De Novo Design of secondary structures: Synthesis and conformational studies

Chemists have long sought to extrapolate the power of biological catalysis and recognition to synthetic systems. These efforts have focused largely on low molecular weight catalysts and receptors; however, biological systems themselves rely almost exclusively on polymers, proteins and RNA, to perform complex chemical functions. Proteins and RNA are unique in their ability to adopt compact, well-ordered conformations, and specific folding provides precise spatial orientation of the functional groups that comprise the “active site”. These features suggest that identification of new polymer backbones with discrete and predictable folding propensities (“foldamers”) will provide a basis for design of molecular machines with unique capabilities. The foldamer approach complements current efforts to design unnatural properties into polypeptides and polynucleotides. The aim of this thesis is the synthesis and conformational studies of new classes of foldamers, using a peptidomimetic approach. Moreover their attitude to be utilized as ionophores, catalysts, and nanobiomaterials were analyzed in solution and in the solid state. This thesis is divided in thematically chapters that are reported below. It begins with a very general introduction (page 4) which is useful, but not strictly necessary, to the expert reader. It is worth mentioning that paragraph I.3 (page 22) is the starting point of this work and paragraph I.5 (page 32) isrequired to better understand the results of chapters 4 and 5. In chapter 1 (page 39) is reported the synthesis and conformational analysis of a novel class of foldamers containing (S)-β3-homophenylglycine [(S)-β3-hPhg] and D- 4-carboxy-oxazolidin-2-one (D-Oxd) residues in alternate order is reported. The experimental conformational analysis performed in solution by IR, 1HNMR, and CD spectroscopy unambiguously proved that these oligomers fold into ordered structures with increasing sequence length. Theoretical calculations employing ab initio MO theory suggest a helix with 11-membered hydrogenbonded rings as the preferred secondary structure type. The novel structures enrich the field of peptidic foldamers and might be useful in the mimicry of native peptides. In chapter 2 cyclo-(L-Ala-D-Oxd)3 and cyclo-(L-Ala-DOxd) 4 were prepared in the liquid phase with good overall yields and were utilized for bivalent ions chelation (Ca2+, Mg2+, Cu2+, Zn2+ and Hg2+); their chelation skill was analyzed with ESI-MS, CD and 1HNMR techniques and the best results were obtained with cyclo-(L-Ala-D-Oxd)3 and Mg2+ or Ca2+. Chapter 3 describes an application of oligopeptides as catalysts for aldol reactions. Paragraph 3.1 concerns the use of prolinamides as catalysts of the cross aldol addition of hydroxyacetone to aromatic aldeydes, whereas paragraphs 3.2 and 3.3 are about the catalyzed aldol addition of acetone to isatins. By means of DFT and AIM calculations, the steric and stereoelectronic effects that control the enantioselectivity in the cross-aldol addition of acetone to isatin catalysed by L-proline have been studied, also in the presence of small quantities of water. In chapter 4 is reported the synthesis and the analysis of a new fiber-like material, obtained from the selfaggregation of the dipeptide Boc-L-Phe-D-Oxd-OBn, which spontaneously forms uniform fibers consisting of parallel infinite linear chains arising from singleintermolecular N-H···O=C hydrogen bonds. This is the absolute borderline case of a parallel β-sheet structure. Longer oligomers of the same series with general formula Boc-(L-Phe-D-Oxd)n-OBn (where n = 2-5), are described in chapter 5. Their properties in solution and in the solid state were analyzed, in correlation with their attitude to form intramolecular hydrogen bond. In chapter 6 is reported the synthesis of imidazolidin-2- one-4-carboxylate and (tetrahydro)-pyrimidin-2-one-5- carboxylate, via an efficient modification of the Hofmann rearrangement. The reaction affords the desired compounds from protected asparagine or glutamine in good to high yield, using PhI(OAc)2 as source of iodine(III).

Electrochemistry of carbon based engineered structures

The main aims of my PhD research work have been the investigation of the redox, photophysical and electronic properties of carbon nanotubes (CNT) and their possible uses as functional substrates for the (electro)catalytic production of oxygen and as molecular connectors for Quantum-dot Molecular Automata. While for CNT many and diverse applications in electronics, in sensors and biosensors field, as a structural reinforcing in composite materials have long been proposed, the study of their properties as individual species has been for long a challenging task. CNT are in fact virtually insoluble in any solvent and, for years, most of the studies has been carried out on bulk samples (bundles). In Chapter 2 an appropriate description of carbon nanotubes is reported, about their production methods and the functionalization strategies for their solubilization. In Chapter 3 an extensive voltammetric and vis-NIR spectroelectrochemical investigation of true solutions of unfunctionalized individual single wall CNT (SWNT) is reported that permitted to determine for the first time the standard electrochemical potentials of reduction and oxidation as a function of the tube diameter of a large number of semiconducting SWNTs. We also established the Fermi energy and the exciton binding energy for individual tubes in solution and, from the linear correlation found between the potentials and the optical transition energies, one to calculate the redox potentials of SWNTs that are insufficiently abundant or absent in the samples. In Chapter 4 we report on very efficient and stable nano-structured, oxygen-evolving anodes (OEA) that were obtained by the assembly of an oxygen evolving polyoxometalate cluster, (a totally inorganic ruthenium catalyst) with a conducting bed of multiwalled carbon nanotubes (MWCNT). Here, MWCNT were effectively used as carrier of the polyoxometallate for the electrocatalytic production of oxygen and turned out to greatly increase both the efficiency and stability of the device avoiding the release of the catalysts. Our bioinspired electrode addresses the major challenge of artificial photosynthesis, i.e. efficient water oxidation, taking us closer to when we might power the planet with carbon-free fuels. In Chapter 5 a study on surface-active chiral bis-ferrocenes conveniently designed in order to act as prototypical units for molecular computing devices is reported. Preliminary electrochemical studies in liquid environment demonstrated the capability of such molecules to enter three indistinguishable oxidation states. Side chains introduction allowed to organize them in the form of self-assembled monolayers (SAM) onto a surface and to study the molecular and redox properties on solid substrates. Electrochemical studies on SAMs of these molecules confirmed their attitude to undergo fast (Nernstian) electron transfer processes generating, in the positive potential region, either the full oxidized Fc+-Fc+ or the partly oxidized Fc+-Fc species. Finally, in Chapter 6 we report on a preliminary electrochemical study of graphene solutions prepared according to an original procedure recently described in the literature. Graphene is the newly-born of carbon nanomaterials and is certainly bound to be among the most promising materials for the next nanoelectronic generation.

Studio di alcuni tratti del temperamento nel cane

Il temperamento può essere definito come l’attitudine che un cane esprime verso le persone e verso altri animali, la combinazione di tratti fisici e mentali, acquisiti e non, che determinano il comportamento del cane. Tale parametro delinea perciò il carattere di un individuo, inclinazioni e tendenze, eccitabilità, tristezza, rabbia e il modo caratteristico di comportarsi di un individuo, con particolare riferimento alle interazioni sociali. La presente tesi di Dottorato rappresenta uno studio su alcuni tratti del temperamento nel cane domestico elaborato in 3 progetti sperimentali. Nei primi due progetti sono state analizzate le differenze attitudinali tra alcune razze canine attraverso l’applicazione di un test di temperamento in cuccioli di 60 giorni e in cani adulti, per valutare e confrontarne il temperamento, la socialità ed identificare profili tipici di razza. Nel terzo progetto un campione di cani morsicatori di canile e di proprietà è stato confrontato con due rispettivi gruppi di controllo. Analizzando i risultati è stato possibile mettere in evidenza caratteristiche di razza omogenee nell’interazione con stimoli inanimati, nelle interazioni sociali e in relazione alla possessività e sono stati delineati profili di razza sia nei cuccioli sia negli adulti. Si sono tuttavia, osservate variabilità individuali, intra-razza e intra-cucciolata, a testimonianza dell’influenza complessa e multifattoriale delle componenti genetica e ambientale sul comportamento dei cani. Il confronto tra cani morsicatori di canile e di proprietà ha messo in luce interessanti differenze tra i soggetti in termini di reattività, socievolezza, propensione all’interazione con il proprietario o con un estraneo, comportamenti di evitamento e velocità di reazione agli stimoli presentati. Il test applicato è risultato un valido strumento per valutare il temperamento di cani dichiarati aggressivi che sono stati sottoposti a situazioni nuove e a stimoli sconosciuti per poter ottenere una migliore visione d’insieme del temperamento del soggetto.

Nonlinear Approaches to Attitude Control Using Magnetic and Mechanical Actuation

This thesis argues the attitude control problem of nanosatellites, which has been a challenging issue over the years for the scientific community and still constitutes an active area of research. The interest is increasing as more than 70% of future satellite launches are nanosatellites. Therefore, new challenges appear with the miniaturisation of the subsystems and improvements must be reached. In this framework, the aim of this thesis is to develop novel control approaches for three-axis stabilisation of nanosatellites equipped with magnetorquers and reaction wheels, to improve the performance of the existent control strategies and demonstrate the stability of the system. In particular, this thesis is focused on the development of non-linear control techniques to stabilise full-actuated nanosatellites, and in the case of underactuation, in which the number of control variables is less than the degrees of freedom of the system. The main contributions are, for the first control strategy proposed, to demonstrate global asymptotic stability derived from control laws that stabilise the system in a target frame, a fixed direction of the orbit frame. Simulation results show good performance, also in presence of disturbances, and a theoretical selection of the magnetic control gain is given. The second control approach presents instead, a novel stable control methodology for three-axis stabilisation in underactuated conditions. The control scheme consists of the dynamical implementation of an attitude manoeuvre planning by means of a switching control logic. A detailed numerical analysis of the control law gains and the effect on the convergence time, total integrated and maximum torque is presented demonstrating the good performance and robustness also in the presence of disturbances.

Monitoring Complex Processes to Verify System Conformance: A Declarative Rule-Based Framework

Over the last 60 years, computers and software have favoured incredible advancements in every field. Nowadays, however, these systems are so complicated that it is difficult – if not challenging – to understand whether they meet some requirement or are able to show some desired behaviour or property. This dissertation introduces a Just-In-Time (JIT) a posteriori approach to perform the conformance check to identify any deviation from the desired behaviour as soon as possible, and possibly apply some corrections. The declarative framework that implements our approach – entirely developed on the promising open source forward-chaining Production Rule System (PRS) named Drools – consists of three components: 1. a monitoring module based on a novel, efficient implementation of Event Calculus (EC), 2. a general purpose hybrid reasoning module (the first of its genre) merging temporal, semantic, fuzzy and rule-based reasoning, 3. a logic formalism based on the concept of expectations introducing Event-Condition-Expectation rules (ECE-rules) to assess the global conformance of a system. The framework is also accompanied by an optional module that provides Probabilistic Inductive Logic Programming (PILP). By shifting the conformance check from after execution to just in time, this approach combines the advantages of many a posteriori and a priori methods proposed in literature. Quite remarkably, if the corrective actions are explicitly given, the reactive nature of this methodology allows to reconcile any deviations from the desired behaviour as soon as it is detected. In conclusion, the proposed methodology brings some advancements to solve the problem of the conformance checking, helping to fill the gap between humans and the increasingly complex technology.

Fault detection, diagnosis and active fault tolerant control for a satellite attitude control system

Modern control systems are becoming more and more complex and control algorithms more and more sophisticated. Consequently, Fault Detection and Diagnosis (FDD) and Fault Tolerant Control (FTC) have gained central importance over the past decades, due to the increasing requirements of availability, cost efficiency, reliability and operating safety. This thesis deals with the FDD and FTC problems in a spacecraft Attitude Determination and Control System (ADCS). Firstly, the detailed nonlinear models of the spacecraft attitude dynamics and kinematics are described, along with the dynamic models of the actuators and main external disturbance sources. The considered ADCS is composed of an array of four redundant reaction wheels. A set of sensors provides satellite angular velocity, attitude and flywheel spin rate information. Then, general overviews of the Fault Detection and Isolation (FDI), Fault Estimation (FE) and Fault Tolerant Control (FTC) problems are presented, and the design and implementation of a novel diagnosis system is described. The system consists of a FDI module composed of properly organized model-based residual filters, exploiting the available input and output information for the detection and localization of an occurred fault. A proper fault mapping procedure and the nonlinear geometric approach are exploited to design residual filters explicitly decoupled from the external aerodynamic disturbance and sensitive to specific sets of faults. The subsequent use of suitable adaptive FE algorithms, based on the exploitation of radial basis function neural networks, allows to obtain accurate fault estimations. Finally, this estimation is actively exploited in a FTC scheme to achieve a suitable fault accommodation and guarantee the desired control performances. A standard sliding mode controller is implemented for attitude stabilization and control. Several simulation results are given to highlight the performances of the overall designed system in case of different types of faults affecting the ADCS actuators and sensors.

Exploring Quantum Speed-up Through Cluster-state Computers

The aim of this thesis is to investigate the nature of quantum computation and the question of the quantum speed-up over classical computation by comparing two different quantum computational frameworks, the traditional quantum circuit model and the cluster-state quantum computer. After an introductory survey of the theoretical and epistemological questions concerning quantum computation, the first part of this thesis provides a presentation of cluster-state computation suitable for a philosophical audience. In spite of the computational equivalence between the two frameworks, their differences can be considered as structural. Entanglement is shown to play a fundamental role in both quantum circuits and cluster-state computers; this supports, from a new perspective, the argument that entanglement can reasonably explain the quantum speed-up over classical computation. However, quantum circuits and cluster-state computers diverge with regard to one of the explanations of quantum computation that actually accords a central role to entanglement, i.e. the Everett interpretation. It is argued that, while cluster-state quantum computation does not show an Everettian failure in accounting for the computational processes, it threatens that interpretation of being not-explanatory. This analysis presented here should be integrated in a more general work in order to include also further frameworks of quantum computation, e.g. topological quantum computation. However, what is revealed by this work is that the speed-up question does not capture all that is at stake: both quantum circuits and cluster-state computers achieve the speed-up, but the challenges that they posit go besides that specific question. Then, the existence of alternative equivalent quantum computational models suggests that the ultimate question should be moved from the speed-up to a sort of “representation theorem” for quantum computation, to be meant as the general goal of identifying the physical features underlying these alternative frameworks that allow for labelling those frameworks as “quantum computation”.

Numerical assessment of the water injection application to GDI engines

A possible future scenario for the water injection (WI) application has been explored as an advanced strategy for modern GDI engines. The aim is to verify whether the PWI (Port Water Injection) and DWI (Direct Water Injection) architectures can replace current fuel enrichment strategies to limit turbine inlet temperatures (TiT) and knock engine attitude. In this way, it might be possible to extend the stoichiometric mixture condition over the entire engine map, meeting possible future restrictions in the use of AES (Auxiliary Emission Strategies) and future emission limitations. The research was first addressed through a comprehensive assessment of the state-of-the-art of the technology and the main effects of the chemical-physical water properties. Then, detailed chemical kinetics simulations were performed in order to compute the effects of WI on combustion development and auto-ignition. The latter represents an important methodology step for accurate numerical combustion simulations. The water injection was then analysed in detail for a PWI system, through an experimental campaign for macroscopic and microscopic injector characterization inside a test chamber. The collected data were used to perform a numerical validation of the spray models, obtaining an excellent matching in terms of particle size and droplet velocity distributions. Finally, a wide range of three-dimensional CFD simulations of a virtual high-bmep engine were realized and compared, exploring also different engine designs and water/fuel injection strategies under non-reacting and reacting flow conditions. According to the latter, it was found that thanks to the introduction of water, for both PWI and DWI systems, it could be possible to obtain an increase of the target performance and an optimization of the bsfc (Break Specific Fuel Consumption), lowering the engine knock risk at the same time, while the TiT target has been achieved hardly only for one DWI configuration.

A double chance to investigate populist influence: The Five Star Movement.

In the last decade, new kinds of European populist parties and movements characterized by a left wing, right wing or “eclectic” attitude have succeeded in entering in governments where they could exert a direct populist influence on their coalition partners or, conversely, become victims themselves of the influence of the institutional background. Such a scenario brought this research to formulate two questions: (i) “To what extent did populist parties succeed in influencing their government coalition partners, leading them to adopt populist rhetoric and change their policy positions?” and (ii) “Have populist parties been able to retain their populist “outside mainstream politics” identity, or have they been assimilated to mainstream parties?”. As a case study this project chose the Italian Five Star Movement. Since 2018 this eclectic populist actor has experienced three different governments first with the radical right wing populist League (2018-2019) and then with the mainstream center left Democratic Party (2019-2021). In addition to this, currently the Five Star Movement is a coalition partner of the ongoing Draghi’s government. Theoretically based on the ideological definition of populism (Mudde, 2004), on a new “revised” model of the inclusionary - exclusionary framework to classify populist parties and on a novel definition of “populist influence”,this research made use of both quantitative (bidimensional and text analysis) and qualitative methods (semi-structured interviews) and mainly focuses on the years 2017- 2020.The importance of this study is threefold. First it contributes to the study of populist influence in government in relation to the ideological attachment of the political actors involved. Second, it contributes to understand if populists in power necessarily need to tone down their anti-system character in order to survive. Third, this study introduces conceptual and methodological novelties within the study of populism and populist influence in government.

Simulation of optical observables for space missions to small bodies

The navigation of deep space spacecraft requires accurate measurement of the probe’s state and attitude with respect to a body whose ephemerides may not be known with good accuracy. The heliocentric state of the spacecraft is estimated through radiometric techniques (ranging, Doppler, and Delta-DOR), while optical observables can be introduced to improve the uncertainty in the relative position and attitude with respect to the target body. In this study, we analyze how simulated optical observables affect the estimation of parameters in an orbit determination problem, considering the case of the ESA’s Hera mission towards the binary asteroid system composed of Didymos and Dimorphos. To this extent, a shape model and a photometric function are used to create synthetic onboard camera images. Then, using a stereophotoclinometry technique on some of the simulated images, we create a database of maplets that describe the 3D geometry of the surface around a set of landmarks. The matching of maplets with the simulated images provides the optical observables, expressed as pixel coordinates in the camera frame, which are fed to an orbit determination filter to estimate a certain number of solve-for parameters. The noise introduced in the output optical observables by the image processing can be quantified using as a metric the quality of the residuals, which is used to fine-tune the maplet-matching parameters. In particular, the best results are obtained when using small maplets, with high correlation coefficients and occupation factors.

Development of unsupervised learning methods with applications to life sciences data

Machine Learning makes computers capable of performing tasks typically requiring human intelligence. A domain where it is having a considerable impact is the life sciences, allowing to devise new biological analysis protocols, develop patients’ treatments efficiently and faster, and reduce healthcare costs. This Thesis work presents new Machine Learning methods and pipelines for the life sciences focusing on the unsupervised field. At a methodological level, two methods are presented. The first is an “Ab Initio Local Principal Path” and it is a revised and improved version of a pre-existing algorithm in the manifold learning realm. The second contribution is an improvement over the Import Vector Domain Description (one-class learning) through the Kullback-Leibler divergence. It hybridizes kernel methods to Deep Learning obtaining a scalable solution, an improved probabilistic model, and state-of-the-art performances. Both methods are tested through several experiments, with a central focus on their relevance in life sciences. Results show that they improve the performances achieved by their previous versions. At the applicative level, two pipelines are presented. The first one is for the analysis of RNA-Seq datasets, both transcriptomic and single-cell data, and is aimed at identifying genes that may be involved in biological processes (e.g., the transition of tissues from normal to cancer). In this project, an R package is released on CRAN to make the pipeline accessible to the bioinformatic Community through high-level APIs. The second pipeline is in the drug discovery domain and is useful for identifying druggable pockets, namely regions of a protein with a high probability of accepting a small molecule (a drug). Both these pipelines achieve remarkable results. Lastly, a detour application is developed to identify the strengths/limitations of the “Principal Path” algorithm by analyzing Convolutional Neural Networks induced vector spaces. This application is conducted in the music and visual arts domains.

Physical activity as a tool to improve the quality of life for individuals with hip or knee osteoarthritis

Total hip and knee replacements (THR/TKR) are considered the gold standard surgical treatments for end-stage osteoarthritis (OA), effectively alleviating pain, enhancing joint mobility and quality of life (QoL). Maintaining an active lifestyle and regular physical activity (PA) is crucial for these patients, as it can increase bone density and stability of joint prosthesis. This thesis aims to: (1) systematically review recommendations from healthcare professionals; (2) explore interventions promoting an active lifestyle post-THR and TKR; (3) investigate the primary causes of stiffness post-TKR; (4) design an exercise protocol to enhance QoL post-THR and TKR; (5) evaluate orthopedic surgeons' attitudes toward PA for patients post-THR/TKR; and (6) assess changes in QoL after a specifically designed PA intervention. The initial review revealed consensus on permissible sports activities post-surgery, but few studies addressed interventions targeting PA behaviors. Subsequently, findings highlighted key factors contributing to post-TKR stiffness, including mispositioned components, psychological distress, and obesity. Building on these insights, a PA intervention was implemented, followed by a survey investigating orthopedic surgeons' attitudes towards PA, which demonstrated a general positive attitude. Lastly, a pilot randomized controlled trial demonstrated significant enhancements in QoL, physical function, and clinical outcomes following a three-month adapted PA intervention. Future research should focus on raising awareness among individuals and healthcare professionals, fostering engagement in PA programs, and promoting active lifestyles. PA represents a valuable strategy for mitigating the burden of chronic diseases on society.