Novel investigation methods in Computational Social Dynamics and Complex Systems

In this thesis the evolution of the techno-social systems analysis methods will be reported, through the explanation of the various research experience directly faced. The first case presented is a research based on data mining of a dataset of words association named Human Brain Cloud: validation will be faced and, also through a non-trivial modeling, a better understanding of language properties will be presented. Then, a real complex system experiment will be introduced: the WideNoise experiment in the context of the EveryAware european project. The project and the experiment course will be illustrated and data analysis will be displayed. Then the Experimental Tribe platform for social computation will be introduced . It has been conceived to help researchers in the implementation of web experiments, and aims also to catalyze the cumulative growth of experimental methodologies and the standardization of tools cited above. In the last part, three other research experience which already took place on the Experimental Tribe platform will be discussed in detail, from the design of the experiment to the analysis of the results and, eventually, to the modeling of the systems involved. The experiments are: CityRace, about the measurement of human traffic-facing strategies; laPENSOcosì, aiming to unveil the political opinion structure; AirProbe, implemented again in the EveryAware project framework, which consisted in monitoring air quality opinion shift of a community informed about local air pollution. At the end, the evolution of the technosocial systems investigation methods shall emerge together with the opportunities and the threats offered by this new scientific path.

Computational insight into materials properties

The aim of the work was to explore the practical applicability of molecular dynamics at different length and time scales. From nanoparticles system over colloids and polymers to biological systems like membranes and finally living cells, a broad range of materials was considered from a theoretical standpoint. In this dissertation five chemistry-related problem are addressed by means of theoretical and computational methods. The main results can be outlined as follows. (1) A systematic study of the effect of the concentration, chain length, and charge of surfactants on fullerene aggregation is presented. The long-discussed problem of the location of C60 in micelles was addressed and fullerenes were found in the hydrophobic region of the micelles. (2) The interactions between graphene sheet of increasing size and phospholipid membrane are quantitatively investigated. (3) A model was proposed to study structure, stability, and dynamics of MoS2, a material well-known for its tribological properties. The telescopic movement of nested nanotubes and the sliding of MoS2 layers is simulated. (4) A mathematical model to gain understaning of the coupled diffusion-swelling process in poly(lactic-co-glycolic acid), PLGA, was proposed. (5) A soft matter cell model is developed to explore the interaction of living cell with artificial surfaces. The effect of the surface properties on the adhesion dynamics of cells are discussed.

Engineering Complex Computational Ecosystems

Self-organising pervasive ecosystems of devices are set to become a major vehicle for delivering infrastructure and end-user services. The inherent complexity of such systems poses new challenges to those who want to dominate it by applying the principles of engineering. The recent growth in number and distribution of devices with decent computational and communicational abilities, that suddenly accelerated with the massive diffusion of smartphones and tablets, is delivering a world with a much higher density of devices in space. Also, communication technologies seem to be focussing on short-range device-to-device (P2P) interactions, with technologies such as Bluetooth and Near-Field Communication gaining greater adoption. Locality and situatedness become key to providing the best possible experience to users, and the classic model of a centralised, enormously powerful server gathering and processing data becomes less and less efficient with device density. Accomplishing complex global tasks without a centralised controller responsible of aggregating data, however, is a challenging task. In particular, there is a local-to-global issue that makes the application of engineering principles challenging at least: designing device-local programs that, through interaction, guarantee a certain global service level. In this thesis, we first analyse the state of the art in coordination systems, then motivate the work by describing the main issues of pre-existing tools and practices and identifying the improvements that would benefit the design of such complex software ecosystems. The contribution can be divided in three main branches. First, we introduce a novel simulation toolchain for pervasive ecosystems, designed for allowing good expressiveness still retaining high performance. Second, we leverage existing coordination models and patterns in order to create new spatial structures. Third, we introduce a novel language, based on the existing ``Field Calculus'' and integrated with the aforementioned toolchain, designed to be usable for practical aggregate programming.

"Experimental and computational approaches to historical masonry structures: A study in the direction of filling the gap"

The assessment of historical structures is a significant need for the next generations, as historical monuments represent the community’s identity and have an important cultural value to society. Most of historical structures built by using masonry which is one of the oldest and most common construction materials used in the building sector since the ancient time. Also it is considered a complex material, as it is a composition of brick units and mortar, which affects the structural performance of the building by having different mechanical behaviour with respect to different geometry and qualities given by the components.

Computational Modelling of Cardiac Electrophysiology: from Cell to Bedside

Heart diseases are the leading cause of death worldwide, both for men and women. However, the ionic mechanisms underlying many cardiac arrhythmias and genetic disorders are not completely understood, thus leading to a limited efficacy of the current available therapies and leaving many open questions for cardiac electrophysiologists. On the other hand, experimental data availability is still a great issue in this field: most of the experiments are performed in vitro and/or using animal models (e.g. rabbit, dog and mouse), even when the final aim is to better understand the electrical behaviour of in vivo human heart either in physiological or pathological conditions. Computational modelling constitutes a primary tool in cardiac electrophysiology: in silico simulations, based on the available experimental data, may help to understand the electrical properties of the heart and the ionic mechanisms underlying a specific phenomenon. Once validated, mathematical models can be used for making predictions and testing hypotheses, thus suggesting potential therapeutic targets. This PhD thesis aims to apply computational cardiac modelling of human single cell action potential (AP) to three clinical scenarios, in order to gain new insights into the ionic mechanisms involved in the electrophysiological changes observed in vitro and/or in vivo. The first context is blood electrolyte variations, which may occur in patients due to different pathologies and/or therapies. In particular, we focused on extracellular Ca2+ and its effect on the AP duration (APD). The second context is haemodialysis (HD) therapy: in addition to blood electrolyte variations, patients undergo a lot of other different changes during HD, e.g. heart rate, cell volume, pH, and sympatho-vagal balance. The third context is human hypertrophic cardiomyopathy (HCM), a genetic disorder characterised by an increased arrhythmic risk, and still lacking a specific pharmacological treatment.

Aggregate Programming in Scala: a Core Library and Actor-Based Platform for Distributed Computational Fields

La programmazione aggregata è un paradigma che supporta la programmazione di sistemi di dispositivi, adattativi ed eventualmente a larga scala, nel loro insieme -- come aggregati. L'approccio prevalente in questo contesto è basato sul field calculus, un calcolo formale che consente di definire programmi aggregati attraverso la composizione funzionale di campi computazionali, creando i presupposti per la specifica di pattern di auto-organizzazione robusti. La programmazione aggregata è attualmente supportata, in modo più o meno parziale e principalmente per la simulazione, da DSL dedicati (cf., Protelis), ma non esistono framework per linguaggi mainstream finalizzati allo sviluppo di applicazioni. Eppure, un simile supporto sarebbe auspicabile per ridurre tempi e sforzi d'adozione e per semplificare l'accesso al paradigma nella costruzione di sistemi reali, nonché per favorire la ricerca stessa nel campo. Il presente lavoro consiste nello sviluppo, a partire da un prototipo della semantica operazionale del field calculus, di un framework per la programmazione aggregata in Scala. La scelta di Scala come linguaggio host nasce da motivi tecnici e pratici. Scala è un linguaggio moderno, interoperabile con Java, che ben integra i paradigmi ad oggetti e funzionale, ha un sistema di tipi espressivo, e fornisce funzionalità avanzate per lo sviluppo di librerie e DSL. Inoltre, la possibilità di appoggiarsi, su Scala, ad un framework ad attori solido come Akka, costituisce un altro fattore trainante, data la necessità di colmare l'abstraction gap inerente allo sviluppo di un middleware distribuito. Nell'elaborato di tesi si presenta un framework che raggiunge il triplice obiettivo: la costruzione di una libreria Scala che realizza la semantica del field calculus in modo corretto e completo, la realizzazione di una piattaforma distribuita Akka-based su cui sviluppare applicazioni, e l'esposizione di un'API generale e flessibile in grado di supportare diversi scenari.

Computational biomechanics to simulate the femoropopliteal intersection during knee flexion: a preliminary study

To assess if finite element (FE) models can be used to predict deformation of the femoropopliteal segment during knee flexion.

Au@Hg nanoalloy formation through direct amalgamation: Structural, spectroscopic, and computational evidence for slow nanoscale diffusion

Dynamic core-shell nanoparticles have received increasing attention in recent years. This paper presents a detailed study of Au-Hg nanoalloys, whose composing elements show a large difference in cohesive energy. A simple method to prepare Au@Hg particles with precise control over the composition up to 15 atom% mercury is introduced, based on reacting a citrate stabilized gold sol with elemental mercury. Transmission electron microscopy shows an increase of particle size with increasing mercury content and, together with X-ray powder diffraction, points towards the presence of a core-shell structure with a gold core surrounded by an Au-Hg solid solution layer. The amalgamation process is described by pseudo-zero-order reaction kinetics, which indicates slow dissolution of mercury in water as the rate determining step, followed by fast scavenging by nanoparticles in solution. Once adsorbed at the surface, slow diffusion of Hg into the particle lattice occurs, to a depth of ca. 3 nm, independent of Hg concentration. Discrete dipole approximation calculations relate the UV-vis spectra to the microscopic details of the nanoalloy structure. Segregation energies and metal distribution in the nanoalloys were modeled by density functional theory calculations. The results indicate slow metal interdiffusion at the nanoscale, which has important implications for synthetic methods aimed at core-shell particles.

Can wild ungulate carcasses provide enough biomass to maintain avian scavenger populations? An empirical assessment using a bio-inspired computational model

Background The reduction in the amount of food available for European avian scavengers as a consequence of restrictive public health policies is a concern for managers and conservationists. Since 2002, the application of several sanitary regulations has limited the availability of feeding resources provided by domestic carcasses, but theoretical studies assessing whether the availability of food resources provided by wild ungulates are enough to cover energetic requirements are lacking. Methodology/Findings We assessed food provided by a wild ungulate population in two areas of NE Spain inhabited by three vulture species and developed a P System computational model to assess the effects of the carrion resources provided on their population dynamics. We compared the real population trend with to a hypothetical scenario in which only food provided by wild ungulates was available. Simulation testing of the model suggests that wild ungulates constitute an important food resource in the Pyrenees and the vulture population inhabiting this area could grow if only the food provided by wild ungulates would be available. On the contrary, in the Pre-Pyrenees there is insufficient food to cover the energy requirements of avian scavenger guilds, declining sharply if biomass from domestic animals would not be available. Conclusions/Significance Our results suggest that public health legislation can modify scavenger population trends if a large number of domestic ungulate carcasses disappear from the mountains. In this case, food provided by wild ungulates could be not enough and supplementary feeding could be necessary if other alternative food resources are not available (i.e. the reintroduction of wild ungulates), preferably in European Mediterranean scenarios sharing similar and socio-economic conditions where there are low densities of wild ungulates. Managers should anticipate the conservation actions required by assessing food availability and the possible scenarios in order to make the most suitable decisions.