Structural analysis of combinatorial optimization problem characteristics and their resolution using hybrid approaches

Many combinatorial problems coming from the real world may not have a clear and well defined structure, typically being dirtied by side constraints, or being composed of two or more sub-problems, usually not disjoint. Such problems are not suitable to be solved with pure approaches based on a single programming paradigm, because a paradigm that can effectively face a problem characteristic may behave inefficiently when facing other characteristics. In these cases, modelling the problem using different programming techniques, trying to ”take the best” from each technique, can produce solvers that largely dominate pure approaches. We demonstrate the effectiveness of hybridization and we discuss about different hybridization techniques by analyzing two classes of problems with particular structures, exploiting Constraint Programming and Integer Linear Programming solving tools and Algorithm Portfolios and Logic Based Benders Decomposition as integration and hybridization frameworks.

Institutional Processes and Discursive Strategies: Rhetoric and Vocabulary Analysis of CSR and Sustainability

The candidate tackled an important issue in contemporary management: the role of CSR and Sustainability. The research proposal focused on a longitudinal and inductive research, directed to specify the evolution of CSR and contribute to the new institutional theory, in particular institutional work framework, and to the relation between institutions and discourse analysis. The documental analysis covers all the evolution of CSR, focusing also on a number of important networks and associations. Some of the methodologies employed in the thesis have been employed as a consequence of data analysis, in a truly inductive research process. The thesis is composed by two section. The first section mainly describes the research process and the analyses results. The candidates employed several research methods: a longitudinal content analysis of documents, a vocabulary research with statistical metrics as cluster analysis and factor analysis, a rhetorical analysis of justifications. The second section puts in relation the analysis results with theoretical frameworks and contributions. The candidate confronted with several frameworks: Actor-Network-Theory, Institutional work and Boundary Work, Institutional Logic. Chapters are focused on different issues: a historical reconstruction of CSR; a reflection about symbolic adoption of recurrent labels; two case studies of Italian networks, in order to confront institutional and boundary works; a theoretical model of institutional change based on contradiction and institutional complexity; the application of the model to CSR and Sustainability, proposing Sustainability as a possible institutional logic.

Essays on the Empirical Analysis of Economic and Political Development in Sub-Saharan Africa

In Sub-Saharan Africa, non-democratic events, like civil wars and coup d'etat, destroy economic development. This study investigates both domestic and spatial effects on the likelihood of civil wars and coup d'etat. To civil wars, an increase of income growth is one of common research conclusions to stop wars. This study adds a concern on ethnic fractionalization. IV-2SLS is applied to overcome causality problem. The findings document that income growth is significant to reduce number and degree of violence in high ethnic fractionalized countries, otherwise they are trade-off. Income growth reduces amount of wars, but increases its violent level, in the countries with few large ethnic groups. Promoting growth should consider ethnic composition. This study also investigates the clustering and contagion of civil wars using spatial panel data models. Onset, incidence and end of civil conflicts spread across the network of neighboring countries while peace, the end of conflicts, diffuse only with the nearest neighbor. There is an evidence of indirect links from neighboring income growth, without too much inequality, to reduce the likelihood of civil wars. To coup d'etat, this study revisits its diffusion for both all types of coups and only successful ones. The results find an existence of both domestic and spatial determinants in different periods. Domestic income growth plays major role to reduce the likelihood of coup before cold war ends, while spatial effects do negative afterward. Results on probability to succeed coup are similar. After cold war ends, international organisations seriously promote democracy with pressure against coup d'etat, and it seems to be effective. In sum, this study indicates the role of domestic ethnic fractionalization and the spread of neighboring effects to the likelihood of non-democratic events in a country. Policy implementation should concern these factors.

Analysis of eruptive and seismic sequences to improve the short-and long-term eruption forecasting

Forecasting the time, location, nature, and scale of volcanic eruptions is one of the most urgent aspects of modern applied volcanology. The reliability of probabilistic forecasting procedures is strongly related to the reliability of the input information provided, implying objective criteria for interpreting the historical and monitoring data. For this reason both, detailed analysis of past data and more basic research into the processes of volcanism, are fundamental tasks of a continuous information-gain process; in this way the precursor events of eruptions can be better interpreted in terms of their physical meanings with correlated uncertainties. This should lead to better predictions of the nature of eruptive events. In this work we have studied different problems associated with the long- and short-term eruption forecasting assessment. First, we discuss different approaches for the analysis of the eruptive history of a volcano, most of them generally applied for long-term eruption forecasting purposes; furthermore, we present a model based on the characteristics of a Brownian passage-time process to describe recurrent eruptive activity, and apply it for long-term, time-dependent, eruption forecasting (Chapter 1). Conversely, in an effort to define further monitoring parameters as input data for short-term eruption forecasting in probabilistic models (as for example, the Bayesian Event Tree for eruption forecasting -BET_EF-), we analyze some characteristics of typical seismic activity recorded in active volcanoes; in particular, we use some methodologies that may be applied to analyze long-period (LP) events (Chapter 2) and volcano-tectonic (VT) seismic swarms (Chapter 3); our analysis in general are oriented toward the tracking of phenomena that can provide information about magmatic processes. Finally, we discuss some possible ways to integrate the results presented in Chapters 1 (for long-term EF), 2 and 3 (for short-term EF) in the BET_EF model (Chapter 4).

Structure of the Southern Tyrrhenian subduction system: insights from seismological analysis of anisotropy and attenuation

The Southern Tyrrhenian subduction system shows a complex interaction among asthenospheric flow, subducting slab and overriding plate. To shed light on the deformations and mechanical properties of the slab and surrounding mantle, I investigated seismic anisotropy and attenuation properties through the subduction region. I used both teleseisms and slab earthquakes, analyzing shear-wave splitting on SKS and S phases, respectively. The fast polarization directions φ, and the delay time, δt, were retrieved using the method of Silver and Chan [1991. SKS and S φ reveal a complex anisotropy pattern across the subduction zone. SKS-rays sample primarily the sub-slab region showing rotation of fast directions following the curved shape of the slab and very strong anisotropy. S-rays sample mainly the slab, showing variable φ and a smaller δt. SKS and S splitting reveals a well developed toroidal flow at SW edge of the slab, while at its NE edge the pattern is not very clear. This suggests that the anisotropy is controlled by the slab rollback, responsible for about 100 km slab parallel φ in the sub-slab mantle. The slab is weakly anisotropic, suggesting the asthenosphere as main source of anisotropy. To investigate the physical properties of the slab and surrounding regions, I analyzed the seismic P and S wave attenuation. By inverting high-quality S-waves t* from slab earthquakes, 3D attenuation models down to 300 km were obtained. Attenuation results image the slab as low-attenuation body, but with heterogeneous QS and QP structure showing spot of high attenuation , between 100-200 km depth, which could be due dehydration associated to the slab metamorphism. A low QS anomaly is present in the mantle wedge beneath the Aeolian volcanic arc and could indicate mantle melting and slab dehydration.

Analysis of cerebral and autonomic response to respiratory events in patients with Sleep Apnea Syndrome

The arousal scoring in Obstructive Sleep Apnea Syndrome (OSAS) is important to clarify the impact of the disease on sleep but the currently applied American Academy of Sleep Medicine (AASM) definition may underestimate the subtle alterations of sleep. The aims of the present study were to evaluate the impact of respiratory events on cortical and autonomic arousal response and to quantify the additional value of cyclic alternating pattern (CAP) and pulse wave amplitude (PWA) for a more accurate detection of respiratory events and sleep alterations in OSAS patients. A retrospective revision of 19 polysomnographic recordings of OSAS patients was carried out. Analysis was focused on quantification of apneas (AP), hypopneas (H) and flow limitation (FL) events, and on investigation of cerebral and autonomic activity. Only 41.1% of FL events analyzed in non rapid eye movement met the AASM rules for the definition of respiratory event-related arousal (RERA), while 75.5% of FL events ended with a CAP A phase. The dual response (EEG-PWA) was the most frequent response for all subtypes of respiratory event with a progressive reduction from AP to H and FL. 87.7% of respiratory events with EEG activation showed also a PWA drop and 53,4% of the respiratory events without EEG activation presented a PWA drop. The relationship between the respiratory events and the arousal response is more complex than that suggested by the international classification. In the estimation of the response to respiratory events, the CAP scoring and PWA analysis can offer more extensive information compared to the AASM rules. Our data confirm also that the application of PWA scoring improves the detection of respiratory events and could reduce the underestimation of OSAS severity compared to AASM arousal.

Regulating Vertical Agreements: A Comparative Law & Economics analysis of Brazil and Europe

This PhD thesis discusses antitrust enforcement of anti-competitive vertical agreements in Europe and in Brazil from an institutional perspective. It considers both the evolution of the legal framework and the application of the existing policies, with the analysis of case studies. The research highlights the main challenges of the current approaches adopted by the competition authorities in these jurisdictions and formulates specific proposals for future improvements. Because the Brazilian competition rules were originally inspired by the European legal framework, this thesis also summarizes the contemporary discussions regarding comparative law and the efficiency of transplanting laws and good practices. In a Law & Economics perspective, vertical agreements have always been a paradoxical topic and constitute one of the most dynamic disputes for antitrust enforcement. The reason for that concern is the fact that those contracts among companies are complex in nature. Taking into account this background, the thesis provides an original analysis of the pro- and anti-competitive effects of vertical agreements, based on the classical literature of Law & Economics. One of the novelties of the research is the extension of the economic analysis of vertical agreements to also consider new forms of contractual abuses in the context of digital markets, such as the contractual restrictions that are being put I practice in e-commerce platforms. The international comparative approach focuses on the Brazilian and European experiences, and opens up a reflection about the policy recommendations applied to several countries with similar economic and institutional realities.

Analysis of efficacy and safety of CAR T-cell therapy in relapsed/refractory lymphomas: current indications and future perspectives

In the last few years, the introduction of chimeric antigen receptor (CAR) T-cell therapy into clinical practice has revolutionized the approach to patients with relapsed/refractory (R/R) large B-cell lymphoma (LBCL), whose outcome used to be dismal with median overall survival (OS) of approximately 6 months with standard salvage therapy. At our Institute, we started treating diffuse large B-cell lymphoma (DLBCL) patients with CAR T-cell products in August 2019 and they received either axicabtagene ciloleucel (axi-cel) and tisagenlecleucel (tisa-cel) as per regulatory indications. This research project presents the 2-year follow-up of the first 53 treated patients. Our first aim is to investigate the feasibility of this treatment strategy in a real-world setting, although the reimbursement criteria set by the Italian Medicines Agency (Agenzia Italiana del Farmaco, AIFA) are very similar to the inclusion criteria of clinical trials and stricter than those established by the regulatory authorities of many foreign countries. One month after infusion, the ORR was 66% with 19 patients already in CR (38%). Restaging at 3, 6 and 12 months post-infusion shows that early CRs tend to be maintained over time and, moreover, that a considerable number of PRs and a few SDs can improve into a CR. The safety data were consistent with what is reported in the literature; toxicity was generally manageable, largely due to the increasing expertise in handling the specific adverse events related to CAR T-cell therapy. Our results confirms that CAR T-cell therapy is both safe and effective in a real-life setting and that it represents a crucial weapon in a subset of patients who were previously doomed to an inevitably severe prognosis.

Contributions to the performance analysis of continuum parallel robots

Continuum parallel robots (CPRs) are manipulators employing multiple flexible beams arranged in parallel and connected to a rigid end-effector. CPRs promise higher payload and accuracy than serial CRs while keeping great flexibility. As the risk of injury during accidental contacts between a human and a CPR should be reduced, CPRs may be used in large-scale collaborative tasks or assisted robotic surgery. There exist various CPR designs, but the prototype conception is rarely based on performance considerations, and the CPRs realization in mainly based on intuitions or rigid-link parallel manipulators architectures. This thesis focuses on the performance analysis of CPRs, and the tools needed for such evaluation, such as workspace computation algorithms. In particular, workspace computation strategies for CPRs are essential for the performance assessment, since the CPRs workspace may be used as a performance index or it can serve for optimal-design tools. Two new workspace computation algorithms are proposed in this manuscript, the former focusing on the workspace volume computation and the certification of its numerical results, while the latter aims at computing the workspace boundary only. Due to the elastic nature of CPRs, a key performance indicator for these robots is the stability of their equilibrium configurations. This thesis proposes the experimental validation of the equilibrium stability assessment on a real prototype, demonstrating limitations of some commonly used assumptions. Additionally, a performance index measuring the distance to instability is originally proposed in this manuscript. Differently from the majority of the existing approaches, the clear advantage of the proposed index is a sound physical meaning; accordingly, the index can be used for a more straightforward performance quantification, and to derive robot specifications.

High-resolution stratigraphy of Central and Southern Adriatic Quaternary deposits of sub-Milankovian climate change on Mediterranean circulation

This volume is a collection of the work done in a three years-lasting PhD, focused in the analysis of Central and Southern Adriatic marine sediments, deriving from the collection of a borehole and many cores, achieved thanks to the good seismic-stratigraphic knowledge of the study area. The work was made out within European projects EC-EURODELTA (coordinated by Fabio Trincardi, ISMAR-CNR), EC-EUROSTRATAFORM (coordinated by Phil P. E. Weaver, NOC, UK), and PROMESS1 (coordinated by Serge Bernè, IFREMER, France). The analysed sedimentary successions presented highly expanded stratigraphic intervals, particularly for the last 400 kyr, 60 kyr and 6 kyr BP. These three different time-intervals resulted in a tri-partition of the PhD thesis. The study consisted of the analysis of planktic and benthic foraminifers’ assemblages (more than 560 samples analysed), as well as in preparing the material for oxygen and carbon stable isotope analyses, and interpreting and discussing the obtained dataset. The chronologic framework of the last 400 kyr was achieved for borehole PRAD1-2 (within the work-package WP6 of PROMESS1 project), collected in 186.5 m water depth. The proposed chronology derives from a multi-disciplinary approach, consisting of the integration of numerous and independent proxies, some of which analysed by other specialists within the project. The final framework based on: micropaleontology (calcareous nannofossils and foraminifers’ bioevents), climatic cyclicity (foraminifers’ assemblages), geochemistry (oxygen stable isotope, made out on planktic and benthic records), paleomagnetism, radiometric ages (14C AMS), teprhochronology, identification of sapropel-equivalent levels (Se). It’s worth to note the good consistency between the oxygen stable isotope curve obtained for borehole PRAD1-2 and other deeper Mediterranean records. The studied proxies allowed the recognition of all the isotopic intervals from MIS10 to MIS1 in PRAD1-2 record, and the base of the borehole has been ascribed to the early MIS11. Glacial and interglacial intervals identified in the Central Adriatic record have been analysed in detail for the paleo-environmental reconstruction, as well. For instance, glacial stages MIS6, MIS8 and MIS10 present peculiar foraminifers’ assemblages, composed by benthic species typical of polar regions and no longer living in the Central Adriatic nowadays. Moreover, a deepening trend in the paleo-bathymetry during glacial intervals was observed, from MIS10 (inner-shelf environment) to MIS4 (mid-shelf environment).Ten sapropel-equivalent levels have been recognised in PRAD1-2 Central Adriatic record. They showed different planktic foraminifers’ assemblages, which allowed the first distinction of events occurred during warm-climate (Se5, Se7), cold-climate (Se4, Se6 and Se8) and temperate-intermediate-climate (Se1, Se3, Se9, Se’, Se10) conditions, consistently with literature. Cold-climate sapropel equivalents are characterised by the absence of an oligotrophic phase, whereas warm-temeprate-climate sapropel equivalents present both the oligotrophic and the eutrophic phases (except for Se1). Sea floor conditions vary, according to benthic foraminifers’ assemblages, from relatively well oxygenated (Se1, Se3), to dysoxic (Se9, Se’, Se10), to highly dysoxic (Se4, Se6, Se8) to events during which benthic foraminifers are absent (Se5, Se7). These two latter levels are also characterised by the lamination of the sediment, feature never observed in literature in such shallow records. The enhanced stratification of the water column during the events Se8, Se7, Se6, Se5, Se4, and the concurring strong dilution of shallow water, pointed out by the isotope record, lead to the hypothesis of a period of intense precipitation in the Central Adriatic region, possibly due to a northward shift of the African Monsoon. Finally, the expression of Central Adriatic PRAD1-2 Se5 equivalent was compared with the same event, as registered in other Eastern Mediterranean areas. The sequence of substantially the same planktic foraminifers’ bioevents has been consistently recognised, indicating a similar evolution of the water column all over the Eastern Mediterranean; yet, the synchronism of these events cannot be demonstrated. A high resolution analysis of late Holocene (last 6000 years BP) climate change was carried out for the Adriatic area, through the recognition of planktic and benthic foraminifers’ bioevents. In particular, peaks of planktic Globigerinoides sacculifer (four during the last 5500 years BP in the most expanded core) have been interpreted, based on the ecological requirements of this species, as warm-climate, arid intervals, correspondent to periods of relative climatic optimum, such as, for instance, the Medieval Warm Period, the Roman Age, the Late Bronze Age and the Copper Age. Consequently, the minima in the abundance of this biomarker could correspond to relatively cooler and more rainy periods. These conclusions are in good agreement with the isotopic and the pollen data. The Last Occurrence (LO) of G. sacculifer has been dated in this work at an average age of 550 years BP, and it is the best bioevent approximating the base of the Little Ice Age in the Adriatic. Recent literature reports the same bioevent in the Levantine Basin, showing a rather consistent age. Therefore, the LO of G. sacculifer has the potential to be extended to all the Eastern Mediterranean. Within the Little Ice Age, benthic foraminifer V. complanata shows two distinct peaks in the shallower Adriatic cores analysed, collected hundred kilometres apart, inside the mud belt environment. Based on the ecological requirements of this species, these two peaks have been interpreted as the more intense (cold and rainy) oscillations inside the LIA. The chronologic framework of the analysed cores is robust, being based on several range-finding 14C AMS ages, on estimates of the secular variation of the magnetic field, on geochemical estimates of the activity depth of 210Pb short-lived radionuclide (for the core-top ages), and is in good agreement with tephrochronologic, pollen and foraminiferal data. The intra-holocenic climate oscillations find out in the Adriatic have been compared with those pointed out in literature from other records of the Northern Hemisphere, and the chronologic constraint seems quite good. Finally, the sedimentary successions analysed allowed the review and the update of the foraminifers’ ecobiostratigraphy available from literature for the Adriatic region, thanks to the achievement of 16 ecobiozones for the last 60 kyr BP. Some bioevents are restricted to the Central Adriatic (for instance the LO of benthic Hyalinea balthica , approximating the MIS3/MIS2 boundary), others occur all over the Adriatic basin (for instance the LO of planktic Globorotalia inflata during MIS3, individuating Dansgaard-Oeschger cycle 8 (Denekamp)).

Design and Characterization of Curved and Spherical Flexure Hinges for Planar and Spatial Compliant Mechanisms

A flexure hinge is a flexible connector that can provide a limited rotational motion between two rigid parts by means of material deformation. These connectors can be used to substitute traditional kinematic pairs (like bearing couplings) in rigid-body mechanisms. When compared to their rigid-body counterpart, flexure hinges are characterized by reduced weight, absence of backlash and friction, part-count reduction, but restricted range of motion. There are several types of flexure hinges in the literature that have been studied and characterized for different applications. In our study, we have introduced new types of flexures with curved structures i.e. circularly curved-beam flexures and spherical flexures. These flexures have been utilized for both planar applications (e.g. articulated robotic fingers) and spatial applications (e.g. spherical compliant mechanisms). We have derived closed-form compliance equations for both circularly curved-beam flexures and spherical flexures. Each element of the spatial compliance matrix is analytically computed as a function of hinge dimensions and employed material. The theoretical model is then validated by comparing analytical data with the results obtained through Finite Element Analysis. A case study is also presented for each class of flexures, concerning the potential applications in the optimal design of planar and spatial compliant mechanisms. Each case study is followed by comparing the performance of these novel flexures with the performance of commonly used geometries in terms of principle compliance factors, parasitic motions and maximum stress demands. Furthermore, we have extended our study to the design and analysis of serial and parallel compliant mechanisms, where the proposed flexures have been employed to achieve spatial motions e.g. compliant spherical joints.

Plutarch's chemistry of stones and metals: conceptions and explanations. With an appendix on the TheSu XML annotation scheme

This dissertation presents a systematic and analytic overview of most of the information related to stones, minerals, and stone masonry which is found in the corpus of Plutarch of Chaeronea, combined with most of the information on metals and metalworking which is connected to the former. This survey is intended as a first step in the reconstruction of the full landscape of ‘chemical’ ideas occurring in Plutarch’s writings; accordingly, the exposition of the relevant passages, the assessment of their possible interpretations, the discussion on their implications, and their contextualization in the ancient traditions have been conducted with a special interest in the ‘mineralogical’ and ‘metallurgic’ themes developed in the frame of natural philosophy and meteorology. Although in this perspective physical etiology could have come to acquire central prominence, non-etiological information on Plutarch’s ideas on the nature and behaviour of stones and metals has been treated as equally relevant to reach a fuller understanding of how Plutarch conceptualized and visualized them in general, in- and outside the frame of philosophical explanation. Such extensive outline of Plutarch’s ideas on stones and metals is a prerequisite for an accurate inquiry into his use of the two in analogies, metaphors, and symbols: to predispose this kind of research was another aim of the present survey, and this aim has contributed to shape it; moreover, a special attention has been paid to the analysis of analogical and figurative speaking due to the nature itself of a large part of Plutarch’s references to stones and metals, which are either metaphorical, presented in close association with metaphors, or framed in analogies. Much of the information used for the present overview has been extracted —always with supporting argumentation— from the implications of such metaphors and analogies.

Analysis of extracellular vesicles from patients with advanced pancreatic cancer identifies miRNAs with predictive value for treatment with gemcitabine + nab-paclitaxel

Pancreatic cancer (PC) is the seventh leading cause of cancer death. Despite recent therapy advancements, 5-year survival is 11%. Resistance to therapy is common, and no predictive factors, except for BRCA1/2 and PALB2 mutations, can drive treatment selection. Based on the easy isolation of extracellular vesicles (EVs) from blood and the role of EV-borne miRNAs in chemoresistance, we analyzed EVs and their miRNA content in order to identify predictive factors. First, we analyzed samples from 28 PC patients and 7 healthy subjects, in order to establish methods for isolation and analysis of EVs and their miRNA content. We observed a significantly different expression of 28 miRNAs, including oncogenic or tumor suppressor miRNAs, showing the ability of our approach to detect candidate biomarkers. Then, we analyzed samples of 21 advanced PC patients, collected before first-line treatment with gemcitabine + nab-paclitaxel, and compared findings in responders and non-responders. EVs have been analyzed with Nanoparticle tracking analysis, flow cytometry and RNA-Seq; then, laboratory results have been matched with clinical data. Nanoparticle tracking analysis did not show any significant difference. Flow cytometry showed a lower expression of SSE4 and CD81 in responders. Finally, miRNA analysis showed 25 upregulated and 19 downregulated miRNAs in responders. In particular, in responders we observed upregulation of miR-141-3p, miR-141-5p, miR-200a-3p, miR-200b-3p, miR-200c-3p, miR-375-3p, miR-429, miR-545-5p. These miRNAs have targets with a previously reported role in PC. In conclusion, we show the feasibility of the proposed approach to identify EV-derived biomarkers with predictive value for therapy with gemcitabine + nab-paclitaxel in PC. Our findings highlight the possibility to exploit liquid biopsy for personalized treatment in PC, in order to maximize chances of response and patients’ outcome. These findings are worthy of further investigation: in the same setting, with different chemotherapy schedules, and in different disease settings such as preoperative therapy.

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.

Analysis of optimal control problems for the incompressible MHD equations and implementation in a finite element multiphysics code

This thesis deals with the study of optimal control problems for the incompressible Magnetohydrodynamics (MHD) equations. Particular attention to these problems arises from several applications in science and engineering, such as fission nuclear reactors with liquid metal coolant and aluminum casting in metallurgy. In such applications it is of great interest to achieve the control on the fluid state variables through the action of the magnetic Lorentz force. In this thesis we investigate a class of boundary optimal control problems, in which the flow is controlled through the boundary conditions of the magnetic field. Due to their complexity, these problems present various challenges in the definition of an adequate solution approach, both from a theoretical and from a computational point of view. In this thesis we propose a new boundary control approach, based on lifting functions of the boundary conditions, which yields both theoretical and numerical advantages. With the introduction of lifting functions, boundary control problems can be formulated as extended distributed problems. We consider a systematic mathematical formulation of these problems in terms of the minimization of a cost functional constrained by the MHD equations. The existence of a solution to the flow equations and to the optimal control problem are shown. The Lagrange multiplier technique is used to derive an optimality system from which candidate solutions for the control problem can be obtained. In order to achieve the numerical solution of this system, a finite element approximation is considered for the discretization together with an appropriate gradient-type algorithm. A finite element object-oriented library has been developed to obtain a parallel and multigrid computational implementation of the optimality system based on a multiphysics approach. Numerical results of two- and three-dimensional computations show that a possible minimum for the control problem can be computed in a robust and accurate manner.