) at the Ghent University, Belgium, from january to june 2007. All-Optical Label Swapping (AOLS) forms a key technology towards the implementation of All-Optical Packet Switching nodes (AOPS) for the future optical Internet. The capital expenditures of the deployment of AOLS increases with the size of the label spaces (i.e. the number of used labels), since a special optical device is needed for each recognized label on every node. Label space sizes are affected by the wayin which demands are routed. For instance, while shortest-path routing leads to the usage of fewer labels but high link utilization, minimum interference routing leads to the opposite. This project studies and proposes All-Optical Label Stacking (AOLStack), which is an extension of the AOLS architecture. AOLStack aims at reducing label spaces while easing the compromise with link utilization. In this project, an Integer Lineal Program is proposed with the objective of analyzing the softening of the aforementioned trade-off due to AOLStack. Furthermore, a heuristic aiming at finding good solutions in polynomial-time is proposed as well. Simulation results show that AOLStack either a) reduces the label spaces with a low increase in the link utilization or, similarly, b) uses better the residual bandwidth to decrease the number of labels even more.

Creation of a carrier-grade telco based on a voice over IP backbone

En aquesta memòria l'autor, fent servir un enfoc modern, redissenya i implementa la plataforma que una empresa de telecomunicacions del segle 21 necessita per poder donar serveis de telefonia i comunicacions als seus usuaris i clients. Al llarg d'aquesta exposició es condueix al lector des d'una fase inicial de disseny fins a la implementació i posada en producció del sistema final desenvolupat, centrant-nos en solucionar les necessitats actuals que això implica. Aquesta memòria cubreix el software, hardware i els processos de negoci associats al repte de fer realitat aquest objectiu, i presenta al lector les múltiples tecnologies emprades per aconseguir-ho, fent emfàsi en la convergència actual de xarxes cap al concepte de xarxes IP i basant-se en aquesta tendència i utilitzant aquesta tecnologia de veu sobre IP per donar forma a la plataforma que finalment, de forma pràctica, es posa en producció.

Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Calibration of a Structured Light-Based Stereo Catadioptric Sensor

Catadioptric sensors are combinations of mirrors and lenses made in order to obtain a wide field of view. In this paper we propose a new sensor that has omnidirectional viewing ability and it also provides depth information about the nearby surrounding. The sensor is based on a conventional camera coupled with a laser emitter and two hyperbolic mirrors. Mathematical formulation and precise specifications of the intrinsic and extrinsic parameters of the sensor are discussed. Our approach overcomes limitations of the existing omni-directional sensors and eventually leads to reduced costs of production

MAPI: towards the integrated exploitation of bioinformatics Web Services.

BACKGROUND. Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. RESULTS. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. CONCLUSIONS. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

Do labour mobility and networks foster geographical knowledge diffusion? The case of European regions

The goal of this paper is twofold: first, we aim to assess the role played by inventors’ cross-regional mobility and networks of collaboration in fostering knowledge diffusion across regions and subsequent innovation. Second, we intend to evaluate the feasibility of using mobility and networks information to build cross-regional interaction matrices to be used within the spatial econometrics toolbox. To do so, we depart from a knowledge production function where regional innovation intensity is a function not only of the own regional innovation inputs but also external accessible R&D gained through interregional interactions. Differently from much of the previous literature, cross-section gravity models of mobility and networks are estimated to use the fitted values to build our ‘spatial’ weights matrices, which characterize the intensity of knowledge interactions across a panel of 269 regions covering most European countries over 6 years.

Uncorrelatedness in growing networks with preferential survival of nodes

The emergence of uncorrelated growing networks is proved when nodes are removed either uniformly or under the preferential survival rule recently observed in the World Wide Web evolution. To this aim, the rate equation for the joint probability of degrees is derived, and stationary symmetrical solutions are obtained, by passing to the continuum limit. When a uniformly random removal of extant nodes and linear preferential attachment of new nodes are at work, we prove that the only stationary solution corresponds to uncorrelated networks for any removal rate r ∈ (0,1). In the more general case of preferential survival of nodes, uncorrelated solutions are also obtained. These results generalize the uncorrelatedness displayed by the (undirected) Barab´asi-Albert network model to models with uniformly random and selective (against low degrees) removal of nodes

Evolutionary games on complex networks : the emergence and maintenance of cooperation

Abstract The object of game theory lies in the analysis of situations where different social actors have conflicting requirements and where their individual decisions will all influence the global outcome. In this framework, several games have been invented to capture the essence of various dilemmas encountered in many common important socio-economic situations. Even though these games often succeed in helping us understand human or animal behavior in interactive settings, some experiments have shown that people tend to cooperate with each other in situations for which classical game theory strongly recommends them to do the exact opposite. Several mechanisms have been invoked to try to explain the emergence of this unexpected cooperative attitude. Among them, repeated interaction, reputation, and belonging to a recognizable group have often been mentioned. However, the work of Nowak and May (1992) showed that the simple fact of arranging the players according to a spatial structure and only allowing them to interact with their immediate neighbors is sufficient to sustain a certain amount of cooperation even when the game is played anonymously and without repetition. Nowak and May's study and much of the following work was based on regular structures such as two-dimensional grids. Axelrod et al. (2002) showed that by randomizing the choice of neighbors, i.e. by actually giving up a strictly local geographical structure, cooperation can still emerge, provided that the interaction patterns remain stable in time. This is a first step towards a social network structure. However, following pioneering work by sociologists in the sixties such as that of Milgram (1967), in the last few years it has become apparent that many social and biological interaction networks, and even some technological networks, have particular, and partly unexpected, properties that set them apart from regular or random graphs. Among other things, they usually display broad degree distributions, and show small-world topological structure. Roughly speaking, a small-world graph is a network where any individual is relatively close, in terms of social ties, to any other individual, a property also found in random graphs but not in regular lattices. However, in contrast with random graphs, small-world networks also have a certain amount of local structure, as measured, for instance, by a quantity called the clustering coefficient. In the same vein, many real conflicting situations in economy and sociology are not well described neither by a fixed geographical position of the individuals in a regular lattice, nor by a random graph. Furthermore, it is a known fact that network structure can highly influence dynamical phenomena such as the way diseases spread across a population and ideas or information get transmitted. Therefore, in the last decade, research attention has naturally shifted from random and regular graphs towards better models of social interaction structures. The primary goal of this work is to discover whether or not the underlying graph structure of real social networks could give explanations as to why one finds higher levels of cooperation in populations of human beings or animals than what is prescribed by classical game theory. To meet this objective, I start by thoroughly studying a real scientific coauthorship network and showing how it differs from biological or technological networks using divers statistical measurements. Furthermore, I extract and describe its community structure taking into account the intensity of a collaboration. Finally, I investigate the temporal evolution of the network, from its inception to its state at the time of the study in 2006, suggesting also an effective view of it as opposed to a historical one. Thereafter, I combine evolutionary game theory with several network models along with the studied coauthorship network in order to highlight which specific network properties foster cooperation and shed some light on the various mechanisms responsible for the maintenance of this same cooperation. I point out the fact that, to resist defection, cooperators take advantage, whenever possible, of the degree-heterogeneity of social networks and their underlying community structure. Finally, I show that cooperation level and stability depend not only on the game played, but also on the evolutionary dynamic rules used and the individual payoff calculations. Synopsis Le but de la théorie des jeux réside dans l'analyse de situations dans lesquelles différents acteurs sociaux, avec des objectifs souvent conflictuels, doivent individuellement prendre des décisions qui influenceront toutes le résultat global. Dans ce cadre, plusieurs jeux ont été inventés afin de saisir l'essence de divers dilemmes rencontrés dans d'importantes situations socio-économiques. Bien que ces jeux nous permettent souvent de comprendre le comportement d'êtres humains ou d'animaux en interactions, des expériences ont montré que les individus ont parfois tendance à coopérer dans des situations pour lesquelles la théorie classique des jeux prescrit de faire le contraire. Plusieurs mécanismes ont été invoqués pour tenter d'expliquer l'émergence de ce comportement coopératif inattendu. Parmi ceux-ci, la répétition des interactions, la réputation ou encore l'appartenance à des groupes reconnaissables ont souvent été mentionnés. Toutefois, les travaux de Nowak et May (1992) ont montré que le simple fait de disposer les joueurs selon une structure spatiale en leur permettant d'interagir uniquement avec leurs voisins directs est suffisant pour maintenir un certain niveau de coopération même si le jeu est joué de manière anonyme et sans répétitions. L'étude de Nowak et May, ainsi qu'un nombre substantiel de travaux qui ont suivi, étaient basés sur des structures régulières telles que des grilles à deux dimensions. Axelrod et al. (2002) ont montré qu'en randomisant le choix des voisins, i.e. en abandonnant une localisation géographique stricte, la coopération peut malgré tout émerger, pour autant que les schémas d'interactions restent stables au cours du temps. Ceci est un premier pas en direction d'une structure de réseau social. Toutefois, suite aux travaux précurseurs de sociologues des années soixante, tels que ceux de Milgram (1967), il est devenu clair ces dernières années qu'une grande partie des réseaux d'interactions sociaux et biologiques, et même quelques réseaux technologiques, possèdent des propriétés particulières, et partiellement inattendues, qui les distinguent de graphes réguliers ou aléatoires. Entre autres, ils affichent en général une distribution du degré relativement large ainsi qu'une structure de "petit-monde". Grossièrement parlant, un graphe "petit-monde" est un réseau où tout individu se trouve relativement près de tout autre individu en termes de distance sociale, une propriété également présente dans les graphes aléatoires mais absente des grilles régulières. Par contre, les réseaux "petit-monde" ont, contrairement aux graphes aléatoires, une certaine structure de localité, mesurée par exemple par une quantité appelée le "coefficient de clustering". Dans le même esprit, plusieurs situations réelles de conflit en économie et sociologie ne sont pas bien décrites ni par des positions géographiquement fixes des individus en grilles régulières, ni par des graphes aléatoires. De plus, il est bien connu que la structure même d'un réseau peut passablement influencer des phénomènes dynamiques tels que la manière qu'a une maladie de se répandre à travers une population, ou encore la façon dont des idées ou une information s'y propagent. Ainsi, durant cette dernière décennie, l'attention de la recherche s'est tout naturellement déplacée des graphes aléatoires et réguliers vers de meilleurs modèles de structure d'interactions sociales. L'objectif principal de ce travail est de découvrir si la structure sous-jacente de graphe de vrais réseaux sociaux peut fournir des explications quant aux raisons pour lesquelles on trouve, chez certains groupes d'êtres humains ou d'animaux, des niveaux de coopération supérieurs à ce qui est prescrit par la théorie classique des jeux. Dans l'optique d'atteindre ce but, je commence par étudier un véritable réseau de collaborations scientifiques et, en utilisant diverses mesures statistiques, je mets en évidence la manière dont il diffère de réseaux biologiques ou technologiques. De plus, j'extrais et je décris sa structure de communautés en tenant compte de l'intensité d'une collaboration. Finalement, j'examine l'évolution temporelle du réseau depuis son origine jusqu'à son état en 2006, date à laquelle l'étude a été effectuée, en suggérant également une vue effective du réseau par opposition à une vue historique. Par la suite, je combine la théorie évolutionnaire des jeux avec des réseaux comprenant plusieurs modèles et le réseau de collaboration susmentionné, afin de déterminer les propriétés structurelles utiles à la promotion de la coopération et les mécanismes responsables du maintien de celle-ci. Je mets en évidence le fait que, pour ne pas succomber à la défection, les coopérateurs exploitent dans la mesure du possible l'hétérogénéité des réseaux sociaux en termes de degré ainsi que la structure de communautés sous-jacente de ces mêmes réseaux. Finalement, je montre que le niveau de coopération et sa stabilité dépendent non seulement du jeu joué, mais aussi des règles de la dynamique évolutionnaire utilisées et du calcul du bénéfice d'un individu.