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.

Studies of pure rotational spectra of isolated molecules and molecular adducts using pulsed jet Fourier transform microwave (PJ-FTM) spectroscopy

This thesis focuses on studying molecular structure and internal dynamics by using pulsed jet Fourier transform microwave (PJ-FTMW) spectroscopy combined with theoretical calculations. Several kinds of interesting chemical problems are investigated by analyzing the MW spectra of the corresponding molecular systems. First, the general aspects of rotational spectroscopy are summarized, and then the basic theory on molecular rotation and experimental method are described briefly. ab initio and density function theory (DFT) calculations that used in this thesis to assist the assignment of rotational spectrum are also included. From chapter 3 to chapter 8, several molecular systems concerning different kind of general chemical problems are presented. In chapter 3, the conformation and internal motions of dimethyl sulfate are reported. The internal rotations of the two methyl groups split each rotational transition into several components line, allowing for the determination of accurate values of the V3 barrier height to internal rotation and of the orientation of the methyl groups with respect to the principal axis system. In chapter 4 and 5, the results concerning two kinds of carboxylic acid bi-molecules, formed via two strong hydrogen bonds, are presented. This kind of adduct is interesting also because a double proton transfer can easily take place, connecting either two equivalent or two non-equivalent molecular conformations. Chapter 6 concerns a medium strong hydrogen bonded molecular complex of alcohol with ether. The dimer of ethanol-dimethylether was chosen as the model system for this purpose. Chapter 7 focuses on weak halogen…H hydrogen bond interaction. The nature of O-H…F and C-H…Cl interaction has been discussed through analyzing the rotational spectra of CH3CHClF/H2O. In chapter 8, two molecular complexes concerning the halogen bond interaction are presented.

New computational biology tools for the systematic analysis of the structure and expression of human genes

From the late 1980s, the automation of sequencing techniques and the computer spread gave rise to a flourishing number of new molecular structures and sequences and to proliferation of new databases in which to store them. Here are presented three computational approaches able to analyse the massive amount of publicly avalilable data in order to answer to important biological questions. The first strategy studies the incorrect assignment of the first AUG codon in a messenger RNA (mRNA), due to the incomplete determination of its 5' end sequence. An extension of the mRNA 5' coding region was identified in 477 in human loci, out of all human known mRNAs analysed, using an automated expressed sequence tag (EST)-based approach. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 and the consequences for the functional studies are discussed. The second approach analyses the codon bias, the phenomenon in which distinct synonymous codons are used with different frequencies, and, following integration with a gene expression profile, estimates the total number of codons present across all the expressed mRNAs (named here "codonome value") in a given biological condition. Systematic analyses across different pathological and normal human tissues and multiple species shows a surprisingly tight correlation between the codon bias and the codonome bias. The third approach is useful to studies the expression of human autism spectrum disorder (ASD) implicated genes. ASD implicated genes sharing microRNA response elements (MREs) for the same microRNA are co-expressed in brain samples from healthy and ASD affected individuals. The different expression of a recently identified long non coding RNA which have four MREs for the same microRNA could disrupt the equilibrium in this network, but further analyses and experiments are needed.

Biochemistry in healthy and neoplastic human tissues: metabolic alteration revealed by HR-MAS nuclear magnetic resonance spectroscopy

This thesis is focused on the metabolomic study of human cancer tissues by ex vivo High Resolution-Magic Angle Spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy. This new technique allows for the acquisition of spectra directly on intact tissues (biopsy or surgery), and it has become very important for integrated metabonomics studies. The objective is to identify metabolites that can be used as markers for the discrimination of the different types of cancer, for the grading, and for the assessment of the evolution of the tumour. Furthermore, an attempt to recognize metabolites, that although involved in the metabolism of tumoral tissues in low concentration, can be important modulators of neoplastic proliferation, was performed. In addition, NMR data was integrated with statistical techniques in order to obtain semi-quantitative information about the metabolite markers. In the case of gliomas, the NMR study was correlated with gene expression of neoplastic tissues. Chapter 1 begins with a general description of a new “omics” study, the metabolomics. The study of metabolism can contribute significantly to biomedical research and, ultimately, to clinical medical practice. This rapidly developing discipline involves the study of the metabolome: the total repertoire of small molecules present in cells, tissues, organs, and biological fluids. Metabolomic approaches are becoming increasingly popular in disease diagnosis and will play an important role on improving our understanding of cancer mechanism. Chapter 2 addresses in more detail the basis of NMR Spectroscopy, presenting the new HR-MAS NMR tool, that is gaining importance in the examination of tumour tissues, and in the assessment of tumour grade. Some advanced chemometric methods were used in an attempt to enhance the interpretation and quantitative information of the HR-MAS NMR data are and presented in chapter 3. Chemometric methods seem to have a high potential in the study of human diseases, as it permits the extraction of new and relevant information from spectroscopic data, allowing a better interpretation of the results. Chapter 4 reports results obtained from HR-MAS NMR analyses performed on different brain tumours: medulloblastoma, meningioms and gliomas. The medulloblastoma study is a case report of primitive neuroectodermal tumor (PNET) localised in the cerebellar region by Magnetic Resonance Imaging (MRI) in a 3-year-old child. In vivo single voxel 1H MRS shows high specificity in detecting the main metabolic alterations in the primitive cerebellar lesion; which consist of very high amounts of the choline-containing compounds and of very low levels of creatine derivatives and N-acetylaspartate. Ex vivo HR-MAS NMR, performed at 9.4 Tesla on the neoplastic specimen collected during surgery, allows the unambiguous identification of several metabolites giving a more in-depth evaluation of the metabolic pattern of the lesion. The ex vivo HR-MAS NMR spectra show higher detail than that obtained in vivo. In addition, the spectroscopic data appear to correlate with some morphological features of the medulloblastoma. The present study shows that ex vivo HR-MAS 1H NMR is able to strongly improve the clinical possibility of in vivo MRS and can be used in conjunction with in vivo spectroscopy for clinical purposes. Three histological subtypes of meningiomas (meningothelial, fibrous and oncocytic) were analysed both by in vivo and ex vivo MRS experiments. The ex vivo HR-MAS investigations are very helpful for the assignment of the in vivo resonances of human meningiomas and for the validation of the quantification procedure of in vivo MR spectra. By using one- and two dimensional experiments, several metabolites in different histological subtypes of meningiomas, were identified. The spectroscopic data confirmed the presence of the typical metabolites of these benign neoplasms and, at the same time, that meningomas with different morphological characteristics have different metabolic profiles, particularly regarding macromolecules and lipids. The profile of total choline metabolites (tCho) and the expression of the Kennedy pathway genes in biopsies of human gliomas were also investigated using HR-MAS NMR, and microfluidic genomic cards. 1H HR-MAS spectra, allowed the resolution and relative quantification by LCModel of the resonances from choline (Cho), phosphorylcholine (PC) and glycerolphorylcholine (GPC), the three main components of the combined tCho peak observed in gliomas by in vivo 1H MRS spectroscopy. All glioma biopsies depicted an increase in tCho as calculated from the addition of Cho, PC and GPC HR-MAS resonances. However, the increase was constantly derived from augmented GPC in low grade NMR gliomas or increased PC content in the high grade gliomas, respectively. This circumstance allowed the unambiguous discrimination of high and low grade gliomas by 1H HR-MAS, which could not be achieved by calculating the tCho/Cr ratio commonly used by in vivo 1H MR spectroscopy. The expression of the genes involved in choline metabolism was investigated in the same biopsies. The present findings offer a convenient procedure to classify accurately glioma grade using 1H HR-MAS, providing in addition the genetic background for the alterations of choline metabolism observed in high and low gliomas grade. Chapter 5 reports the study on human gastrointestinal tract (stomach and colon) neoplasms. The human healthy gastric mucosa, and the characteristics of the biochemical profile of human gastric adenocarcinoma in comparison with that of healthy gastric mucosa were analyzed using ex vivo HR-MAS NMR. Healthy human mucosa is mainly characterized by the presence of small metabolites (more than 50 identified) and macromolecules. The adenocarcinoma spectra were dominated by the presence of signals due to triglycerides, that are usually very low in healthy gastric mucosa. The use of spin-echo experiments enable us to detect some metabolites in the unhealthy tissues and to determine their variation with respect to the healthy ones. Then, the ex vivo HR-MAS NMR analysis was applied to human gastric tissue, to obtain information on the molecular steps involved in the gastric carcinogenesis. A microscopic investigation was also carried out in order to identify and locate the lipids in the cellular and extra-cellular environments. Correlation of the morphological changes detected by transmission (TEM) and scanning (SEM) electron microscopy, with the metabolic profile of gastric mucosa in healthy, gastric atrophy autoimmune diseases (AAG), Helicobacter pylori-related gastritis and adenocarcinoma subjects, were obtained. These ultrastructural studies of AAG and gastric adenocarcinoma revealed lipid intra- and extra-cellularly accumulation associated with a severe prenecrotic hypoxia and mitochondrial degeneration. A deep insight into the metabolic profile of human healthy and neoplastic colon tissues was gained using ex vivo HR-MAS NMR spectroscopy in combination with multivariate methods: Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA). The NMR spectra of healthy tissues highlight different metabolic profiles with respect to those of neoplastic and microscopically normal colon specimens (these last obtained at least 15 cm far from the adenocarcinoma). Furthermore, metabolic variations are detected not only for neoplastic tissues with different histological diagnosis, but also for those classified identical by histological analysis. These findings suggest that the same subclass of colon carcinoma is characterized, at a certain degree, by metabolic heterogeneity. The statistical multivariate approach applied to the NMR data is crucial in order to find metabolic markers of the neoplastic state of colon tissues, and to correctly classify the samples. Significant different levels of choline containing compounds, taurine and myoinositol, were observed. Chapter 6 deals with the metabolic profile of normal and tumoral renal human tissues obtained by ex vivo HR-MAS NMR. The spectra of human normal cortex and medulla show the presence of differently distributed osmolytes as markers of physiological renal condition. The marked decrease or disappearance of these metabolites and the high lipid content (triglycerides and cholesteryl esters) is typical of clear cell renal carcinoma (RCC), while papillary RCC is characterized by the absence of lipids and very high amounts of taurine. This research is a contribution to the biochemical classification of renal neoplastic pathologies, especially for RCCs, which can be evaluated by in vivo MRS for clinical purposes. Moreover, these data help to gain a better knowledge of the molecular processes envolved in the onset of renal carcinogenesis.

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.

Architettura delle centrali idroelettriche italiane 1910-1940. L'esperienza di Giovanni Muzio e Piero Portaluppi

Oggetto della ricerca è il tema dello spazio delle centrali idroelettriche costruite nella prima metà del Novecento dagli architetti Giovanni Muzio e Piero Portaluppi. L’individuazione del tema sorge dalla volontà di indagare quali siano stati gli sviluppi dal punto di vista architettonico all’interno di un genere così specifico durante un periodo di tempo in cui gli stili architettonici e le tendenze hanno subito stravolgimenti ed evoluzioni che ancora oggi trovano una difficile connotazione e definizione precisa. L’analisi dell’architettura delle centrali idroelettriche, effettuata ripercorrendo le principali vicende del settore idroelettrico dalla fine del secolo scorso al secondo dopoguerra, oltre a considerare il rapporto con il contesto territoriale e culturale del nostro Paese vuole prendere in considerazione anche il particolare rapporto che in più casi si è venuto a creare tra committenti e progettisti. Compito della tesi è rileggere un settore poco indagato finora e capire se vi sia stata effettivamente una evoluzione architettonica dal punto di vista tipologico o se la centrale sia stata sempre affrontata come semplice esercizio di “vestizione” di un involucro precostituito da precise esigenze tecniche. La ricerca infatti si pone come obiettivo lo studio delle centrali non solo dal punto di vista tipologico e spaziale dei suoi principali elementi, ma si pone come obiettivo anche lo studio della loro distribuzione nel sito in cui sono sorte, distribuzione che spesso ha portato alla formazione di una sorta di vera e propria “città elettrica”, in cui la composizione dei vari elementi segue una logica compositiva ben precisa. Dal punto di vista del contributo originale la ricerca vuole proporre una serie di riflessioni ed elaborati inerenti alcune centrali non ancora indagate. Nel caso specifico di Portaluppi l’apporto originale consiste nell’aver portato alla luce notizie inerenti centrali che sono sempre state poste in secondo piano rispetto le ben più note e studiate centrali della Val d’Ossola. Nel caso invece di Muzio il contributo consiste in una analisi approfondita e in una comparazione di documenti che di solito sono sempre stati pubblicati come semplice apparato iconografico, ma che messi a confronto danno una lettura di quelle che sono state le fasi e le elaborazioni progettuali apportate dall’autore. Il tema della ricerca è stato affrontato poi attraverso una lettura delle fonti dirette relative agli scritti degli autori, con una contemporanea lettura di testi, articoli e interventi tratti dalle riviste appartenenti al periodo in esame per comprendere al meglio il panorama culturale e architettonico che hanno fatto da scenario alle esperienze di entrambe le figure oggetto di studio. Infine la ricerca si è concentrata sull’analisi di alcune opere in particolare - due centrali idroelettriche per ciascun autore oggetto della tesi - scelte perché considerate rappresentative sia per impianto spaziale e tipologico, sia per le scelte compositive e stilistiche adottate. La lettura dei manufatti architettonici scelti è stata condotta con l’analisi di copie di elaborati grafici originali, foto d’epoca e altri documenti reperiti grazie ad una ricerca condotta in vari archivi. Le centrali scelte nell’ambito delle esperienze maturate da Muzio e Portaluppi sono state individuate per rappresentare il quadro relativo allo sviluppo e alla ricerca di un nuovo linguaggio formale da adottare nell’ambito dell’architettura di questi manufatti. Per entrambi i protagonisti oggetto della ricerca sono state individuate due centrali in grado di dare una visione il più possibile completa dell’evoluzione della tematica delle centrali idroelettriche all’interno della loro esperienza, prendendo in considerazione soprattutto gli aspetti legati all’evoluzione del loro linguaggio compositivo e stilistico. L’individuazione delle centrali da analizzare è stata dettata prendendo in considerazione alcuni fattori come il tipo di impianto, le relazioni e confronto con il contesto geografico e naturale e le soluzioni adottate.

Securitization and Special Purpose Vehicles in an International Setting: a Systemic View

The present work tries to display a comprehensive and comparative study of the different legal and regulatory problems involved in international securitization transactions. First, an introduction to securitization is provided, with the basic elements of the transaction, followed by the different varieties of it, including dynamic securitization and synthetic securitization structures. Together with this introduction to the intricacies of the structure, a insight into the influence of securitization in the financial and economic crisis of 2007-2009 is provided too; as well as an overview of the process of regulatory competition and cooperation that constitutes the framework for the international aspects of securitization. The next Chapter focuses on the aspects that constitute the foundations of structured finance: the inception of the vehicle, and the transfer of risks associated to the securitized assets, with particular emphasis on the validity of those elements, and how a securitization transaction could be threatened at its root. In this sense, special importance is given to the validity of the trust as an instrument of finance, to the assignment of future receivables or receivables in block, and to the importance of formalities for the validity of corporations, trusts, assignments, etc., and the interaction of such formalities contained in general corporate, trust and assignment law with those contemplated under specific securitization regulations. Then, the next Chapter (III) focuses on creditor protection aspects. As such, we provide some insights on the debate on the capital structure of the firm, and its inadequacy to assess the financial soundness problems inherent to securitization. Then, we proceed to analyze the importance of rules on creditor protection in the context of securitization. The corollary is in the rules in case of insolvency. In this sense, we divide the cases where a party involved in the transaction goes bankrupt, from those where the transaction itself collapses. Finally, we focus on the scenario where a substance over form analysis may compromise some of the elements of the structure (notably the limited liability of the sponsor, and/or the transfer of assets) by means of veil piercing, substantive consolidation, or recharacterization theories. Once these elements have been covered, the next Chapters focus on the regulatory aspects involved in the transaction. Chapter IV is more referred to “market” regulations, i.e. those concerned with information disclosure and other rules (appointment of the indenture trustee, and elaboration of a rating by a rating agency) concerning the offering of asset-backed securities to the public. Chapter V, on the other hand, focuses on “prudential” regulation of the entity entrusted with securitizing assets (the so-called Special Purpose vehicle), and other entities involved in the process. Regarding the SPV, a reference is made to licensing requirements, restriction of activities and governance structures to prevent abuses. Regarding the sponsor of the transaction, a focus is made on provisions on sound originating practices, and the servicing function. Finally, we study accounting and banking regulations, including the Basel I and Basel II Frameworks, which determine the consolidation of the SPV, and the de-recognition of the securitized asset from the originating company’s balance-sheet, as well as the posterior treatment of those assets, in particular by banks. Chapters VI-IX are concerned with liability matters. Chapter VI is an introduction to the different sources of liability. Chapter VII focuses on the liability by the SPV and its management for the information supplied to investors, the management of the asset pool, and the breach of loyalty (or fiduciary) duties. Chapter VIII rather refers to the liability of the originator as a result of such information and statements, but also as a result of inadequate and reckless originating or servicing practices. Chapter IX finally focuses on third parties entrusted with the soundness of the transaction towards the market, the so-called gatekeepers. In this respect, we make special emphasis on the liability of indenture trustees, underwriters and rating agencies. Chapters X and XI focus on the international aspects of securitization. Chapter X contains a conflicts of laws analysis of the different aspects of structured finance. In this respect, a study is made of the laws applicable to the vehicle, to the transfer of risks (either by assignment or by means of derivatives contracts), to liability issues; and a study is also made of the competent jurisdiction (and applicable law) in bankruptcy cases; as well as in cases where a substance-over-form is performed. Then, special attention is also devoted to the role of financial and securities regulations; as well as to their territorial limits, and extraterritoriality problems involved. Chapter XI supplements the prior Chapter, for it analyzes the limits to the States’ exercise of regulatory power by the personal and “market” freedoms included in the US Constitution or the EU Treaties. A reference is also made to the (still insufficient) rules from the WTO Framework, and their significance to the States’ recognition and regulation of securitization transactions.

Sostanzialismo e relazionalismo dello spaziotempo alla luce della relatività generale

Until recently the debate on the ontology of spacetime had only a philosophical significance, since, from a physical point of view, General Relativity has been made "immune" to the consequences of the "Hole Argument" simply by reducing the subject to the assertion that solutions of Einstein equations which are mathematically different and related by an active diffeomorfism are physically equivalent. From a technical point of view, the natural reading of the consequences of the "Hole Argument” has always been to go further and say that the mathematical representation of spacetime in General Relativity inevitably contains a “superfluous structure” brought to light by the gauge freedom of the theory. This position of apparent split between the philosophical outcome and the physical one has been corrected thanks to a meticulous and complicated formal analysis of the theory in a fundamental and recent (2006) work by Luca Lusanna and Massimo Pauri entitled “Explaining Leibniz equivalence as difference of non-inertial appearances: dis-solution of the Hole Argument and physical individuation of point-events”. The main result of this article is that of having shown how, from a physical point of view, point-events of Einstein empty spacetime, in a particular class of models considered by them, are literally identifiable with the autonomous degrees of freedom of the gravitational field (the Dirac observables, DO). In the light of philosophical considerations based on realism assumptions of the theories and entities, the two authors then conclude by saying that spacetime point-events have a degree of "weak objectivity", since they, depending on a NIF (non-inertial frame), unlike the points of the homogeneous newtonian space, are plunged in a rich and complex non-local holistic structure provided by the “ontic part” of the metric field. Therefore according to the complex structure of spacetime that General Relativity highlights and within the declared limits of a methodology based on a Galilean scientific representation, we can certainly assert that spacetime has got "elements of reality", but the inevitably relational elements that are in the physical detection of point-events in the vacuum of matter (highlighted by the “ontic part” of the metric field, the DO) are closely dependent on the choice of the global spatiotemporal laboratory where the dynamics is expressed (NIF). According to the two authors, a peculiar kind of structuralism takes shape: the point structuralism, with common features both of the absolutist and substantival tradition and of the relationalist one. The intention of this thesis is that of proposing a method of approaching the problem that is, at least at the beginning, independent from the previous ones, that is to propose an approach based on the possibility of describing the gravitational field at three distinct levels. In other words, keeping the results achieved by the work of Lusanna and Pauri in mind and following their underlying philosophical assumptions, we intend to partially converge to their structuralist approach, but starting from what we believe is the "foundational peculiarity" of General Relativity, which is that characteristic inherent in the elements that constitute its formal structure: its essentially geometric nature as a theory considered regardless of the empirical necessity of the measure theory. Observing the theory of General Relativity from this perspective, we can find a "triple modality" for describing the gravitational field that is essentially based on a geometric interpretation of the spacetime structure. The gravitational field is now "visible" no longer in terms of its autonomous degrees of freedom (the DO), which, in fact, do not have a tensorial and, therefore, nor geometric nature, but it is analyzable through three levels: a first one, called the potential level (which the theory identifies with the components of the metric tensor), a second one, known as the connections level (which in the theory determine the forces acting on the mass and, as such, offer a level of description related to the one that the newtonian gravitation provides in terms of components of the gravitational field) and, finally, a third level, that of the Riemann tensor, which is peculiar to General Relativity only. Focusing from the beginning on what is called the "third level" seems to present immediately a first advantage: to lead directly to a description of spacetime properties in terms of gauge-invariant quantites, which allows to "short circuit" the long path that, in the treatises analyzed, leads to identify the "ontic part” of the metric field. It is then shown how to this last level it is possible to establish a “primitive level of objectivity” of spacetime in terms of the effects that matter exercises in extended domains of spacetime geometrical structure; these effects are described by invariants of the Riemann tensor, in particular of its irreducible part: the Weyl tensor. The convergence towards the affirmation by Lusanna and Pauri that the existence of a holistic, non-local and relational structure from which the properties quantitatively identified of point-events depend (in addition to their own intrinsic detection), even if it is obtained from different considerations, is realized, in our opinion, in the assignment of a crucial role to the degree of curvature of spacetime that is defined by the Weyl tensor even in the case of empty spacetimes (as in the analysis conducted by Lusanna and Pauri). In the end, matter, regarded as the physical counterpart of spacetime curvature, whose expression is the Weyl tensor, changes the value of this tensor even in spacetimes without matter. In this way, going back to the approach of Lusanna and Pauri, it affects the DOs evolution and, consequently, the physical identification of point-events (as our authors claim). In conclusion, we think that it is possible to see the holistic, relational, and non-local structure of spacetime also through the "behavior" of the Weyl tensor in terms of the Riemann tensor. This "behavior" that leads to geometrical effects of curvature is characterized from the beginning by the fact that it concerns extensive domains of the manifold (although it should be pointed out that the values of the Weyl tensor change from point to point) by virtue of the fact that the action of matter elsewhere indefinitely acts. Finally, we think that the characteristic relationality of spacetime structure should be identified in this "primitive level of organization" of spacetime.

Ernesto Nathan Rogers e le preesistenze ambientali. Itinerario teorico, 1948-1964

La tesi indaga il significato del concetto di “preesistenze ambientali” nel pensiero teorico dell’architetto Ernesto Nathan Rogers. Il tema è scelto come punto di vista privilegiato per indagare il contributo di Rogers al dibattito sull’eredità del Movimento Moderno in un momento, il secondo dopoguerra, in cui si intensifica la necessità di soffermare l’attenzione delle riflessioni teoriche sulle relazioni tra ambiente e progetto. Il problema fu inteso come la ricerca di un linguaggio adeguato all’era macchinista e di un ordine formale per lo sviluppo urbano recente da costruire in funzione del suo rapporto con la città consolidata. Esso fu sviluppato, all’interno dell’opera teorica rogersiana, come riflessione sulla dialettica contrapposizione tra intuizione e trasmissione del sapere, contingenza e universalità. La tesi mostra le ricche connessioni culturali tramite cui tale dialettica è capace di animare un discorso unitario che va dall’insegnamento del Movimento Moderno alle ricerche tipologiche e urbane della cultura italiana degli anni Sessanta. Riportando il concetto di preesistenze ambientali alla sua accezione originale, da un lato attraverso la ricostruzione delle relazioni intellettuali instaurate da Rogers con il Movimento Moderno e i CIAM, dall’altro mediante l’approfondimento del progetto editoriale costruito durante la direzione della rivista “Casabella continuità”, la tesi intende conferire alla nozione il valore di un contributo importante alla teoria della progettazione architettonica urbana. Il concetto di preesistenze ambientali diventa così la chiave analitica per indagare, in particolare, l’influenza del dibattito dell’VIII CIAM su Il Cuore della città e della partecipazione di Rogers al lavoro di redazione dell’Estudio del Plan di Buenos Aires nel 1948-1949 nella maturazione del progetto editoriale di “Casabella continuità” (1954-1965) attraverso l’attribuzione di un preciso valore all’archetipo, alla fenomenologia e alla tradizione nella definizione del rapporto architettura e storia.

Le opere di urbanizzazione a scomputo degli oneri

Le considerazioni sviluppate in questo scritto si pongono come obiettivo quello di fare chiarezza sul delicato tema delle opere di urbanizzazione a scomputo. La normativa concernente la realizzazione delle opere pubbliche a scomputo totale o parziale degli oneri di urbanizzazione è stata oggetto di svariate modifiche e interpretazioni giurisprudenziali, che si sono susseguite dopo l'importante pronuncia della Corte di Giustizia Europea. E' con questa sentenza che i Giudici del Kirchberg introducono un particolare obbligo procedurale a carico dei privati: nel caso in cui singole opere superino i valori di rilevanza europea, esse devono essere affidate, applicando le procedure di gara previste dalla direttiva 37/93/CEE. Va precisato che sino a quel momento l'affidamento diretto delle opere al privato costituiva nell'ottica del Legislatore lo strumento per realizzare le infrastrutture necessarie per consentire gli insediamenti edilizi che la pubblica amministrazione spesso non era in grado di effettuare. In questo panorama legislativo la sentenza della Corte di Giustizia, appare del tutto dirompente. Infatti, introducendo il principio secondo cui anche la realizzazione diretta delle opere di urbanizzazione da parte del privato deve sottostare alle regole delle procedure europee in materia di appalti, mette inevitabilmente a confronto due normative, quella degli appalti pubblici e quella dell'urbanistica, che sino a quel momento erano riuscite a viaggiare in modo parallelo, senza dar luogo a reciproche sovrapposizioni. Il Legislatore nazionale ha, con molta fatica, recepito il principio comunitario ed è stato negli anni quasi costretto, attraverso una serie di modifiche legislative, ad ampliarne la portata. La presente ricerca, dopo aver analizzato i vari correttivi apportati al Codice degli appalti pubblici vuole, quindi, verificare se l'attuale quadro normativo rappresenti un vero punto di equilibrio tra le contrapposte esigenze di pianificazione del territorio e di rispetto dei principi comunitari di concorrenza nella scelta del contraente.

Daniello Bartoli, Il Giappone, Edizione critica

La tesi di ricerca ha portato alla realizzazione di un’edizione critica del Giappone di Daniello Bartoli (1660): per la prima volta la «seconda parte» dell’Asia trova, in questo lavoro, una trascrizione integrale condotta con moderni criteri filologi. Quanto all’esegesi la ricerca ha visto la compilazione di tre «Schedari»: un «Indice dei nomi», che vede l’identificazione dei personaggi storici citati esplicitamente nell’opera, ne traccia un rapido profilo biografico e ne fornisce precisa e aggiornata bibliografia. Per quanto riguarda i missionari evocati dall’autore nel testo, questa sezione indica se (e dove) si tratta di personaggio o di fonte (registrando, nel caso, il luogo o i luoghi in cui Bartoli ricorre a tale testimonianza); un «Indice dei luoghi», che dà l’indicazione moderna del luogo citato e ne fornisce il riscontro con i repertori più aggiornati; un «Lessico» riservato ai termini giapponesi presenti nel testo che vengono spiegati e, là dove possibile, studiati nella loro storia, nella loro presenza nella coeva letteratura di viaggio e corredati di utili riferimenti bibliografici. Le pagine introduttive inquadrano l’opera di Bartoli sia nell’orizzonte biografico dell’autore sia nel milieu gesuitico barocco, fornendo puntuali coordinate storiche grazie alle quali recuperare il più ampio contesto delle missioni gesuitiche nell’Estremo Oriente tra Cinque e Seicento. Particolare attenzione è stata riservata al modo di intendere il compito dello storico da parte di Bartoli: una storiografia la sua che s’intreccia in modi affatto peculiari alle diverse forme stilistiche e dinamiche retoriche richieste dalle altre due grandi attività a cui egli dedicò impegno e passione: l’insegnamento e la predicazione.

Essays in structural heuristics

This dissertation introduces and develops a new method of rational reconstruction called structural heuristics. Structural heuristics takes assignment of structure to any given object of investigation as the starting point for its rational reconstruction. This means to look at any given object as a system of relations and of transformation laws for those relations. The operational content of this heuristics can be summarized as follows: when facing any given system the best way to approach it is to explicitly look for a possible structure of it. The utilization of structural heuristics allows structural awareness, which is considered a fundamental epistemic disposition, as well as a fundamental condition for the rational reconstruction of systems of knowledge. In this dissertation, structural heuristics is applied to reconstructing the domain of economic knowledge. This is done by exploring four distinct areas of economic research: (i) economic axiomatics; (ii) realism in economics; (iii) production theory; (iv) economic psychology. The application of structural heuristics to these fields of economic inquiry shows the flexibility and potential of structural heuristics as epistemic tool for theoretical exploration and reconstruction.