Electrochemiluminescence: insights into the mechanisms and nanomaterial-based applications

Biomarkers are biological indicators of human health conditions. Their ultra-sensitive quantification is of paramount importance in clinical monitoring and early disease diagnosis. Biosensors are simple and easy-to-use analytical devices and, in their world, electrochemiluminescence (ECL) is one of the most promising analytical techniques that needs an ever-increasing sensitivity for improving its clinical effectiveness. Scope of this project was the investigation of the ECL generation mechanisms for enhancing the ECL intensity also through the identification of suitable nanostructures. The combination of nanotechnologies, microscopy and ECL has proved to be a very successful strategy to improve the analytical efficiency of ECL in one of its most promising bioanalytical approaches, the bead-based immunoassay. Nanosystems, such as [Ru(bpy)3]2+-dye-doped nanoparticles (DDSNPs) and Bodipy Carbon Nanodots, have been used to improve the sensitivity of ECL techniques thanks to their advantageous and tuneable properties, reaching a signal increase of 750% in DDSNPs-bead-based immunoassay system. In this thesis, an investigation of size and distance effects on the ECL mechanisms was carried out through the innovative combination of ECL microscopy and electrochemical mapping of radicals. It allowed the discovery of an unexpected and highly efficient mechanistic path for ECL generation at small distances from the electrode surface. It was exploited and enhanced through the addition of a branched amine DPIBA to the usual coreactant TPrA solution for enhancing the ECL efficiency until a maximum of 128%. Finally, a beads-based immunoassay and an immunosensor specific for cardiac Troponin I were built exploiting previous results and carbon nanotubes features. They created a conductive layer around beads enhancing the signal by 70% and activating an ECL mechanism unobserved before in such systems. In conclusion, the combination of ECL microscopy and nanotechnology and the deep understanding of the mechanisms responsible for the ECL emission led to a great enhancement in the signal.

QoS-aware architectures, technologies, and middleware for the cloud continuum

The recent trend of moving Cloud Computing capabilities to the Edge of the network is reshaping how applications and their middleware supports are designed, deployed, and operated. This new model envisions a continuum of virtual resources between the traditional cloud and the network edge, which is potentially more suitable to meet the heterogeneous Quality of Service (QoS) requirements of diverse application domains and next-generation applications. Several classes of advanced Internet of Things (IoT) applications, e.g., in the industrial manufacturing domain, are expected to serve a wide range of applications with heterogeneous QoS requirements and call for QoS management systems to guarantee/control performance indicators, even in the presence of real-world factors such as limited bandwidth and concurrent virtual resource utilization. The present dissertation proposes a comprehensive QoS-aware architecture that addresses the challenges of integrating cloud infrastructure with edge nodes in IoT applications. The architecture provides end-to-end QoS support by incorporating several components for managing physical and virtual resources. The proposed architecture features: i) a multilevel middleware for resolving the convergence between Operational Technology (OT) and Information Technology (IT), ii) an end-to-end QoS management approach compliant with the Time-Sensitive Networking (TSN) standard, iii) new approaches for virtualized network environments, such as running TSN-based applications under Ultra-low Latency (ULL) constraints in virtual and 5G environments, and iv) an accelerated and deterministic container overlay network architecture. Additionally, the QoS-aware architecture includes two novel middlewares: i) a middleware that transparently integrates multiple acceleration technologies in heterogeneous Edge contexts and ii) a QoS-aware middleware for Serverless platforms that leverages coordination of various QoS mechanisms and virtualized Function-as-a-Service (FaaS) invocation stack to manage end-to-end QoS metrics. Finally, all architecture components were tested and evaluated by leveraging realistic testbeds, demonstrating the efficacy of the proposed solutions.

Semantic coordination through programmable Tuple spaces

Two of the main features of today complex software systems like pervasive computing systems and Internet-based applications are distribution and openness. Distribution revolves around three orthogonal dimensions: (i) distribution of control|systems are characterised by several independent computational entities and devices, each representing an autonomous and proactive locus of control; (ii) spatial distribution|entities and devices are physically distributed and connected in a global (such as the Internet) or local network; and (iii) temporal distribution|interacting system components come and go over time, and are not required to be available for interaction at the same time. Openness deals with the heterogeneity and dynamism of system components: complex computational systems are open to the integration of diverse components, heterogeneous in terms of architecture and technology, and are dynamic since they allow components to be updated, added, or removed while the system is running. The engineering of open and distributed computational systems mandates for the adoption of a software infrastructure whose underlying model and technology could provide the required level of uncoupling among system components. This is the main motivation behind current research trends in the area of coordination middleware to exploit tuple-based coordination models in the engineering of complex software systems, since they intrinsically provide coordinated components with communication uncoupling and further details in the references therein. An additional daunting challenge for tuple-based models comes from knowledge-intensive application scenarios, namely, scenarios where most of the activities are based on knowledge in some form|and where knowledge becomes the prominent means by which systems get coordinated. Handling knowledge in tuple-based systems induces problems in terms of syntax - e.g., two tuples containing the same data may not match due to differences in the tuple structure - and (mostly) of semantics|e.g., two tuples representing the same information may not match based on a dierent syntax adopted. Till now, the problem has been faced by exploiting tuple-based coordination within a middleware for knowledge intensive environments: e.g., experiments with tuple-based coordination within a Semantic Web middleware (surveys analogous approaches). However, they appear to be designed to tackle the design of coordination for specic application contexts like Semantic Web and Semantic Web Services, and they result in a rather involved extension of the tuple space model. The main goal of this thesis was to conceive a more general approach to semantic coordination. In particular, it was developed the model and technology of semantic tuple centres. It is adopted the tuple centre model as main coordination abstraction to manage system interactions. A tuple centre can be seen as a programmable tuple space, i.e. an extension of a Linda tuple space, where the behaviour of the tuple space can be programmed so as to react to interaction events. By encapsulating coordination laws within coordination media, tuple centres promote coordination uncoupling among coordinated components. Then, the tuple centre model was semantically enriched: a main design choice in this work was to try not to completely redesign the existing syntactic tuple space model, but rather provide a smooth extension that { although supporting semantic reasoning { keep the simplicity of tuple and tuple matching as easier as possible. By encapsulating the semantic representation of the domain of discourse within coordination media, semantic tuple centres promote semantic uncoupling among coordinated components. The main contributions of the thesis are: (i) the design of the semantic tuple centre model; (ii) the implementation and evaluation of the model based on an existent coordination infrastructure; (iii) a view of the application scenarios in which semantic tuple centres seem to be suitable as coordination media.

A clustering method for robust and reliable large scale functional and structural protein sequence annotation

Bioinformatics, in the last few decades, has played a fundamental role to give sense to the huge amount of data produced. Obtained the complete sequence of a genome, the major problem of knowing as much as possible of its coding regions, is crucial. Protein sequence annotation is challenging and, due to the size of the problem, only computational approaches can provide a feasible solution. As it has been recently pointed out by the Critical Assessment of Function Annotations (CAFA), most accurate methods are those based on the transfer-by-homology approach and the most incisive contribution is given by cross-genome comparisons. In the present thesis it is described a non-hierarchical sequence clustering method for protein automatic large-scale annotation, called “The Bologna Annotation Resource Plus” (BAR+). The method is based on an all-against-all alignment of more than 13 millions protein sequences characterized by a very stringent metric. BAR+ can safely transfer functional features (Gene Ontology and Pfam terms) inside clusters by means of a statistical validation, even in the case of multi-domain proteins. Within BAR+ clusters it is also possible to transfer the three dimensional structure (when a template is available). This is possible by the way of cluster-specific HMM profiles that can be used to calculate reliable template-to-target alignments even in the case of distantly related proteins (sequence identity < 30%). Other BAR+ based applications have been developed during my doctorate including the prediction of Magnesium binding sites in human proteins, the ABC transporters superfamily classification and the functional prediction (GO terms) of the CAFA targets. Remarkably, in the CAFA assessment, BAR+ placed among the ten most accurate methods. At present, as a web server for the functional and structural protein sequence annotation, BAR+ is freely available at http://bar.biocomp.unibo.it/bar2.0.

Orchestration of multiscale model for computational oncology

Cancer is a challenging disease that involves multiple types of biological interactions in different time and space scales. Often computational modelling has been facing problems that, in the current technology level, is impracticable to represent in a single space-time continuum. To handle this sort of problems, complex orchestrations of multiscale models is frequently done. PRIMAGE is a large EU project that aims to support personalized childhood cancer diagnosis and prognosis. The goal is to do so predicting the growth of the solid tumour using multiscale in-silico technologies. The project proposes an open cloud-based platform to support decision making in the clinical management of paediatric cancers. The orchestration of predictive models is in general complex and would require a software framework that support and facilitate such task. The present work, proposes the development of an updated framework, referred herein as the VPH-HFv3, as a part of the PRIMAGE project. This framework, a complete re-writing with respect to the previous versions, aims to orchestrate several models, which are in concurrent development, using an architecture as simple as possible, easy to maintain and with high reusability. This sort of problem generally requires unfeasible execution times. To overcome this problem was developed a strategy of particularisation, which maps the upper-scale model results into a smaller number and homogenisation which does the inverse way and analysed the accuracy of this approach.

Distributed and synchronized measurements for the wide-area observation of electric power systems in distorted and low-inertia conditions

With the aim of heading towards a more sustainable future, there has been a noticeable increase in the installation of Renewable Energy Sources (RES) in power systems in the latest years. Besides the evident environmental benefits, RES pose several technological challenges in terms of scheduling, operation, and control of transmission and distribution power networks. Therefore, it raised the necessity of developing smart grids, relying on suitable distributed measurement infrastructure, for instance, based on Phasor Measurement Units (PMUs). Not only are such devices able to estimate a phasor, but they can also provide time information which is essential for real-time monitoring. This Thesis falls within this context by analyzing the uncertainty requirements of PMUs in distribution and transmission applications. Concerning the latter, the reliability of PMU measurements during severe power system events is examined, whereas for the first, typical configurations of distribution networks are studied for the development of target uncertainties. The second part of the Thesis, instead, is dedicated to the application of PMUs in low-inertia power grids. The replacement of traditional synchronous machines with inertia-less RES is progressively reducing the overall system inertia, resulting in faster and more severe events. In this scenario, PMUs may play a vital role in spite of the fact that no standard requirements nor target uncertainties are yet available. This Thesis deeply investigates PMU-based applications, by proposing a new inertia index relying only on local measurements and evaluating their reliability in low-inertia scenarios. It also develops possible uncertainty intervals based on the electrical instrumentation currently used in power systems and assesses the interoperability with other devices before and after contingency events.

Synthesis, multiscale-multiphase characterization and applications of thiophene-based biohybrids

Biohybrid derivatives of π-conjugated materials are emerging as powerful tools to study biological events through the (opto)electronic variations of the π-conjugated moieties, as well as to direct and govern the self-assembly properties of the organic materials through the organization principles of the bio component. So far, very few examples of thiophene-based biohybrids have been reported. The aim of this Ph. D thesis has been the development of oligothiophene-oligonucleotide hybrid derivatives as tools, on one side, to detect DNA hybridisation events and, on the other, as model compounds to investigate thiophene-nucleobase interactions in the solid state. To obtain oligothiophene bioconjugates with the required high level of purity, we first developed new synthetic ecofriendly protocols for the synthesis of thiophene oligomers. Our innovative heterogeneous Suzuki coupling methodology, carried out in EtOH/water or isopropanol under microwave irradiation, allowed us to obtain alkyl substituted oligothiophenes and thiophene based co-oligomers in high yields and very short reaction times, free from residual metals and with improved film forming properties. These methodologies were subsequently applied in the synthesis of oligothiophene-oligonucleotide conjugates. Oligothiophene-5-labeled deoxyuridines were synthesized and incorporated into 19-meric oligonucletide sequences. We showed that the oligothiophene-labeled oligonucletide sequences obtained can be used as probes to detect a single nucleotide polymorphism (SNP) in complementary DNA target sequences. In fact, all the probes showed marked variations in emission intensity upon hybridization with a complementary target sequence. The observed variations in emitted light were comparable or even superior to those reported in similar studies, showing that the biohybrids can potentially be useful to develop biosensors for the detection of DNA mismatches. Finally, water-soluble, photoluminescent and electroactive dinucleotide-hybrid derivatives of quaterthiophene and quinquethiophene were synthesized. By means of a combination of spectroscopy and microscopy techniques, electrical characterizations, microfluidic measurements and theoretical calculations, we were able to demonstrate that the self-assembly modalities of the biohybrids in thin films are driven by the interplay of intra and intermolecular interactions in which the π-stacking between the oligothiophene and nucleotide bases plays a major role.

Design and fabrication of MOMS-based ultrasonic probes for minimally invasive endoscopic applications

A Micro-opto-mechanical systems (MOMS) based technology for the fabrication of ultrasonic probes on optical fiber is presented. Thanks to the high miniaturization level reached, the realization of an ultrasonic system constituted by ultrasonic generating and detecting elements, suitable for minimally invasive applications or Non Destructive Evaluation (NDE) of materials at high resolution, is demonstrated. The ultrasonic generation is realized by irradiating a highly absorbing carbon film patterned on silicon micromachined structures with a nanosecond pulsed laser source, generating a mechanical shock wave due to the thermal expansion of the film induced by optical energy conversion into heat. The short duration of the pulsed laser, together with an appropriate emitter design, assure high frequency and wide band ultrasonic generation. The acoustic detection is also realized on a MOMS device using an interferometric receiver, fabricated with a Fabry-Perot optical cavity realized by means of a patterned SU-8 and two Al metallization levels. In order to detect the ultrasonic waves, the cavity is interrogated by a laser beam measuring the reflected power with a photodiode. Various issues related to the design and fabrication of these acoustic probes are investigated in this thesis. First, theoretical models are developed to characterize the opto-acoustic behavior of the devices and estimate their expected acoustic performances. Tests structures are realized to derive the relevant physical parameters of the materials constituting the MOMS devices and determine the conditions theoretically assuring the best acoustic emission and detection performances. Moreover, by exploiting the models and the theoretical results, prototypes of acoustic probes are designed and their fabrication process developed by means of an extended experimental activity.

Thiophene- Based Materials for Photovoltaic Applications

Thiophene oligomers (OTs) and polymers (PTs) are currently attracting remarkable attention as organic materials showing semiconducting, fluorescent, nonlinear optical and liquid crystalline properties. All these properties can be fine-tuned through minor structural modifications. As a consequence, thiophene oligomers and polymers are among the most investigated compounds for applications in organic electronics, optoelectronics and thin film devices such as field effect transistors (FETs), light emitting diodes (LEDs) and photovoltaic devices (PVDs). Our research aims to explore the self-assembly features and the optical, electrical and photovoltaic properties of a class of thiophene based materials so far scarcely investigated, namely that of oligo- and polythiophenes head-to-head substituted with alkyl or S-alkyl chains. In particular, we synthesized these compounds in short reaction times, high yields, high purity and environmentally friendly procedures taking advantage of ultrasound (US) and microwave (MW) enabling technologies in Suzuki-Miyaura cross-couplings.

Design and implementation of a novel multi-constellation FPGA-based dual frequency GNSS receiver for space applications

The PhD activity described in the document is part of the Microsatellite and Microsystem Laboratory of the II Faculty of Engineering, University of Bologna. The main objective is the design and development of a GNSS receiver for the orbit determination of microsatellites in low earth orbit. The development starts from the electronic design and goes up to the implementation of the navigation algorithms, covering all the aspects that are involved in this type of applications. The use of GPS receivers for orbit determination is a consolidated application used in many space missions, but the development of the new GNSS system within few years, such as the European Galileo, the Chinese COMPASS and the Russian modernized GLONASS, proposes new challenges and offers new opportunities to increase the orbit determination performances. The evaluation of improvements coming from the new systems together with the implementation of a receiver that is compatible with at least one of the new systems, are the main activities of the PhD. The activities can be divided in three section: receiver requirements definition and prototype implementation, design and analysis of the GNSS signal tracking algorithms, and design and analysis of the navigation algorithms. The receiver prototype is based on a Virtex FPGA by Xilinx, and includes a PowerPC processor. The architecture follows the software defined radio paradigm, so most of signal processing is performed in software while only what is strictly necessary is done in hardware. The tracking algorithms are implemented as a combination of Phase Locked Loop and Frequency Locked Loop for the carrier, and Delay Locked Loop with variable bandwidth for the code. The navigation algorithm is based on the extended Kalman filter and includes an accurate LEO orbit model.

Constraint based methods for allocation and scheduling of periodic applications

This work presents exact algorithms for the Resource Allocation and Cyclic Scheduling Problems (RA&CSPs). Cyclic Scheduling Problems arise in a number of application areas, such as in hoist scheduling, mass production, compiler design (implementing scheduling loops on parallel architectures), software pipelining, and in embedded system design. The RA&CS problem concerns time and resource assignment to a set of activities, to be indefinitely repeated, subject to precedence and resource capacity constraints. In this work we present two constraint programming frameworks facing two different types of cyclic problems. In first instance, we consider the disjunctive RA&CSP, where the allocation problem considers unary resources. Instances are described through the Synchronous Data-flow (SDF) Model of Computation. The key problem of finding a maximum-throughput allocation and scheduling of Synchronous Data-Flow graphs onto a multi-core architecture is NP-hard and has been traditionally solved by means of heuristic (incomplete) algorithms. We propose an exact (complete) algorithm for the computation of a maximum-throughput mapping of applications specified as SDFG onto multi-core architectures. Results show that the approach can handle realistic instances in terms of size and complexity. Next, we tackle the Cyclic Resource-Constrained Scheduling Problem (i.e. CRCSP). We propose a Constraint Programming approach based on modular arithmetic: in particular, we introduce a modular precedence constraint and a global cumulative constraint along with their filtering algorithms. Many traditional approaches to cyclic scheduling operate by fixing the period value and then solving a linear problem in a generate-and-test fashion. Conversely, our technique is based on a non-linear model and tackles the problem as a whole: the period value is inferred from the scheduling decisions. The proposed approaches have been tested on a number of non-trivial synthetic instances and on a set of realistic industrial instances achieving good results on practical size problem.

Automatic Deployment of Applications in the Cloud

In distributed systems like clouds or service oriented frameworks, applications are typically assembled by deploying and connecting a large number of heterogeneous software components, spanning from fine-grained packages to coarse-grained complex services. The complexity of such systems requires a rich set of techniques and tools to support the automation of their deployment process. By relying on a formal model of components, a technique is devised for computing the sequence of actions allowing the deployment of a desired configuration. An efficient algorithm, working in polynomial time, is described and proven to be sound and complete. Finally, a prototype tool implementing the proposed algorithm has been developed. Experimental results support the adoption of this novel approach in real life scenarios.

Electrochemical surface modification of Single walled carbon nanotubes and graphene-based electrodes for (bio)sensing applications

Sensors are devices that have shown widespread use, from the detection of gas molecules to the tracking of chemical signals in biological cells. Single walled carbon nanotube (SWCNT) and graphene based electrodes have demonstrated to be an excellent material for the development of electrochemical biosensors as they display remarkable electronic properties and the ability to act as individual nanoelectrodes, display an excellent low-dimensional charge carrier transport, and promote surface electrocatalysis. The present work aims at the preparation and investigation of electrochemically modified SWCNT and graphene-based electrodes for applications in the field of biosensors. We initially studied SWCNT films and focused on their topography and surface composition, electrical and optical properties. Parallel to SWCNTs, graphene films were investigated. Higher resistance values were obtained in comparison with nanotubes films. The electrochemical surface modification of both electrodes was investigated following two routes (i) the electrografting of aryl diazonium salts, and (ii) the electrophylic addition of 1, 3-benzodithiolylium tetrafluoroborate (BDYT). Both the qualitative and quantitative characteristics of the modified electrode surfaces were studied such as the degree of functionalization and their surface composition. The combination of Raman, X-ray photoelectron spectroscopy, atomic force microscopy, electrochemistry and other techniques, has demonstrated that selected precursors could be covalently anchored to the nanotubes and graphene-based electrode surfaces through novel carbon-carbon formation.