Estudo da dinâmica de populações utilizando a técnica de polinômios de colocação

Pós-graduação em Engenharia Elétrica - FEB

Estimulador elétrico funcional com utilização de ponte H e fonte de corrente no estágio de potência

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estimulador elétrico funcional com utilização de ponte H e fonte de corrente no estágio de potência

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Tokamak TCABR: Acquisition system, data analysis, and remote participation using MDSplus

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way to control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and this private system makes it difficult to follow the work remotely. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The choice of MDSplus (Model Driven System plus) is proved by the fact that it is widely utilized, and the scientists from different institutions may use the same system in different experiments in different tokamaks without the need to know how each system treats its acquisition system and data analysis. Another important point is the fact that the MDSplus has a library system that allows communication between different types of language (JAVA, Fortran, C, C++, Python) and programs such as MATLAB, IDL, OCTAVE. In the case of tokamak TCABR interfaces (object of this paper) between the system already in use and MDSplus were developed, instead of using the MDSplus at all stages, from the control, and data acquisition to the data analysis. This was done in the way to preserve a complex system already in operation and otherwise it would take a long time to migrate. This implementation also allows add new components using the MDSplus fully at all stages. (c) 2012 Elsevier B.V. All rights reserved.

Constitutive models for biodegradable thermoplastic ropes for ligament repair

The concept behind a biodegradable ligament device is to temporarily replace the biomechanical functions of the ruptured ligament, while it progressively regenerates its capacities. However, there is a lack of methods to predict the mechanical behaviour evolution of the biodegradable devices during degradation, which is an important aspect of the project. In this work, a hyper elastic constitutive model will be used to predict the mechanical behaviour of a biodegradable rope made of aliphatic polyesters. A numerical approach using ABAQUS is presented, where the material parameters of the model proposal are automatically updated in correspondence to the degradation time, by means of a script in PYTHON. In this method we also use a User Material subroutine (UMAT) to apply a failure criterion base on the strength that decreases according to a first order differential equation. The parameterization of the material model proposal for different degradation times were achieved by fitting the theoretical curves with the experimental data of tensile tests on fibres. To model all the rope behaviour we had considered one step of homogenisation considering the fibres architectures in an elementary volume. (C) 2012 Elsevier Ltd. All rights reserved.

Simulador virtual de técnicas de endoscopia rígida para formación sanitaria

[ES] En este proyecto se trata el proceso de análisis y desarrollo llevado a cabo con el objetivo de construir un prototipo funcional de simulador virtual de endoscopia rígida monocanal orientado a la histeroscopia. Para el desarrollo del prototipo se toma como base el entorno ESQUI, un entorno de simulación virtual médica de código libre. Este entorno provee una librería, basada a su vez en la conocida librería gráfica VTK(Visual ToolKit), cuyo propósito es poner a disposición del programador toda la algoritmia necesaria para construir una simulación médica virtual. En este proyecto, esta librería se depuró y amplió para mejorar el soporte a las técnicas de endoscopia rígida que se persiguen simular. Por otro lado se emplea el Simball 4D, un dispositivo de interfaz humana de la empresa G-coder Systems, para capturar la interacción del usuario emulando la morfología y dinámica de un endoscopio rígido. Todos estos elementos se conectan con una interfaz gráfica sencilla, intuitiva y práctica soportada por wxWidgets y utilizando Python como lenguaje de scripting. Finalmente, se analiza el prototipo resultante y se proponen una serie de líneas futuras de cara a la aplicación didáctica del mismo, tanto en relación a los objetivos conceptuales del prototipo como a los aspectos específicos del entorno ESQUI.

Reidentificación de personas y objetos mediante aprendizaje semisupervisado

[ES]La reidentificación consiste en volver a identificar a un individuo/objeto que ya se ha detectado previamente desde distintas cámaras. En este proyecto se exploran diferentes técnicas para la reidentificación de personas. Se implementan y prueban técnicas que no requieren de aprendizaje previo para realizar una ordenación inicial, al ser este tipo de métodos los que mayor aplicación tienen en un escenario real. Así mismo se usan técnicas de reordenación sobre esta ordenación inicial utilizando la información de un operador humano, aplicando entre otros métodos aprendizaje semisupervisado. Para realizar todo el proceso y facilitar la combinación y automatización de las diversas técnicas se crea un framework denominado PyReID basado en Python y OpenCV, de software libre y disponible públicamente en Github.

Enabling computationally intensive bioinformatics applications on the Grid platform

Bioinformatics is a recent and emerging discipline which aims at studying biological problems through computational approaches. Most branches of bioinformatics such as Genomics, Proteomics and Molecular Dynamics are particularly computationally intensive, requiring huge amount of computational resources for running algorithms of everincreasing complexity over data of everincreasing size. In the search for computational power, the EGEE Grid platform, world's largest community of interconnected clusters load balanced as a whole, seems particularly promising and is considered the new hope for satisfying the everincreasing computational requirements of bioinformatics, as well as physics and other computational sciences. The EGEE platform, however, is rather new and not yet free of problems. In addition, specific requirements of bioinformatics need to be addressed in order to use this new platform effectively for bioinformatics tasks. In my three years' Ph.D. work I addressed numerous aspects of this Grid platform, with particular attention to those needed by the bioinformatics domain. I hence created three major frameworks, Vnas, GridDBManager and SETest, plus an additional smaller standalone solution, to enhance the support for bioinformatics applications in the Grid environment and to reduce the effort needed to create new applications, additionally addressing numerous existing Grid issues and performing a series of optimizations. The Vnas framework is an advanced system for the submission and monitoring of Grid jobs that provides an abstraction with reliability over the Grid platform. In addition, Vnas greatly simplifies the development of new Grid applications by providing a callback system to simplify the creation of arbitrarily complex multistage computational pipelines and provides an abstracted virtual sandbox which bypasses Grid limitations. Vnas also reduces the usage of Grid bandwidth and storage resources by transparently detecting equality of virtual sandbox files based on content, across different submissions, even when performed by different users. BGBlast, evolution of the earlier project GridBlast, now provides a Grid Database Manager (GridDBManager) component for managing and automatically updating biological flatfile databases in the Grid environment. GridDBManager sports very novel features such as an adaptive replication algorithm that constantly optimizes the number of replicas of the managed databases in the Grid environment, balancing between response times (performances) and storage costs according to a programmed cost formula. GridDBManager also provides a very optimized automated management for older versions of the databases based on reverse delta files, which reduces the storage costs required to keep such older versions available in the Grid environment by two orders of magnitude. The SETest framework provides a way to the user to test and regressiontest Python applications completely scattered with side effects (this is a common case with Grid computational pipelines), which could not easily be tested using the more standard methods of unit testing or test cases. The technique is based on a new concept of datasets containing invocations and results of filtered calls. The framework hence significantly accelerates the development of new applications and computational pipelines for the Grid environment, and the efforts required for maintenance. An analysis of the impact of these solutions will be provided in this thesis. This Ph.D. work originated various publications in journals and conference proceedings as reported in the Appendix. Also, I orally presented my work at numerous international conferences related to Grid and bioinformatics.

Ottimizzazione strutturale in ambiente Salome-Meca/CAE

La tesi tratta aspetti relativi all'ottimizzazione strutturale. Algoritmi di ottimizzazione scritti in linguaggio di programmazione Python, sia basati sul metodo del simplesso che di tipo gentico, sono stati integrati in ambiente Salome-Meca/CAE ed applicati ad esempi di interesse strutturale.

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Progettazione e implementazione di una rete di sensori mobili Arduino per scenari di Disaster Recovery

Sommario Il progetto descritto in questo documento consiste nella realizzazione di una prima applicazione pratica di uno specifico studio di ricerca rivolto al ripristino di reti wireless in scenari post-calamità naturali. In principio è stata descritta un’ampia analisi delle problematiche di rete che si vengono a creare in seguito ad eventi catastrofici. Successivamente, analizzando le varie tecniche e tecnologie oggetto di studio di diversi gruppi di ricerca, si è scelto di collaborare con il progetto STEM-Mesh, essendo ancora in fase sperimentale, il quale affronta il problema di ristabilire la connettività di rete in questi particolari scenari, attraverso l’utilizzo di tecnologie Cognitive Radio (CR), mobilità controllata e principi di reti auto-organizzanti. Di questo primo approccio pratico sono state poi descritte le fasi di progettazione, implementazione e testing. Nella fase di progettazione sono state studiate le componenti hardware e software che rispettassero il più possibile i requisiti e le caratteristiche dei dispositivi “staminali” STEM-Node cuore del progetto STEM-Mesh, ovvero dei dispositivi wireless altamente auto-riconfiguranti ed auto-organizzanti che possono diventare dispositivi sostituivi ai nodi compromessi in una rete, riconfigurandosi appunto in base alle funzionalità interrotte. Nella fase di implementazione si è passati alla stesura del codice, in Python e Wiring, abilitante il dispositivo STEM-Node. Infine nella fase di testing si è verificato che i risultati fossero quelli desiderati e che il sistema realizzato funzionasse come previsto.

Nanoparticelle e condizione mesoscopica: esempi di proprieta fisiche e analisi di micrografie elettroniche

Nel capitolo 1 si definisce la condizione mesoscopica e sono descritte le tecnologie utilizzate per la produzione e il deposito di particelle. Inoltre si discute come l’organizzazione dei gruppi di particelle sia influenzata dalla loro superficie e dalla loro reciproca interazione. Nel capitolo 2 si presenta un software per l'analisi di micrografie elettroniche, come è stato sviluppato, la sua portata, i limiti. Si descrivono gli algoritmi di base utilizzati per processare l’immagine e ottenere aree e perimetri delle nanoparticelle campionate. Infine il capitolo 3 contiene i risultati dell’analisi immagine e le relative conclusioni fisiche.

Automated Analysis Methods for the Assessment of Bicycle Infrastructure and Demand

A first phase of the research activity has been related to the study of the state of art of the infrastructures for cycling, bicycle use and methods for evaluation. In this part, the candidate has studied the "bicycle system" in countries with high bicycle use and in particular in the Netherlands. Has been carried out an evaluation of the questionnaires of the survey conducted within the European project BICY on mobility in general in 13 cities of the participating countries. The questionnaire was designed, tested and implemented, and was later validated by a test in Bologna. The results were corrected with information on demographic situation and compared with official data. The cycling infrastructure analysis was conducted on the basis of information from the OpenStreetMap database. The activity consisted in programming algorithms in Python that allow to extract data from the database infrastructure for a region, to sort and filter cycling infrastructure calculating some attributes, such as the length of the arcs paths. The results obtained were compared with official data where available. The structure of the thesis is as follows: 1. Introduction: description of the state of cycling in several advanced countries, description of methods of analysis and their importance to implement appropriate policies for cycling. Supply and demand of bicycle infrastructures. 2. Survey on mobility: it gives details of the investigation developed and the method of evaluation. The results obtained are presented and compared with official data. 3. Analysis cycling infrastructure based on information from the database of OpenStreetMap: describes the methods and algorithms developed during the PhD. The results obtained by the algorithms are compared with official data. 4. Discussion: The above results are discussed and compared. In particular the cycle demand is compared with the length of cycle networks within a city. 5. Conclusions

Dynamic networks, text analysis and Gephi: the art math

In numerosi campi scientici l'analisi di network complessi ha portato molte recenti scoperte: in questa tesi abbiamo sperimentato questo approccio sul linguaggio umano, in particolare quello scritto, dove le parole non interagiscono in modo casuale. Abbiamo quindi inizialmente presentato misure capaci di estrapolare importanti strutture topologiche dai newtork linguistici(Degree, Strength, Entropia, . . .) ed esaminato il software usato per rappresentare e visualizzare i grafi (Gephi). In seguito abbiamo analizzato le differenti proprietà statistiche di uno stesso testo in varie sue forme (shuffolato, senza stopwords e senza parole con bassa frequenza): il nostro database contiene cinque libri di cinque autori vissuti nel XIX secolo. Abbiamo infine mostrato come certe misure siano importanti per distinguere un testo reale dalle sue versioni modificate e perché la distribuzione del Degree di un testo normale e di uno shuffolato abbiano lo stesso andamento. Questi risultati potranno essere utili nella sempre più attiva analisi di fenomeni linguistici come l'autorship attribution e il riconoscimento di testi shuffolati.