Application Platforms for the Internet of Things: Theory, Architecture, Protocols, Data Formats, and Privacy

The Internet of Things (IoT) is the next industrial revolution: we will interact naturally with real and virtual devices as a key part of our daily life. This technology shift is expected to be greater than the Web and Mobile combined. As extremely different technologies are needed to build connected devices, the Internet of Things field is a junction between electronics, telecommunications and software engineering. Internet of Things application development happens in silos, often using proprietary and closed communication protocols. There is the common belief that only if we can solve the interoperability problem we can have a real Internet of Things. After a deep analysis of the IoT protocols, we identified a set of primitives for IoT applications. We argue that each IoT protocol can be expressed in term of those primitives, thus solving the interoperability problem at the application protocol level. Moreover, the primitives are network and transport independent and make no assumption in that regard. This dissertation presents our implementation of an IoT platform: the Ponte project. Privacy issues follows the rise of the Internet of Things: it is clear that the IoT must ensure resilience to attacks, data authentication, access control and client privacy. We argue that it is not possible to solve the privacy issue without solving the interoperability problem: enforcing privacy rules implies the need to limit and filter the data delivery process. However, filtering data require knowledge of how the format and the semantics of the data: after an analysis of the possible data formats and representations for the IoT, we identify JSON-LD and the Semantic Web as the best solution for IoT applications. Then, this dissertation present our approach to increase the throughput of filtering semantic data by a factor of ten.

Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

Innovative architecture of on-board and on-ground radio systems for space communication

The radio communication system is one of the most critical system of the overall satellite platform: it often represents the only way of communication, between a spacecraft and the Ground Segment or among a constellation of satellites. This thesis focuses on specific innovative architectures for on-board and on-ground radio systems. In particular, this work is an integral part of a space program started in 2004 at the University of Bologna, Forlì campus, which led to the completion of the microsatellite ALMASat-1, successfully launched on-board the VEGA maiden flight. The success of this program led to the development of a second microsatellite, named ALMASat-EO, a three-axis stabilized microsatellite able to capture images of the Earth surface. Therefore, the first objective of this study was focused on the investigation of an innovative, efficient and low cost architecture for on-board radio communication systems. The TT&C system and the high data rate transmitter for images downlink design and realization are thoroughly described in this work, together with the development of the embedded hardware and the adopted antenna systems. Moreover, considering the increasing interest in the development of constellations of microsatellite, in particular those flying in close formations, a careful analysis has been carried out for the development of innovative communication protocols for inter-satellite links. Furthermore, in order to investigate the system aspects of space communications, a study has been carried out at ESOC having as objective the design, implementation and test of two experimental devices for the enhancement of the ESA GS. Thus, a significant portion of this thesis is dedicated to the description of the results of a method for improving the phase stability of GS radio frequency equipments by means of real-time phase compensation and a new way to perform two antennas arraying tracking using already existing ESA tracking stations facilities.

Development of JADE, a new software for the verification and validation of nuclear data libraries

Nuclear cross sections are the pillars onto which the transport simulation of particles and radiations is built on. Since the nuclear data libraries production chain is extremely complex and made of different steps, it is mandatory to foresee stringent verification and validation procedures to be applied to it. The work here presented has been focused on the development of a new python based software called JADE, whose objective is to give a significant help in increasing the level of automation and standardization of these procedures in order to reduce the time passing between new libraries releases and, at the same time, increasing their quality. After an introduction to nuclear fusion (which is the field where the majority of the V\&V action was concentrated for the time being) and to the simulation of particles and radiations transport, the motivations leading to JADE development are discussed. Subsequently, the code general architecture and the implemented benchmarks (both experimental and computational) are described. After that, the results coming from the major application of JADE during the research years are presented. At last, after a final discussion on the objective reached by JADE, the possible brief, mid and long time developments for the project are discussed.

Decentralized systems for the protection and portability of personal data

The General Data Protection Regulation (GDPR) has been designed to help promote a view in favor of the interests of individuals instead of large corporations. However, there is the need of more dedicated technologies that can help companies comply with GDPR while enabling people to exercise their rights. We argue that such a dedicated solution must address two main issues: the need for more transparency towards individuals regarding the management of their personal information and their often hindered ability to access and make interoperable personal data in a way that the exercise of one's rights would result in straightforward. We aim to provide a system that helps to push personal data management towards the individual's control, i.e., a personal information management system (PIMS). By using distributed storage and decentralized computing networks to control online services, users' personal information could be shifted towards those directly concerned, i.e., the data subjects. The use of Distributed Ledger Technologies (DLTs) and Decentralized File Storage (DFS) as an implementation of decentralized systems is of paramount importance in this case. The structure of this dissertation follows an incremental approach to describing a set of decentralized systems and models that revolves around personal data and their subjects. Each chapter of this dissertation builds up the previous one and discusses the technical implementation of a system and its relation with the corresponding regulations. We refer to the EU regulatory framework, including GDPR, eIDAS, and Data Governance Act, to build our final system architecture's functional and non-functional drivers. In our PIMS design, personal data is kept in a Personal Data Space (PDS) consisting of encrypted personal data referring to the subject stored in a DFS. On top of that, a network of authorization servers acts as a data intermediary to provide access to potential data recipients through smart contracts.

Digital 3D reconstruction as a research environment in art and architecture history: uncertainty classification and visualisation

The dissertation addresses the still not solved challenges concerned with the source-based digital 3D reconstruction, visualisation and documentation in the domain of archaeology, art and architecture history. The emerging BIM methodology and the exchange data format IFC are changing the way of collaboration, visualisation and documentation in the planning, construction and facility management process. The introduction and development of the Semantic Web (Web 3.0), spreading the idea of structured, formalised and linked data, offers semantically enriched human- and machine-readable data. In contrast to civil engineering and cultural heritage, academic object-oriented disciplines, like archaeology, art and architecture history, are acting as outside spectators. Since the 1990s, it has been argued that a 3D model is not likely to be considered a scientific reconstruction unless it is grounded on accurate documentation and visualisation. However, these standards are still missing and the validation of the outcomes is not fulfilled. Meanwhile, the digital research data remain ephemeral and continue to fill the growing digital cemeteries. This study focuses, therefore, on the evaluation of the source-based digital 3D reconstructions and, especially, on uncertainty assessment in the case of hypothetical reconstructions of destroyed or never built artefacts according to scientific principles, making the models shareable and reusable by a potentially wide audience. The work initially focuses on terminology and on the definition of a workflow especially related to the classification and visualisation of uncertainty. The workflow is then applied to specific cases of 3D models uploaded to the DFG repository of the AI Mainz. In this way, the available methods of documenting, visualising and communicating uncertainty are analysed. In the end, this process will lead to a validation or a correction of the workflow and the initial assumptions, but also (dealing with different hypotheses) to a better definition of the levels of uncertainty.

Data driven regularization models of non-linear ill-posed inverse problems in imaging

Imaging technologies are widely used in application fields such as natural sciences, engineering, medicine, and life sciences. A broad class of imaging problems reduces to solve ill-posed inverse problems (IPs). Traditional strategies to solve these ill-posed IPs rely on variational regularization methods, which are based on minimization of suitable energies, and make use of knowledge about the image formation model (forward operator) and prior knowledge on the solution, but lack in incorporating knowledge directly from data. On the other hand, the more recent learned approaches can easily learn the intricate statistics of images depending on a large set of data, but do not have a systematic method for incorporating prior knowledge about the image formation model. The main purpose of this thesis is to discuss data-driven image reconstruction methods which combine the benefits of these two different reconstruction strategies for the solution of highly nonlinear ill-posed inverse problems. Mathematical formulation and numerical approaches for image IPs, including linear as well as strongly nonlinear problems are described. More specifically we address the Electrical impedance Tomography (EIT) reconstruction problem by unrolling the regularized Gauss-Newton method and integrating the regularization learned by a data-adaptive neural network. Furthermore we investigate the solution of non-linear ill-posed IPs introducing a deep-PnP framework that integrates the graph convolutional denoiser into the proximal Gauss-Newton method with a practical application to the EIT, a recently introduced promising imaging technique. Efficient algorithms are then applied to the solution of the limited electrods problem in EIT, combining compressive sensing techniques and deep learning strategies. Finally, a transformer-based neural network architecture is adapted to restore the noisy solution of the Computed Tomography problem recovered using the filtered back-projection method.

An architecture for network acceleration as a service in the cloud continuum

The pervasive availability of connected devices in any industrial and societal sector is pushing for an evolution of the well-established cloud computing model. The emerging paradigm of the cloud continuum embraces this decentralization trend and envisions virtualized computing resources physically located between traditional datacenters and data sources. By totally or partially executing closer to the network edge, applications can have quicker reactions to events, thus enabling advanced forms of automation and intelligence. However, these applications also induce new data-intensive workloads with low-latency constraints that require the adoption of specialized resources, such as high-performance communication options (e.g., RDMA, DPDK, XDP, etc.). Unfortunately, cloud providers still struggle to integrate these options into their infrastructures. That risks undermining the principle of generality that underlies the cloud computing scale economy by forcing developers to tailor their code to low-level APIs, non-standard programming models, and static execution environments. This thesis proposes a novel system architecture to empower cloud platforms across the whole cloud continuum with Network Acceleration as a Service (NAaaS). To provide commodity yet efficient access to acceleration, this architecture defines a layer of agnostic high-performance I/O APIs, exposed to applications and clearly separated from the heterogeneous protocols, interfaces, and hardware devices that implement it. A novel system component embodies this decoupling by offering a set of agnostic OS features to applications: memory management for zero-copy transfers, asynchronous I/O processing, and efficient packet scheduling. This thesis also explores the design space of the possible implementations of this architecture by proposing two reference middleware systems and by adopting them to support interactive use cases in the cloud continuum: a serverless platform and an Industry 4.0 scenario. A detailed discussion and a thorough performance evaluation demonstrate that the proposed architecture is suitable to enable the easy-to-use, flexible integration of modern network acceleration into next-generation cloud platforms.