Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Analisi di pushover 3D per strutture in c.a.

In the present study, a new pushover procedure for 3D frame structures is proposed, based on the application of a set of horizontal force and torque distributions at each floor level; in order to predict the most severe configurations of an irregular structure subjected to an earthquake, more than one pushover analysis has to be performed. The proposed method is validated by a consistent comparison of results from static pushover and dynamic simulations in terms of different response parameters, such as displacements, rotations, floor shears and floor torques. Starting from the linear analysis, the procedure is subsequently extended to the nonlinear case. The results confirm the effectiveness of the proposed procedure to predict the structural behaviour in the most severe configurations.

Studio e ricostruzione delle distribuzioni granulometriche interne al grano in motori a propellente solido

The main purposes of this essay were to investigate in detail the burning rate anomaly phenomenon, also known as "Hump Effect", in solid rocket motors casted in mandrel and the mechanisms at the base of it, as well as the developing of a numeric code, in Matlab environment, in order to obtain a forecasting tool to generate concentration and orientation maps of the particles within the grain. The importance of these analysis is due to the fact that the forecasts of ballistics curves in new motors have to be improved in order to reduce the amount of experimental tests needed for the characterization of their ballistic behavior. This graduate work is divided into two parts. The first one is about bidimensional and tridimensional simulations on z9 motor casting process. The simulations have been carried out respectively with Fluent and Flow 3D. The second one is about the analysis of fluid dynamic data and the developing of numeric codes which give information about the concentration and orientation of particles within the grain based on fluid strain rate information which are extrapolated from CFD software.

User centered retrofit: The case of kadk campus, Copenhagen, (dk)

The following research thesis is about a retrofit project made in Denmark, Copenhagen, and carried out on one of the buildings belonging to the Royal Danish Academy. The key assumption and base of the entire research process is that, up to now, the standard procedure in retrofit cases like this provides as comparative method between de facto and design, the use of Energy Simulation software. These programs generally divide the space into different thermal zones, assigning to each of them different levels of employment, activities, set-point temperatures set for cooling and heating analysis and so on, but always providing average and constant values, usually taken in the middle point of the single thermal zone. Therefore, the project and its research path stems from the attempt to investigate the potentialities of this kind of designing for retrofit process, as previously anticipated not antithetical but complementary to that classic energy-based retrofit, thus passing from the building scale, and all its thermal zones, to the users' scale, related to humans and microclimates. The main software used in this process is Autodesk Simulation CFD. The idea behind the project is that in certain situations, for example, it will not be necessary to add throughout insulation layers (previously parameterized and optimized with Design Builder), and that even in Winter conditions, due maybe to the users' activities, the increased level of clothing (clo) and the heat produced by equipments, thermal comfort could be achieved also in areas characterized by considerably lower MRT. After the analysis of the State of Art and its simulations, the project has still been supported by the tool itself, the CFD Software, in an iterative process aimed at achieving visible improvements in terms of MRT, on spaces with different needs and characteristics, both in Winter and Summer regimes.