Automatic Design of Boolean Networks for Modelling Differentiation Trees

Real living cell is a complex system governed by many process which are not yet fully understood: the process of cell differentiation is one of these. In this thesis work we make use of a cell differentiation model to develop gene regulatory networks (Boolean networks) with desired differentiation dynamics. To accomplish this task we have introduced techniques of automatic design and we have performed experiments using various differentiation trees. The results obtained have shown that the developed algorithms, except the Random algorithm, are able to generate Boolean networks with interesting differentiation dynamics. Moreover, we have presented some possible future applications and developments of the cell differentiation model in robotics and in medical research. Understanding the mechanisms involved in biological cells can gives us the possibility to explain some not yet understood dangerous disease, i.e the cancer. Le cellula è un sistema complesso governato da molti processi ancora non pienamente compresi: il differenziamento cellulare è uno di questi. In questa tesi utilizziamo un modello di differenziamento cellulare per sviluppare reti di regolazione genica (reti Booleane) con dinamiche di differenziamento desiderate. Per svolgere questo compito abbiamo introdotto tecniche di progettazione automatica e abbiamo eseguito esperimenti utilizzando vari alberi di differenziamento. I risultati ottenuti hanno mostrato che gli algoritmi sviluppati, eccetto l'algoritmo Random, sono in grado di poter generare reti Booleane con dinamiche di differenziamento interessanti. Inoltre, abbiamo presentato alcune possibili applicazioni e sviluppi futuri del modello di differenziamento in robotica e nella ricerca medica. Capire i meccanismi alla base del funzionamento cellulare può fornirci la possibilità di spiegare patologie ancora oggi non comprese, come il cancro.

Organic matter deposition/resuspension in a one-dimensional physical-biogeochemical model. A modelling study

The shallow water configuration of the gulf of Trieste allows the propagation of the stress due to wind and waves along the whole water column down to the bottom. When the stress overcomes a particular threshold it produces resuspension processes of the benthic detritus. The benthic sediments in the North Adriatic are rich of organic matter, transported here by many rivers. This biological active particulate, when remaining in the water, can be transported in all the Adriatic basin by the basin-wide circulation. In this work is presented a first implementation of a resuspension/deposition submodel in the oceanographic coupled physical-biogeochemical 1-dimensional numerical model POM-BFM. At first has been considered the only climatological wind stress forcing, next has been introduced, on the surface, an annual cycle of wave motion and finally have been imposed some exceptional wave event in different periods of the year. The results show a strong relationship between the efficiency of the resuspension process and the stratification of the water column. During summer the strong stratification can contained a great quantity of suspended matter near to the bottom, while during winter even a low concentration of particulate can reach the surface and remains into the water for several months without settling and influencing the biogeochemical system. Looking at the biologic effects, the organic particulate, injected in the water column, allow a sudden growth of the pelagic bacteria which competes with the phytoplankton for nutrients strongly inhibiting its growth. This happen especially during summer when the suspended benthic detritus concentration is greater.

Modelling and Verification of a Correction Factor to Evaluate the Efficiency of Solar Thermal Collectors with the Rapid Test Method

A new method for the evaluation of the efficiency of parabolic trough collectors, called Rapid Test Method, is investigated at the Solar Institut Jülich. The basic concept is to carry out measurements under stagnation conditions. This allows a fast and inexpensive process due to the fact that no working fluid is required. With this approach, the temperature reached by the inner wall of the receiver is assumed to be the stagnation temperature and hence the average temperature inside the collector. This leads to a systematic error which can be rectified through the introduction of a correction factor. A model of the collector is simulated with COMSOL Multipyisics to study the size of the correction factor depending on collector geometry and working conditions. The resulting values are compared with experimental data obtained at a test rig at the Solar Institut Jülich. These results do not match with the simulated ones. Consequentially, it was not pos-sible to verify the model. The reliability of both the model with COMSOL Multiphysics and of the measurements are analysed. The influence of the correction factor on the rapid test method is also studied, as well as the possibility of neglecting it by measuring the receiver’s inner wall temperature where it receives the least amount of solar rays. The last two chapters analyse the specific heat capacity as a function of pressure and tem-perature and present some considerations about the uncertainties on the efficiency curve obtained with the Rapid Test Method.

Experimentally and coupled CFD/CSD assisted structural and aeroelastic modelling of the Javelin UAV outboard wing section

This study presents the procedure followed to make a prediction of the critical flutter speed for a composite UAV wing. At the beginning of the study, there was no information available on the materials used for the construction of the wing, and the wing internal structure was unknown. Ground vibration tests were performed in order to detect the structure’s natural frequencies and mode shapes. From tests, it was found that the wing possesses a high stiffness, presenting well separated first bending and torsional natural frequencies. Two finite element models were developed and matched to experimental results. It has been necessary to introduce some assumptions, due to the uncertainties regarding the structure. The matching process was based on natural frequencies’ sensitivity with respect to a change in the mechanical properties of the materials. Once experimental results were met, average material properties were also found. Aerodynamic coefficients for the wing were obtained by means of a CFD software. The same analysis was also conducted when the wing is deformed in its first four mode shapes. A first approximation for flutter critical speed was made with the classical V - g technique. Finally, wing’s aeroelastic behavior was simulated using a coupled CFD/CSD method, obtaining a more accurate flutter prediction. The CSD solver is based on the time integration of modal dynamic equations, requiring the extraction of mode shapes from the previously performed finite-element analysis. Results show that flutter onset is not a risk for the UAV, occurring at velocities well beyond its operative range.

Analysis, modelling and design of a groin as coastal protection structure at Lido di Dante, Ravenna

An analysis and a subsequent solution is here presented. This document is about a groin design able to contrast the erosion actions given by waves in Lido di Dante. Advantages will be visible also for Fiumi Uniti's inlet, in the north side of the shoreline. Beach future progression and growth will be subjected to monitoring actions in the years after groin construction. The resulting effects of the design will have a positive impact not only on the local fauna and environment, but also, a naturalistic appeal will increase making new type of tourists coming not only for recreational purposes. The design phase is focused on possible design alternatives and their features. Particular interest is given to scouring phenomena all around the groin after its construction. Groin effects will impact not only on its south side, instead they will cause an intense erosion process on the downdrift front. Here, many fishing hut would be in danger, thus a beach revetment structure is needed to avoid any future criticality. In addiction, a numerical model based on a generalized shoreline change numerical model, also known as GENESIS, has been applied to the study area in order to perform a simplistic analysis of the shoreline and its future morphology. Critical zones are visible in proximity of the Fiumi Uniti's river inlet, where currents from the sea and the river itself start the erosion process that is affecting Lido di Dante since mid '80s, or even before. The model is affected by several assumptions that make results not to be interpreted as a real future trend of the shore. Instead the model allows the user to have a more clear view about critical processes induced by monochromatic inputed waves. In conclusion, the thesis introduce a wide analysis on a complex erosion process that is affecting many shoreline nowadays. A groin design is seen as a hard solution it is considered to be the only means able to decrease the rate of erosion.

Optimized methods to digital survey and 3D modelling of cultural heritage assets

Currently making digital 3D models and replicas of the cultural heritage assets play an important role in the preservation and having a high detail source for future research and intervention. In this dissertation, it is tried to assess different methods for digital surveying and making 3D replicas of cultural heritage assets in different scales of size. The methodologies vary in devices, software, workflow, and the amount of skill that is required. The three phases of the 3D modelling process are data acquisition, modelling, and model presentation. Each of these sections is divided into sub-sections and there are several approaches, methods, devices, and software that may be employed, furthermore, the selection process should be based on the operation's goal, available facilities, the scale and properties of the object or structure to be modeled, as well as the operators' expertise and experience. The most key point to remember is that the 3D modelling operation should be properly accurate, precise, and reliable; therefore, there are so many instructions and pieces of advice on how to perform 3D modelling effectively. It is an attempt to compare and evaluate the various ways of each phase in order to explain and demonstrate their differences, benefits, and drawbacks in order to serve as a simple guide for new and/or inexperienced users.

Loading and damage modelling for an integrated SHM system of a prestressed concrete railway bridge in Naples

The thesis explores recent technology developments in the field of structural health monitoring and its application to railway bridge projects. It focuses on two main topics. First, service loads and effect of environmental actions are modelled. In particular, the train moving load and its interaction with rail track is considered with different degrees of detail. Hence, results are compared with real-time experimental measurements. Secondly, the work concerns the identification, definition and modelling process of damages for a prestressed concrete railway bridge, and their implementation inside FEM models. Along with a critical interpretation of the in-field measurements, this approach results in the development of undamaged and damaged databases for the AI-aided detection of anomalies and the definition of threshold levels to prompt automatic alert interventions. In conclusion, an innovative solution for the development of the railway weight-in-motion system is proposed.