Computational methods for genome screening

Motivation An actual issue of great interest, both under a theoretical and an applicative perspective, is the analysis of biological sequences for disclosing the information that they encode. The development of new technologies for genome sequencing in the last years, opened new fundamental problems since huge amounts of biological data still deserve an interpretation. Indeed, the sequencing is only the first step of the genome annotation process that consists in the assignment of biological information to each sequence. Hence given the large amount of available data, in silico methods became useful and necessary in order to extract relevant information from sequences. The availability of data from Genome Projects gave rise to new strategies for tackling the basic problems of computational biology such as the determination of the tridimensional structures of proteins, their biological function and their reciprocal interactions. Results The aim of this work has been the implementation of predictive methods that allow the extraction of information on the properties of genomes and proteins starting from the nucleotide and aminoacidic sequences, by taking advantage of the information provided by the comparison of the genome sequences from different species. In the first part of the work a comprehensive large scale genome comparison of 599 organisms is described. 2,6 million of sequences coming from 551 prokaryotic and 48 eukaryotic genomes were aligned and clustered on the basis of their sequence identity. This procedure led to the identification of classes of proteins that are peculiar to the different groups of organisms. Moreover the adopted similarity threshold produced clusters that are homogeneous on the structural point of view and that can be used for structural annotation of uncharacterized sequences. The second part of the work focuses on the characterization of thermostable proteins and on the development of tools able to predict the thermostability of a protein starting from its sequence. By means of Principal Component Analysis the codon composition of a non redundant database comprising 116 prokaryotic genomes has been analyzed and it has been showed that a cross genomic approach can allow the extraction of common determinants of thermostability at the genome level, leading to an overall accuracy in discriminating thermophilic coding sequences equal to 95%. This result outperform those obtained in previous studies. Moreover, we investigated the effect of multiple mutations on protein thermostability. This issue is of great importance in the field of protein engineering, since thermostable proteins are generally more suitable than their mesostable counterparts in technological applications. A Support Vector Machine based method has been trained to predict if a set of mutations can enhance the thermostability of a given protein sequence. The developed predictor achieves 88% accuracy.

An experimental and theoretical approach to correct for the scattered radiation in an X-ray computer tomography system for industrial applications

The main problem connected to cone beam computed tomography (CT) systems for industrial applications employing 450 kV X-ray tubes is the high amount of scattered radiation which is added to the primary radiation (signal). This stray radiation leads to a significant degradation of the image quality. A better understanding of the scattering and methods to reduce its effects are therefore necessary to improve the image quality. Several studies have been carried out in the medical field at lower energies, whereas studies in industrial CT, especially for energies up to 450 kV, are lacking. Moreover, the studies reported in literature do not consider the scattered radiation generated by the CT system structure and the walls of the X-ray room (environmental scatter). In order to investigate the scattering on CT projections a GEANT4-based Monte Carlo (MC) model was developed. The model, which has been validated against experimental data, has enabled the calculation of the scattering including the environmental scatter, the optimization of an anti-scatter grid suitable for the CT system, and the optimization of the hardware components of the CT system. The investigation of multiple scattering in the CT projections showed that its contribution is 2.3 times the one of primary radiation for certain objects. The results of the environmental scatter showed that it is the major component of the scattering for aluminum box objects of front size 70 x 70 mm2 and that it strongly depends on the thickness of the object and therefore on the projection. For that reason, its correction is one of the key factors for achieving high quality images. The anti-scatter grid optimized by means of the developed MC model was found to reduce the scatter-toprimary ratio in the reconstructed images by 20 %. The object and environmental scatter calculated by means of the simulation were used to improve the scatter correction algorithm which could be patented by Empa. The results showed that the cupping effect in the corrected image is strongly reduced. The developed CT simulation is a powerful tool to optimize the design of the CT system and to evaluate the contribution of the scattered radiation to the image. Besides, it has offered a basis for a new scatter correction approach by which it has been possible to achieve images with the same spatial resolution as state-of-the-art well collimated fan-beam CT with a gain in the reconstruction time of a factor 10. This result has a high economic impact in non-destructive testing and evaluation, and reverse engineering.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Materiali lapidei in provincia di Bologna: studio sulle cave storiche e ipotesi di sostenibilità.

Lo studio effettuato verte sulla ricerca delle cave storiche di pietra da taglio in provincia di Bologna, facendo partire la ricerca al 1870 circa, data in cui si hanno le prime notizie cartacee di cave bolognesi. Nella ricerca si è potuto contare sull’aiuto dei Dott. Stefano Segadelli e Maria Tersa De Nardo, geologi della regione Emilia-Romagna, che hanno messo a disposizione la propria conoscenza e le pubblicazioni della regione a questo scopo. Si è scoperto quindi che non esiste in bibliografia la localizzazione di tali cave e si è cercato tramite l’utilizzo del software ArcGIS , di georeferenziarle, correlandole di informazioni raccolte durante la ricerca. A Bologna al momento attuale non esistono cave di pietra da taglio attive, così tutte le fonti che si sono incontrate hanno fornito dati parziali, che uniti hanno permesso di ottenere una panoramica soddisfacente della situazione a inizio secolo scorso. Le fonti studiate sono state, in breve: il catasto cave della regione Emilia-Romagna, gli shape preesistenti della localizzazione delle cave, le pubblicazioni “Uso del Suolo”, oltre ai dati forniti dai vari Uffici Tecnici dei comuni nei quali erano attive le cave. I litotipi cavati in provincia sono quattro: arenaria, calcare, gesso e ofiolite. Per l’ofiolite si tratta di coltivazioni sporadiche e difficilmente ripetibili dato il rischio che può esserci di incontrare l’amianto in queste formazioni; è quindi probabile che non verranno più aperte. Il gesso era una grande risorsa a fine ‘800, con molte cave aperte nella Vena del Gesso. Questa zona è diventata il Parco dei Gessi Bolognesi, lasciando alla cava di Borgo Rivola il compito di provvedere al fabbisogno regionale. Il calcare viene per lo più usato come inerte, ma non mancano esempi di formazioni adatte a essere usate come blocchi. La vera protagonista del panorama bolognese rimane l’arenaria, che venne usata da sempre per costruire paesi e città in provincia. Le cave, molte e di ridotte dimensioni, sono molto spesso difficili da trovare a causa della conseguente rinaturalizzazione. Ci sono possibilità però di vedere riaprire cave di questo materiale a Monte Finocchia, tramite la messa in sicurezza di una frana, e forse anche tramite la volontà di sindaci di comunità montane, sensibili a questo argomento. Per avere una descrizione “viva” della situazione attuale, sono stati intervistati il Dott. Maurizio Aiuola, geologo della Provincia di Bologna, e il Geom. Massimo Romagnoli della Regione Emilia-Romagna, che hanno fornito una panoramica esauriente dei problemi che hanno portato ad avere in regione dei poli unici estrattivi anziché più cave di modeste dimensioni, e delle possibilità future. Le grandi cave sono, da parte della regione, più facilmente controllabili, essendo poche, e più facilmente ripristinabili data la disponibilità economica di chi la gestisce. Uno dei problemi emersi che contrastano l’apertura di aree estrattive minori, inoltre, è la spietata concorrenza dei materiali esteri, che costano, a parità di qualità, circa la metà del materiale italiano. Un esempio di ciò lo si è potuto esaminare nel comune di Sestola (MO), dove, grazie all’aiuto e alle spiegazioni del Geom. Edo Giacomelli si è documentato come il granito e la pietra di Luserna esteri utilizzati rispondano ai requisiti di resistenza e non gelività che un paese sottoposto ai rigori dell’inverno richiede ai lapidei, al contrario di alcune arenarie già in opera provenienti dal comune di Bagno di Romagna. Alla luce di questo esempio si è proceduto a calcolare brevemente l’ LCA di questo commercio, utilizzando con l’aiuto dell’ Ing. Cristian Chiavetta il software SimaPRO, in cui si è ipotizzato il trasporto di 1000 m3 di arenaria da Shanghai (Cina) a Bologna e da Karachi (Pakistan) a Bologna, comparandolo con le emissioni che possono esserci nel trasporto della stessa quantità di materiale dal comune di Monghidoro (BO) al centro di Bologna. Come previsto, il trasporto da paesi lontani comporta un impatto ambientale quasi non comparabile con quello locale, in termini di consumo di risorse organiche e inorganiche e la conseguente emissione di gas serra. Si è ipotizzato allora una riapertura di cave locali a fini non edilizi ma di restauro; esistono infatti molti edifici e monumenti vincolati in provincia, e quando questi devono essere restaurati, dove si sceglie di cavare il materiale necessario e rispondente a quello già in opera? Al riguardo, si è passati attraverso altre due interviste ai Professori Francesco Eleuteri, architetto presso la Soprintendenza dei Beni Culturali a Bologna e Gian Carlo Grillini, geologo-petrografo e esperto di restauro. Ciò che è emerso è che effettivamente non esiste attualmente una panoramica soddisfacente di quello che è il patrimonio lapideo della provincia, mancando, oltre alla georeferenziazione, una caratterizzazione minero-petrografica e fisico-meccanica adeguata a poter descrivere ciò che veniva anticamente cavato; l’ipotesi di riapertura a fini restaurativi potrebbe esserci, ma non sembra essere la maggiore necessità attualmente, in quanto il restauro viene per lo più fatto senza sostituzioni o integrazioni, tranne rari casi; è pur sempre utile avere una carta alla mano che possa correlare l’edificio storico con la zona di estrazione del materiale, quindi entrambi i professori hanno auspicato una prosecuzione della ricerca. Si può concludere dicendo che la ricerca può proseguire con una migliore e più efficace localizzazione delle cave sul terreno, usando anche come fonte il sapere della popolazione locale, e di procedere con una parte pratica che riguardi la caratterizzazione minero-petrografica e fisico-meccanica. L’utilità di questi dati può esserci nel momento in cui si facciano ricerche storiche sui beni artistici presenti a Bologna, e qualora si ipotizzi una riapertura di una zona estrattiva.

Archaeological Baltic amber: degradation mechanisms and conservation measures

The aim of this project was to achieve a deep understanding of the mechanisms by which Baltic amber degrades, in order to develop techniques for preventive conservation of archaeological amber objects belonging to the National Museum of Denmark’s collections. To examine deterioration of Baltic amber, a starting point was to identify and monitor surface and bulk properties which are affected during degradation. The way to operate consisted of the use of accelerated ageing to initiate degradation of raw Baltic amber samples in different conditions of relative humidity, oxygen exposure or pH and, successively, of the use of non/micro-destructive techniques to identify and quantify changes in visual, chemical and structural properties. A large piece of raw Baltic amber was used to prepare several test samples for two different kinds of accelerated ageing: thermal-ageing and photo-ageing. During the ageing, amber samples were regularly examined through several analytical techniques related to different information: appearance/colour change by visual examination, photography and colorimetry; chemical change by infrared spectroscopy, Raman spectroscopy and elemental analysis; rate of oxidation by oxygen measurement; qualitative analysis of released volatiles by gas chromatography – mass spectrometry. The obtained results were analysed through both critical evaluation and statistical study. After the interpretation of the achieved data, the main relations between amber and environmental factors during the degradation process became clearer and it was possible to identify the major pathways by which amber degrades, such as hydrolysis of esters into alcohols and carboxylic acids, thermal-oxidation and photo-oxidation of terpenoid components, depolymerisation and decomposition of the chemical structure. At the end it was possible to suggest a preventive conservation strategy based on the control of climatic, atmospheric and lighting parameters in the environment where Baltic amber objects are stored and displayed.

Un piano territoriale per la riduzione della concentrazione di CO2 nell'atmosfera e la produzione energetica da fonti rinnovabili per mezzo della filiera delle biomasse

Il progetto propone uno studio per verificare la fattibilita' di un piano territoriale (ideato per il bacino del Po ma di fatto estendibile a tutti i bacini fluviali) per la creazione di una filiera di colture bioenergetiche (biomasse) che, trasportate per mezzo della navigazione fluviale (uno dei mezzi di trasporto a minore emissione di CO2), alimentino una o piu' centrali a nuova tecnologia che associno alla produzione di calore (teleriscaldamento e raffreddamento) e di energia la separazione dei fumi. La CO2 catturata dalla crescita delle biomasse e recuperata dalla combustione, puo' quindi essere segregata nel sottosuolo di aree costiere subsidenti contrastando il fenomeno dell’abbassamento del suolo. Ricavando benefici in tutti i passaggi di attuazione del piano territoriale (lancio dell'agricoltura bioenergetica, rilancio della navigazione a corrente libera, avvio di una economia legata alla logistica del trasporto e dello stoccaggio delle biomasse, generazione di energia pulita, lotta alla subsidenza) il progetto, di fatto, consente di catturare ingenti quantitativi di CO2 dall'atmosfera e di segregarli nel sottosuolo, riducendo l'effetto serra. Nel corso del Dottorato e' stata sviluppata una metodologia di valutazione della sostenibilita' economica ed ambientale del progetto ad un bacino fluviale, che consta di una modulistica di raccolta dei dati di base e di una procedura informatizzata di analisi.

Geolocalizzazione e QRCode come strumenti a supporto di applicazioni turistico-culturali

Gli smartphone, sono dispositivi per la telefonia mobile che oramai includono una serie di funzionalità a supporto della multimedialità e non solo. Divenuti quasi dei notebook in miniatura, ne esistono di vari tipi e dimensioni e anche se la loro potenza di calcolo rimane di gran lunga inferiore a quella di un PC, riescono comunque a effettuare operazioni abbastanza evolute e con prestazioni accettabili. Quello che si vuole realizzare con questo lavoro non è uno studio su questi dispositivi (anche se in parte sarà affrontato), ma un approfondimento sulla possibilità di utilizzare una buona fetta di essi, a supporto dello sviluppo turistico nel nostro paese. In particolare si vuole realizzare una piattaforma mobile che metta in comunicazione individui che vogliono fornire informazione di tipo turistico (beni culturali, eventi, attività commerciali, ecc.) con individui che vogliono fruire di tali contenuti (un qualsiasi turista che sia in grado di utilizzare uno smartphone). Tale applicazione dovrà raccogliere informazioni su una determinata città e riuscire in maniera chiara e intuitiva a dare risposte alle principali domande che un turista si pone: • dove sono? • Cosa c’è d’interessante da visitare nei dintorni? • Interessante questa statua! Di cosa si tratta? • Quali sono gli eventi più interessanti ai quali potrei partecipare? • Ho un leggero appetito dove posso andare a mangiare? • Dove posso fare un po’ di shopping?

Performance evaluation of detectors for digital radiography

To date the hospital radiological workflow is completing a transition from analog to digital technology. Since the X-rays digital detection technologies have become mature, hospitals are trading on the natural devices turnover to replace the conventional screen film devices with digital ones. The transition process is complex and involves not just the equipment replacement but also new arrangements for image transmission, display (and reporting) and storage. This work is focused on 2D digital detector’s characterization with a concern to specific clinical application; the systems features linked to the image quality are analyzed to assess the clinical performances, the conversion efficiency, and the minimum dose necessary to get an acceptable image. The first section overviews the digital detector technologies focusing on the recent and promising technological developments. The second section contains a description of the characterization methods considered in this thesis categorized in physical, psychophysical and clinical; theory, models and procedures are described as well. The third section contains a set of characterizations performed on new equipments that appears to be some of the most advanced technologies available to date. The fourth section deals with some procedures and schemes employed for quality assurance programs.

Produzione e circolazione delle anfore greco italiche in area Adriatica

The present study, being part of a wide research program carried by the University of Bologna (Dipartimento di Scienze della Terra e Geo-Ambientali and Dipartimento di Archeologia) together with the Soprintendenze of Emilia-Romagna and Veneto, is aimed at examining the manufacturing and circulation of Greek Italic amphorae in the Adriatic area. This represents an essential step for the historical and archaeological reconstructions and in particular for: - the identification of local manufacturing though the archaeometric comparisons between ceramic samples and raw materials - the reconstruction of the ancient routes connecting different areas of the Roman world The examined archaeologic sites are representative of the main manufacturing areas in the Adriatic region both along the Italian and Albanian coasts: Adria, Cattolica, Rimini, Spina , Suasa and Phoinike. Notably, the Adriatic region not only represents the manufacturing area, but also coincides with the source area where the raw materials were collected. Archaeometric analyses of representative samples from the different areas of interests, were performed adapting the analytical tecniques used in mineralogy, petrography and geochemistry, to the study of ancient archaeological finds. These data were combined with the ones obtained from the analysis of clays, aimed at characterizing the nature of the raw materials. As a whole, an integration of these data with the available archaeologic observations led to significant advances in the scientific knowledge about of the main types of amphoric manufacturing and distribution in the Adriatic region. In particular, a local manufacturing is suggested for all the archaeological finds from Cattolica and for the main part of the archaeological finds from Suasa. Moreover, the occurrence of commercial routes between the sites of Rimini and Suasa and between Adria, Spina and Suasa is evidenced. On the contrary, for the amphorae from Phoinike a provenance from the examined sites is very unlikely.

Interfaccia web per un sistema di condivisione semantica dell'informazione: studio e implementazione

Questa tesi progettuale nasce per integrare gli sforzi attuali sullo sviluppo del web semantico. La piattaforma di riferimento sulla quale è stato svolto il presente lavoro è SMART-M3. Questa piattaforma mette a disposizione uno spazio condiviso di informazioni, rappresentate e accessibili secondo le tecnologie del web semantico. In questo scenario, nasce la necessità di disporre di un'interfaccia web capace di interagire con la piattaforma - in grado di risolvere la complessità intrinseca dei dati semantici - allo scopo di averne un completo controllo; ricerche precedenti a questo proposito hanno dato come frutto una libreria PHP che mi è stata consegnata come strumento per lo sviluppo dell'interfaccia. La tesi si è articolata in 3 fasi principali: una fase iniziale di documentazione sull'argomento, eseguita principalmente sul libro “A developer's guide to the semantic web” di Liyang Yu e sulla tesi “Ontologie per il web semantico: un'analisi comparativa.” di Indrit Beqiri; una seconda fase, quella principale, di sviluppo del progetto informatico; una terza fase, infine, di sviluppo di questo elaborato di tesi, da considerarsi come la trattazione di tutto il percorso soprascritto, dall'inizio alla fine, secondo l'ordine cronologico in cui si svolto l'intero processo della tesi.

Stochastic models and dynamic measures for the characterization of bistable circuits

During the last few years, a great deal of interest has risen concerning the applications of stochastic methods to several biochemical and biological phenomena. Phenomena like gene expression, cellular memory, bet-hedging strategy in bacterial growth and many others, cannot be described by continuous stochastic models due to their intrinsic discreteness and randomness. In this thesis I have used the Chemical Master Equation (CME) technique to modelize some feedback cycles and analyzing their properties, including experimental data. In the first part of this work, the effect of stochastic stability is discussed on a toy model of the genetic switch that triggers the cellular division, which malfunctioning is known to be one of the hallmarks of cancer. The second system I have worked on is the so-called futile cycle, a closed cycle of two enzymatic reactions that adds and removes a chemical compound, called phosphate group, to a specific substrate. I have thus investigated how adding noise to the enzyme (that is usually in the order of few hundred molecules) modifies the probability of observing a specific number of phosphorylated substrate molecules, and confirmed theoretical predictions with numerical simulations. In the third part the results of the study of a chain of multiple phosphorylation-dephosphorylation cycles will be presented. We will discuss an approximation method for the exact solution in the bidimensional case and the relationship that this method has with the thermodynamic properties of the system, which is an open system far from equilibrium.In the last section the agreement between the theoretical prediction of the total protein quantity in a mouse cells population and the observed quantity will be shown, measured via fluorescence microscopy.

Pyrolysis-Gas Chromatography-Mass Spectometry and Chemometric Analysis for the Characterization of Complex Matrices

The present PhD thesis was focused on the development and application of chemical methodology (Py-GC-MS) and data-processing method by multivariate data analysis (chemometrics). The chromatographic and mass spectrometric data obtained with this technique are particularly suitable to be interpreted by chemometric methods such as PCA (Principal Component Analysis) as regards data exploration and SIMCA (Soft Independent Models of Class Analogy) for the classification. As a first approach, some issues related to the field of cultural heritage were discussed with a particular attention to the differentiation of binders used in pictorial field. A marker of egg tempera the phosphoric acid esterified, a pyrolysis product of lecithin, was determined using HMDS (hexamethyldisilazane) rather than the TMAH (tetramethylammonium hydroxide) as a derivatizing reagent. The validity of analytical pyrolysis as tool to characterize and classify different types of bacteria was verified. The FAMEs chromatographic profiles represent an important tool for the bacterial identification. Because of the complexity of the chromatograms, it was possible to characterize the bacteria only according to their genus, while the differentiation at the species level has been achieved by means of chemometric analysis. To perform this study, normalized areas peaks relevant to fatty acids were taken into account. Chemometric methods were applied to experimental datasets. The obtained results demonstrate the effectiveness of analytical pyrolysis and chemometric analysis for the rapid characterization of bacterial species. Application to a samples of bacterial (Pseudomonas Mendocina), fungal (Pleorotus ostreatus) and mixed- biofilms was also performed. A comparison with the chromatographic profiles established the possibility to: • Differentiate the bacterial and fungal biofilms according to the (FAMEs) profile. • Characterize the fungal biofilm by means the typical pattern of pyrolytic fragments derived from saccharides present in the cell wall. • Individuate the markers of bacterial and fungal biofilm in the same mixed-biofilm sample.

Statistical Physics and Modeling of Human Mobility

In this thesis, we extend some ideas of statistical physics to describe the properties of human mobility. By using a database containing GPS measures of individual paths (position, velocity and covered space at a spatial scale of 2 Km or a time scale of 30 sec), which includes the 2% of the private vehicles in Italy, we succeed in determining some statistical empirical laws pointing out "universal" characteristics of human mobility. Developing simple stochastic models suggesting possible explanations of the empirical observations, we are able to indicate what are the key quantities and cognitive features that are ruling individuals' mobility. To understand the features of individual dynamics, we have studied different aspects of urban mobility from a physical point of view. We discuss the implications of the Benford's law emerging from the distribution of times elapsed between successive trips. We observe how the daily travel-time budget is related with many aspects of the urban environment, and describe how the daily mobility budget is then spent. We link the scaling properties of individual mobility networks to the inhomogeneous average durations of the activities that are performed, and those of the networks describing people's common use of space with the fractional dimension of the urban territory. We study entropy measures of individual mobility patterns, showing that they carry almost the same information of the related mobility networks, but are also influenced by a hierarchy among the activities performed. We discover that Wardrop's principles are violated as drivers have only incomplete information on traffic state and therefore rely on knowledge on the average travel-times. We propose an assimilation model to solve the intrinsic scattering of GPS data on the street network, permitting the real-time reconstruction of traffic state at a urban scale.

Integration of MFA and LCA methodologies: the anthropogenic aluminium cycle in Italy

MFA and LCA methodologies were applied to analyse the anthropogenic aluminium cycle in Italy with focus on historical evolution of stocks and flows of the metal, embodied GHG emissions, and potentials from recycling to provide key features to Italy for prioritizing industrial policy toward low-carbon technologies and materials. Historical trend series were collected from 1947 to 2009 and balanced with data from production, manufacturing and waste management of aluminium-containing products, using a ‘top-down’ approach to quantify the contemporary in-use stock of the metal, and helping to identify ‘applications where aluminium is not yet being recycled to its full potential and to identify present and future recycling flows’. The MFA results were used as a basis for the LCA aimed at evaluating the carbon footprint evolution, from primary and electrical energy, the smelting process and the transportation, embodied in the Italian aluminium. A discussion about how the main factors, according to the Kaya Identity equation, they did influence the Italian GHG emissions pattern over time, and which are the levers to mitigate it, it has been also reported. The contemporary anthropogenic reservoirs of aluminium was estimated at about 320 kg per capita, mainly embedded within the transportation and building and construction sectors. Cumulative in-use stock represents approximately 11 years of supply at current usage rates (about 20 Mt versus 1.7 Mt/year), and it would imply a potential of about 160 Mt of CO2eq emissions savings. A discussion of criticality related to aluminium waste recovery from the transportation and the containers and packaging sectors was also included in the study, providing an example for how MFA and LCA may support decision-making at sectorial or regional level. The research constitutes the first attempt of an integrated approach between MFA and LCA applied to the aluminium cycle in Italy.