Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Processi di morfogenesi delle politiche sociali locali: le sfide della sussidiarietà e della riflessività

La tesi di Martina Visentin, dal titolo “Processi di morfogenesi delle politiche sociali locali: le sfide della sussidiarietà e della riflessività ”, intende analizzare le pratiche di sussidiarietà relative a due progetti di politica familiare nel contesto veneto. La sussidiarietà è intesa come modalità di lavoro entro queste progettualità, strettamente connessa alla riflessività dei servizi che vengono attuati. La tesi è suddivisa nel segente modo. Nela prima parte si esplora la dimensione teorica del principio di sussidiarietà. Tale contestualizzazione è utile per poter arrivare alla dimensione sociologica del concetto e comprendere la portata innovativa dell'attuazione del principio di sussidiarietà. Nella seconda parte si affronta il tema della trasformazione del welfare italiano attraverso lo sguardo dei servizi alla persona. Nello specifico, si evidenzia che, nella realizzazione di tali servizi, la valorizzazione della capacità riflessiva degli attori in gioco non deve mai essere mai essere data per scontata. Pur nella difficoltà e nella consapevolezza che questo implichi l'attuazione di una radicale revisione delle identità, delle funzioni degli attori in gioco (e la conseguente costruzione e riconoscimento di codici propri) e che tale sviluppo è possibile solo entro un quadro di nuova capacità riflessiva. Nella terza parte viene esposto lo studio di casi: I due studi di caso presentati sono: i) il progetto Politiche Familiari del Comune di Montebelluna (Tv) che ha l'obiettivo di promuovere e valorizzare la piena cittadinanza della famiglia; ii) il progetto 'Famiglie in rete', che prevede in tutto il territorio dell' U.l.s.s. n. 8 di Asolo (Tv) la promozione e la creazione di reti di solidarietà tra famiglie. Attraverso di essi si è voluto comprendere come gli attori in gioco debbano cambiare la loro identità e funzione per lavorare sussidiariamente. Infine, nelle conclusioni, vengono esposti i principali risultati della ricerca. Nel tracciare l'emergere di elementi morfostatici e morfogenetici (Archer 1995) si è tentata una valutazione della bontà dei progetti attraverso un'analisi comparativa dei nodi critici e delle potenzialità dei due casi.

Video transmission over wireless channel

This work has been realized by the author in his PhD course in Electrical, Computer Science and Telecommunication at the University of Bologna, Faculty of Engineering, Italy. All the documentation here reported is a summary of years of work, under the supervision of Prof. Oreste Andrisano, coordinator of Wireless Communication Laboratory - WiLab, in Bologna. The subject of this thesis is the transmission of video in a context of heterogeneous network, and in particular, using a wireless channel. All the instrumentation that has been used for the characterization of the telecommunication systems belongs to CNR (National Research Council), CNIT (Italian Inter- University Center), and DEIS (Dept. of Electrical, Computer Science, and Systems). From November 2009 to July 2010, the author spent his time abroad, working in collaboration with DLR - German Aerospace Center in Munich, Germany, on channel coding area, developing a general purpose decoder machine to decode a huge family of iterative codes. A patent concerning Doubly Generalized-Low Density Parity Check codes has been produced by the author as well as some important scientic papers, published on IEEE journals and conferences.

Cooperative and reconfigurable telecommunication systems based on FPGA

This work has been realized by the author in his PhD course in Electronics, Computer Science and Telecommunication at the University of Bologna, Faculty of Engineering, Italy. The subject of this thesis regards important channel estimation aspects in wideband wireless communication systems, such as echo cancellation in digital video broadcasting systems and pilot aided channel estimation through an innovative pilot design in Multi-Cell Multi-User MIMO-OFDM network. All the documentation here reported is a summary of years of work, under the supervision of Prof. Oreste Andrisano, coordinator of Wireless Communication Laboratory - WiLab, in Bologna. All the instrumentation that has been used for the characterization of the telecommunication systems belongs to CNR (National Research Council), CNIT (Italian Inter-University Center), and DEIS (Dept. of Electronics, Computer Science, and Systems). From November 2009 to May 2010, the author spent his time abroad, working in collaboration with DOCOMO - Communications Laboratories Europe GmbH (DOCOMO Euro-Labs) in Munich, Germany, in the Wireless Technologies Research Group. Some important scientific papers, submitted and/or published on IEEE journals and conferences have been produced by the author.

Semantic coordination through programmable Tuple spaces

Two of the main features of today complex software systems like pervasive computing systems and Internet-based applications are distribution and openness. Distribution revolves around three orthogonal dimensions: (i) distribution of control|systems are characterised by several independent computational entities and devices, each representing an autonomous and proactive locus of control; (ii) spatial distribution|entities and devices are physically distributed and connected in a global (such as the Internet) or local network; and (iii) temporal distribution|interacting system components come and go over time, and are not required to be available for interaction at the same time. Openness deals with the heterogeneity and dynamism of system components: complex computational systems are open to the integration of diverse components, heterogeneous in terms of architecture and technology, and are dynamic since they allow components to be updated, added, or removed while the system is running. The engineering of open and distributed computational systems mandates for the adoption of a software infrastructure whose underlying model and technology could provide the required level of uncoupling among system components. This is the main motivation behind current research trends in the area of coordination middleware to exploit tuple-based coordination models in the engineering of complex software systems, since they intrinsically provide coordinated components with communication uncoupling and further details in the references therein. An additional daunting challenge for tuple-based models comes from knowledge-intensive application scenarios, namely, scenarios where most of the activities are based on knowledge in some form|and where knowledge becomes the prominent means by which systems get coordinated. Handling knowledge in tuple-based systems induces problems in terms of syntax - e.g., two tuples containing the same data may not match due to differences in the tuple structure - and (mostly) of semantics|e.g., two tuples representing the same information may not match based on a dierent syntax adopted. Till now, the problem has been faced by exploiting tuple-based coordination within a middleware for knowledge intensive environments: e.g., experiments with tuple-based coordination within a Semantic Web middleware (surveys analogous approaches). However, they appear to be designed to tackle the design of coordination for specic application contexts like Semantic Web and Semantic Web Services, and they result in a rather involved extension of the tuple space model. The main goal of this thesis was to conceive a more general approach to semantic coordination. In particular, it was developed the model and technology of semantic tuple centres. It is adopted the tuple centre model as main coordination abstraction to manage system interactions. A tuple centre can be seen as a programmable tuple space, i.e. an extension of a Linda tuple space, where the behaviour of the tuple space can be programmed so as to react to interaction events. By encapsulating coordination laws within coordination media, tuple centres promote coordination uncoupling among coordinated components. Then, the tuple centre model was semantically enriched: a main design choice in this work was to try not to completely redesign the existing syntactic tuple space model, but rather provide a smooth extension that { although supporting semantic reasoning { keep the simplicity of tuple and tuple matching as easier as possible. By encapsulating the semantic representation of the domain of discourse within coordination media, semantic tuple centres promote semantic uncoupling among coordinated components. The main contributions of the thesis are: (i) the design of the semantic tuple centre model; (ii) the implementation and evaluation of the model based on an existent coordination infrastructure; (iii) a view of the application scenarios in which semantic tuple centres seem to be suitable as coordination media.

Nonlinear / electromagnetic co-simulation and co-design of microwave links in highly polluted and / or strongly inhomogeneous environments

The objective of the Ph.D. thesis is to put the basis of an all-embracing link analysis procedure that may form a general reference scheme for the future state-of-the-art of RF/microwave link design: it is basically meant as a circuit-level simulation of an entire radio link, with – generally multiple – transmitting and receiving antennas examined by EM analysis. In this way the influence of mutual couplings on the frequency-dependent near-field and far-field performance of each element is fully accounted for. The set of transmitters is treated as a unique nonlinear system loaded by the multiport antenna, and is analyzed by nonlinear circuit techniques. In order to establish the connection between transmitters and receivers, the far-fields incident onto the receivers are evaluated by EM analysis and are combined by extending an available Ray Tracing technique to the link study. EM theory is used to describe the receiving array as a linear active multiport network. Link performances in terms of bit error rate (BER) are eventually verified a posteriori by a fast system-level algorithm. In order to validate the proposed approach, four heterogeneous application contexts are provided. A complete MIMO link design in a realistic propagation scenario is meant to constitute the reference case study. The second one regards the design, optimization and testing of various typologies of rectennas for power generation by common RF sources. Finally, the project and implementation of two typologies of radio identification tags, at X-band and V-band respectively. In all the cases the importance of an exhaustive nonlinear/electromagnetic co-simulation and co-design is demonstrated to be essential for any accurate system performance prediction.

Client VoIP su Windows Mobile

Quando si parla di VoIP ci si riferisce ad un insieme di protocolli di comunicazione, tecnologie e metodi di trasmissione che permettono di effettuare conversazioni telefoniche attraverso reti a commutazione di pacchetto basata su IP, come Internet. Si tratta di una tecnologia che ha subito un forte crescita sia in ambito lavorativo che in ambito privato, questo fenomeno è in maggior parte dovuto al successo di applicazioni commerciali come Skype. Anche i dispositivi mobili hanno avuto un grande sviluppo e diffusione, sono passati da essere semplici telefoni cellulari a dispositivi in grado di fornire all’utente funzionalità avanzate come ad esempio navigazione internet, posta elettronica, riproduzione video, possibilità di installare applicazioni aggiuntive. Inoltre anche le reti dati sono migliorate in maniera considerevole negli ultimi anni, offrendo agli utenti una larghezza di banda sempre maggiore anche in mobilità. Tutti questi fattori hanno portato ad una crescente richiesta di applicazioni per dispositivi mobili in grado di sfruttare il VoIP. Per questi motivi si è deciso di progettare e sviluppare un applicazione VoIP per Windows Mobile, che offra tutte le funzioni necessarie ad un uso completo del VoIP e con un’interfaccia utente sia di facile utilizzo, per permettere anche agli utenti meno esperti di poter utilizzare la tecnologia VoIP

Dynamic power management: from portable devices to high performance computing

Electronic applications are nowadays converging under the umbrella of the cloud computing vision. The future ecosystem of information and communication technology is going to integrate clouds of portable clients and embedded devices exchanging information, through the internet layer, with processing clusters of servers, data-centers and high performance computing systems. Even thus the whole society is waiting to embrace this revolution, there is a backside of the story. Portable devices require battery to work far from the power plugs and their storage capacity does not scale as the increasing power requirement does. At the other end processing clusters, such as data-centers and server farms, are build upon the integration of thousands multiprocessors. For each of them during the last decade the technology scaling has produced a dramatic increase in power density with significant spatial and temporal variability. This leads to power and temperature hot-spots, which may cause non-uniform ageing and accelerated chip failure. Nonetheless all the heat removed from the silicon translates in high cooling costs. Moreover trend in ICT carbon footprint shows that run-time power consumption of the all spectrum of devices accounts for a significant slice of entire world carbon emissions. This thesis work embrace the full ICT ecosystem and dynamic power consumption concerns by describing a set of new and promising system levels resource management techniques to reduce the power consumption and related issues for two corner cases: Mobile Devices and High Performance Computing.

Parallel modeling of the electric field distribution in the brain

The term "Brain Imaging" identi�es a set of techniques to analyze the structure and/or functional behavior of the brain in normal and/or pathological situations. These techniques are largely used in the study of brain activity. In addition to clinical usage, analysis of brain activity is gaining popularity in others recent �fields, i.e. Brain Computer Interfaces (BCI) and the study of cognitive processes. In this context, usage of classical solutions (e.g. f MRI, PET-CT) could be unfeasible, due to their low temporal resolution, high cost and limited portability. For these reasons alternative low cost techniques are object of research, typically based on simple recording hardware and on intensive data elaboration process. Typical examples are ElectroEncephaloGraphy (EEG) and Electrical Impedance Tomography (EIT), where electric potential at the patient's scalp is recorded by high impedance electrodes. In EEG potentials are directly generated from neuronal activity, while in EIT by the injection of small currents at the scalp. To retrieve meaningful insights on brain activity from measurements, EIT and EEG relies on detailed knowledge of the underlying electrical properties of the body. This is obtained from numerical models of the electric �field distribution therein. The inhomogeneous and anisotropic electric properties of human tissues make accurate modeling and simulation very challenging, leading to a tradeo�ff between physical accuracy and technical feasibility, which currently severely limits the capabilities of these techniques. Moreover elaboration of data recorded requires usage of regularization techniques computationally intensive, which influences the application with heavy temporal constraints (such as BCI). This work focuses on the parallel implementation of a work-flow for EEG and EIT data processing. The resulting software is accelerated using multi-core GPUs, in order to provide solution in reasonable times and address requirements of real-time BCI systems, without over-simplifying the complexity and accuracy of the head models.

Luoghi di identità e spazi del sacro nella città europea contemporanea

A fronte della frammentarietà e della confusione semantica della città contemporanea, la ricerca sui ‘Luoghi di identità e spazi del sacro nella città europea contemporanea’ ha inteso affrontare il tema della morfologia urbana in termini di significato. La focalizzazione sui temi dell’identità e del sacro nella città odierna è stata intesa quale modalità per tentare di andare alla radice dell’irrisolto problema di mancanza di senso che affligge la compagine urbana contemporanea e per cercare di individuare le cause e, quindi, le possibili azioni necessarie a riportare il costruito nell’ambito della relazione significante. Il campo di indagine è quello delle aree periferiche europee, ma la ricerca si muove da considerazioni di ordine generale relativamente alle reti di relazioni che l’essere umano instaura con il mondo circostante. Il lavoro sviluppa un primo inquadramento del tema di carattere generale, con un riferimento sistematico alla letteratura scientifica, individuando attraverso un sintetico excursus storico, i principi fondamentali della costruzione dell’immagine spaziale e del suo evolversi nel tempo. Su questa base i tre concetti di ‘centralità’, ‘identità’ e ‘sacro’, sono intesi come i cardini del discorso circa gli ambiti di significato e, sulla base di studi di alcune esperienze europee ritenute particolarmente esemplificative, la trattazione di questi tre temi arriva a proporre alcune considerazioni in merito alle caratteristiche che il contesto urbano deve avere per manifestarsi come luogo di costruzione di una identità personale e comunitaria. Nella consapevolezza che l’ampiezza dei temi considerati non ne consente una trattazione esaustiva, le considerazioni fatte sono da intendersi quali spunti di riflessione a riguardo dei metodi e delle modalità di relazione che sono ritenute necessarie per la costruzione di spazi di riferimento orientativo, identitario e socializzante.

Electrothermal characterization and nonlinear modelling of GaN transistors for telecommunication circuit design

This thesis starts showing the main characteristics and application fields of the AlGaN/GaN HEMT technology, focusing on reliability aspects essentially due to the presence of low frequency dispersive phenomena which limit in several ways the microwave performance of this kind of devices. Based on an equivalent voltage approach, a new low frequency device model is presented where the dynamic nonlinearity of the trapping effect is taken into account for the first time allowing considerable improvements in the prediction of very important quantities for the design of power amplifier such as power added efficiency, dissipated power and internal device temperature. An innovative and low-cost measurement setup for the characterization of the device under low-frequency large-amplitude sinusoidal excitation is also presented. This setup allows the identification of the new low frequency model through suitable procedures explained in detail. In this thesis a new non-invasive empirical method for compact electrothermal modeling and thermal resistance extraction is also described. The new contribution of the proposed approach concerns the non linear dependence of the channel temperature on the dissipated power. This is very important for GaN devices since they are capable of operating at relatively high temperatures with high power densities and the dependence of the thermal resistance on the temperature is quite relevant. Finally a novel method for the device thermal simulation is investigated: based on the analytical solution of the tree-dimensional heat equation, a Visual Basic program has been developed to estimate, in real time, the temperature distribution on the hottest surface of planar multilayer structures. The developed solver is particularly useful for peak temperature estimation at the design stage when critical decisions about circuit design and packaging have to be made. It facilitates the layout optimization and reliability improvement, allowing the correct choice of the device geometry and configuration to achieve the best possible thermal performance.