Metaheuristics for Search Problems in Genomics - New Algorithms and Applications

In this thesis we made the first steps towards the systematic application of a methodology for automatically building formal models of complex biological systems. Such a methodology could be useful also to design artificial systems possessing desirable properties such as robustness and evolvability. The approach we follow in this thesis is to manipulate formal models by means of adaptive search methods called metaheuristics. In the first part of the thesis we develop state-of-the-art hybrid metaheuristic algorithms to tackle two important problems in genomics, namely, the Haplotype Inference by parsimony and the Founder Sequence Reconstruction Problem. We compare our algorithms with other effective techniques in the literature, we show strength and limitations of our approaches to various problem formulations and, finally, we propose further enhancements that could possibly improve the performance of our algorithms and widen their applicability. In the second part, we concentrate on Boolean network (BN) models of gene regulatory networks (GRNs). We detail our automatic design methodology and apply it to four use cases which correspond to different design criteria and address some limitations of GRN modeling by BNs. Finally, we tackle the Density Classification Problem with the aim of showing the learning capabilities of BNs. Experimental evaluation of this methodology shows its efficacy in producing network that meet our design criteria. Our results, coherently to what has been found in other works, also suggest that networks manipulated by a search process exhibit a mixture of characteristics typical of different dynamical regimes.

Argumentation and artifacts for intelligent multi-agent systems

Reasoning under uncertainty is a human capacity that in software system is necessary and often hidden. Argumentation theory and logic make explicit non-monotonic information in order to enable automatic forms of reasoning under uncertainty. In human organization Distributed Cognition and Activity Theory explain how artifacts are fundamental in all cognitive process. Then, in this thesis we search to understand the use of cognitive artifacts in an new argumentation framework for an agent-based artificial society.

Copper(I) phenanthroline complexes and supramolecular systems containing fullerenes: Photophysics, photochemistry and potential applications in sustainable energy technologies.

Chemistry can contribute, in many different ways to solve the challenges we are facing to modify our inefficient and fossil-fuel based energy system. The present work was motivated by the search for efficient photoactive materials to be employed in the context of the energy problem: materials to be utilized in energy efficient devices and in the production of renewable electricity and fuels. We presented a new class of copper complexes, that could find application in lighting techhnologies, by serving as luminescent materials in LEC, OLED, WOLED devices. These technologies may provide substantial energy savings in the lighting sector. Moreover, recently, copper complexes have been used as light harvesting compounds in dye sensitized photoelectrochemical solar cells, which offer a viable alternative to silicon-based photovoltaic technologies. We presented also a few supramolecular systems containing fullerene, e.g. dendrimers, dyads and triads.The most complex among these arrays, which contain porphyrin moieties, are presented in the final chapter. They undergo photoinduced energy- and electron transfer processes also with long-lived charge separated states, i.e. the fundamental processes to power artificial photosynthetic systems.

Self-organising coordination systems

Many research fields are pushing the engineering of large-scale, mobile, and open systems towards the adoption of techniques inspired by self-organisation: pervasive computing, but also distributed artificial intelligence, multi-agent systems, social networks, peer-topeer and grid architectures exploit adaptive techniques to make global system properties emerge in spite of the unpredictability of interactions and behaviour. Such a trend is visible also in coordination models and languages, whenever a coordination infrastructure needs to cope with managing interactions in highly dynamic and unpredictable environments. As a consequence, self-organisation can be regarded as a feasible metaphor to define a radically new conceptual coordination framework. The resulting framework defines a novel coordination paradigm, called self-organising coordination, based on the idea of spreading coordination media over the network, and charge them with services to manage interactions based on local criteria, resulting in the emergence of desired and fruitful global coordination properties of the system. Features like topology, locality, time-reactiveness, and stochastic behaviour play a key role in both the definition of such a conceptual framework and the consequent development of self-organising coordination services. According to this framework, the thesis presents several self-organising coordination techniques developed during the PhD course, mainly concerning data distribution in tuplespace-based coordination systems. Some of these techniques have been also implemented in ReSpecT, a coordination language for tuple spaces, based on logic tuples and reactions to events occurring in a tuple space. In addition, the key role played by simulation and formal verification has been investigated, leading to analysing how automatic verification techniques like probabilistic model checking can be exploited in order to formally prove the emergence of desired behaviours when dealing with coordination approaches based on self-organisation. To this end, a concrete case study is presented and discussed.

Development of synthetic molecular circuits for the control of cell systems

Synthetic biology is a young field of applicative research aiming to design and build up artificial biological devices, useful for human applications. How synthetic biology emerged in past years and how the development of the Registry of Standard Biological Parts aimed to introduce one practical starting solution to apply the basics of engineering to molecular biology is presented in chapter 1 in the thesis The same chapter recalls how biological parts can make up a genetic program, the molecular cloning tecnique useful for this purpose, and an overview of the mathematical modeling adopted to describe gene circuit behavior. Although the design of gene circuits has become feasible the increasing complexity of gene networks asks for a rational approach to design gene circuits. A bottom-up approach was proposed, suggesting that the behavior of a complicated system can be predicted from the features of its parts. The option to use modular parts in large-scale networks will be facilitated by a detailed and shared characterization of their functional properties. Such a prediction, requires well-characterized mathematical models of the parts and of how they behave when assembled together. In chapter 2, the feasibility of the bottom-up approach in the design of a synthetic program in Escherichia coli bacterial cells is described. The rational design of gene networks is however far from being established. The synthetic biology approach can used the mathematical formalism to identify biological information not assessable with experimental measurements. In this context, chapter 3 describes the design of a synthetic sensor for identifying molecules of interest inside eukaryotic cells. The Registry of Standard parts collects standard and modular biological parts. To spread the use of BioBricks the iGEM competition was started. The ICM Laboratory, where Francesca Ceroni completed her Ph.D, partecipated with teams of students and Chapter 4 summarizes the projects developed.

Nonlinear Control Strategies for Cooperative Control of Multi-Robot Systems

This thesis deals with distributed control strategies for cooperative control of multi-robot systems. Specifically, distributed coordination strategies are presented for groups of mobile robots. The formation control problem is initially solved exploiting artificial potential fields. The purpose of the presented formation control algorithm is to drive a group of mobile robots to create a completely arbitrarily shaped formation. Robots are initially controlled to create a regular polygon formation. A bijective coordinate transformation is then exploited to extend the scope of this strategy, to obtain arbitrarily shaped formations. For this purpose, artificial potential fields are specifically designed, and robots are driven to follow their negative gradient. Artificial potential fields are then subsequently exploited to solve the coordinated path tracking problem, thus making the robots autonomously spread along predefined paths, and move along them in a coordinated way. Formation control problem is then solved exploiting a consensus based approach. Specifically, weighted graphs are used both to define the desired formation, and to implement collision avoidance. As expected for consensus based algorithms, this control strategy is experimentally shown to be robust to the presence of communication delays. The global connectivity maintenance issue is then considered. Specifically, an estimation procedure is introduced to allow each agent to compute its own estimate of the algebraic connectivity of the communication graph, in a distributed manner. This estimate is then exploited to develop a gradient based control strategy that ensures that the communication graph remains connected, as the system evolves. The proposed control strategy is developed initially for single-integrator kinematic agents, and is then extended to Lagrangian dynamical systems.

Inverse Static Analysis of Massive Parallel Arrays of Three-State Actuators via Artificial Intelligence

Massive parallel robots (MPRs) driven by discrete actuators are force regulated robots that undergo continuous motions despite being commanded through a finite number of states only. Designing a real-time control of such systems requires fast and efficient methods for solving their inverse static analysis (ISA), which is a challenging problem and the subject of this thesis. In particular, five Artificial intelligence methods are proposed to investigate the on-line computation and the generalization error of ISA problem of a class of MPRs featuring three-state force actuators and one degree of revolute motion.

Water, sediment and soil physicochemical interactions in freshwater, brackish and saline systems

The physicochemical interactions between water, sediment and soil deeply influence the formation and development of the ecosystem. In this research, different freshwater, brackish and saline subaqueous environments of Northern Italy were chosen as study area to investigate the physicochemical processes which occur at the interface between water and sediments, as well as the effects of soil submergence on ecosystem development. In the freshwater system of the Reno river basin, the main purpose was to define the heavy metals hazard in water and sediments of natural and artificial water courses. Heavy metals partitioning and speciation allowed to assess the environmental risk linked to the critical action of dredging canal sediments, for the maintenance of the hydraulic safety of plain lands. In addition, some bioremediation techniques were experimented for protecting sediments from heavy metals contamination, and for giving an answer to the problem of sediments management. In the brackish system of S. Vitale park, the development of hydromorphic and subaqueous soils was investigated. The study of soil profiles highlighted the presence of a soil continuum among pedons subjected to different saturation degrees. This investigation allowed to the identification of both morphological and physicochemical indicators, which characterize the formation of subaqueous soils and describe the soil hydromorphism in transitional soil systems. In the saline system of Grado lagoon, an ecosystem approach was used to define the role of water oscillation in soil characterization and plants colonization. This study highlighted the close relationship and the mutual influence of soil submergence and aeration, tide oscillation and vegetation cover, on the soil development. In view of climate change, this study contribute to understand and suppose how soil and landscape could evolve. However, a complete evaluation of hydromorphic soil functionality will be achieved only involving physiological and biochemical expertise in these kind of studies.