A framework for cyber-physical system simulation

In these last years, systems engineering has became one of the major research domains. The complexity of systems has increased constantly and nowadays Cyber-Physical Systems (CPS) are a category of particular interest: these, are systems composed by a cyber part (computer-based algorithms) that monitor and control some physical processes. Their development and simulation are both complex due to the importance of the interaction between the cyber and the physical entities: there are a lot of models written in different languages that need to exchange information among each other. Normally people use an orchestrator that takes care of the simulation of the models and the exchange of informations. This orchestrator is developed manually and this is a tedious and long work. Our proposition is to achieve to generate the orchestrator automatically through the use of Co-Modeling, i.e. by modeling the coordination. Before achieving this ultimate goal, it is important to understand the mechanisms and de facto standards that could be used in a co-modeling framework. So, I studied the use of a technology employed for co-simulation in the industry: FMI. In order to better understand the FMI standard, I realized an automatic export, in the FMI format, of the models realized in an existing software for discrete modeling: TimeSquare. I also developed a simple physical model in the existing open source openmodelica tool. Later, I started to understand how works an orchestrator, developing a simple one: this will be useful in future to generate an orchestrator automatically.

Depth Estimation in Stereo Biomedical Images via Proxy-Supervised Deep Learning

In order to estimate depth through supervised deep learning-based stereo methods, it is necessary to have access to precise ground truth depth data. While the gathering of precise labels is commonly tackled by deploying depth sensors, this is not always a viable solution. For instance, in many applications in the biomedical domain, the choice of sensors capable of sensing depth at small distances with high precision on difficult surfaces (that present non-Lambertian properties) is very limited. It is therefore necessary to find alternative techniques to gather ground truth data without having to rely on external sensors. In this thesis, two different approaches have been tested to produce supervision data for biomedical images. The first aims to obtain input stereo image pairs and disparities through simulation in a virtual environment, while the second relies on a non-learned disparity estimation algorithm in order to produce noisy disparities, which are then filtered by means of hand-crafted confidence measures to create noisy labels for a subset of pixels. Among the two, the second approach, which is referred in literature as proxy-labeling, has shown the best results and has even outperformed the non-learned disparity estimation algorithm used for supervision.

Electrolyte disorders in the human ventricle. A simulation study.

Ventricular cells are immersed in a bath of electrolytes and these ions are essential for a healthy heart and a regular rhythm. Maintaining physiological concentration of them is fundamental for reducing arrhythmias and risk of sudden cardiac death, especially in haemodialysis patients and in the heart diseases treatments. Models of electrically activity of the heart based on mathematical formulation are a part of the efforts to improve the understanding and prediction of heart behaviour. Modern models incorporate the extensive and ever increasing amounts of experimental data in incorporating biophysically detailed mechanisms to allow the detailed study of molecular and subcellular mechanisms of heart disease. The goal of this project was to simulate the effects of changes in potassium and calcium concentrations in the extracellular space between experimental data and and a description incorpored into two modern biophysically detailed models (Grandi et al. Model; O’Hara Rudy Model). Moreover the task was to analyze the changes in the ventricular electrical activity, in particular by studying the modifications on the simulated electrocardiographic signal. We used the cellular information obtained by the heart models in order to build a 1D tissue description. The fibre is composed by 165 cells, it is divided in four groups to differentiate the cell types that compound human ventricular tissue. The main results are the following: Grandi et al. (GBP) model is not even able to reproduce the correct action potential profile in hyperkalemia. Data from hospitalized patients indicates that the action potential duration (APD) should be shorter than physiological state but in this model we have the opposite. From the potassium point of view the results obtained by using O’Hara model (ORD) are in agreement with experimental data for the single cell action potential in hypokalemia and hyperkalemia, most of the currents follow the data from literature. In the 1D simulations we were able to reproduce ECGs signal in most the potassium concentrations we selected for this study and we collected data that can help physician in understanding what happens in ventricular cells during electrolyte disorder. However the model fails in the conduction of the stimulus under hyperkalemic conditions. The model emphasized the ECG modifications when the K+ is slightly more than physiological value. In the calcium setting using the ORD model we found an APD shortening in hypocalcaemia and an APD lengthening in hypercalcaemia, i.e. the opposite to experimental observation. This wrong behaviour is kept in one dimensional simulations bringing a longer QT interval in the ECG under higher [Ca2+]o conditions and vice versa. In conclusion it has highlighted that the actual ventricular models present in literature, even if they are useful in the original form, they need an improvement in the sensitivity of these two important electrolytes. We suggest an use of the GBP model with modifications introduced by Carro et al. who understood that the failure of this model is related to the Shannon et al. model (a rabbit model) from which the GBP model was built. The ORD model should be modified in the Ca2+ - dependent IcaL and in the influence of the Iks in the action potential for letting it him produce a correct action potential under different calcium concentrations. In the 1D tissue maybe a heterogeneity setting of intra and extracellular conductances for the different cell types should improve a reproduction of the ECG signal.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Eye-trauma: Event driven control software for gesture recognition in medical simulation

Il progetto Eye-Trauma si colloca all'interno dello sviluppo di un simulatore chirurgico per traumi alla zona oculare, sviluppato in collaborazione con Simulation Group in Boston, Harvard Medical School e Massachusetts General Hospital. Il simulatore presenta un busto in silicone fornito di moduli intercambiabili della zona oculare, per simulare diversi tipi di trauma. L'utilizzatore è chiamato ad eseguire la procedura medica di saturazione tramite degli strumenti chirurgici su cui sono installati dei sensori di forza e di apertura. I dati collezionati vengono utilizzati all'interno del software per il riconoscimento dei gesti e il controllo real-time della performance. L'algoritmo di gesture recognition, da me sviluppato, si basa sul concetto di macchine a stati; la transizione tra gli stati avviene in base agli eventi rilevati dal simulatore.

Simulation of visible light communications in vehicular networks

The rapid development in the field of lighting and illumination allows low energy consumption and a rapid growth in the use, and development of solid-state sources. As the efficiency of these devices increases and their cost decreases there are predictions that they will become the dominant source for general illumination in the short term. The objective of this thesis is to study, through extensive simulations in realistic scenarios, the feasibility and exploitation of visible light communication (VLC) for vehicular ad hoc networks (VANETs) applications. A brief introduction will introduce the new scenario of smart cities in which visible light communication will become a fundamental enabling technology for the future communication systems. Specifically, this thesis focus on the acquisition of several, frequent, and small data packets from vehicles, exploited as sensors of the environment. The use of vehicles as sensors is a new paradigm to enable an efficient environment monitoring and an improved traffic management. In most cases, the sensed information must be collected at a remote control centre and one of the most challenging aspects is the uplink acquisition of data from vehicles. My thesis discusses the opportunity to take advantage of short range vehicle-to-vehicle (V2V) and vehicle-to-roadside (V2R) communications to offload the cellular networks. More specifically, it discusses the system design and assesses the obtainable cellular resource saving, by considering the impact of the percentage of vehicles equipped with short range communication devices, of the number of deployed road side units, and of the adopted routing protocol. When short range communications are concerned, WAVE/IEEE 802.11p is considered as standard for VANETs. Its use together with VLC will be considered in urban vehicular scenarios to let vehicles communicate without involving the cellular network. The study is conducted by simulation, considering both a simulation platform (SHINE, simulation platform for heterogeneous interworking networks) developed within the Wireless communication Laboratory (Wilab) of the University of Bologna and CNR, and network simulator (NS3). trying to realistically represent all the wireless network communication aspects. Specifically, simulation of vehicular system was performed and introduced in ns-3, creating a new module for the simulator. This module will help to study VLC applications in VANETs. Final observations would enhance and encourage potential research in the area and optimize performance of VLC systems applications in the future.

Frequency-dependent response of snow in uniaxial compression and comparison with numerical simulation

La determinazione del modulo di Young è fondamentale nello studio della propagazione di fratture prima del rilascio di una valanga e per lo sviluppo di affidabili modelli di stabilità della neve. Il confronto tra simulazioni numeriche del modulo di Young e i valori sperimentali mostra che questi ultimi sono tre ordini di grandezza inferiori a quelli simulati (Reuter et al. 2013)⁠. Lo scopo di questo lavoro è stimare il modulo di elasticità studiando la dipendenza dalla frequenza della risposta di diversi tipi di neve a bassa densità, 140-280 kg m-3. Ciò è stato fatto applicando una compressione dinamica uniassiale a -15°C nel range 1-250 Hz utilizzando il Young's modulus device (YMD), prototipo di cycling loading device progettato all'Istituto per lo studio della neve e delle valanghe (SLF). Una risposta viscoelastica della neve è stata identificata a tutte le frequenze considerate, la teoria della viscoelasticità è stata applicata assumendo valida l'ipotesi di risposta lineare della neve. Il valore dello storage modulus, E', a 100 Hz è stato identificato come ragionevolmente rappresentativo del modulo di Young di ciascun campione neve. Il comportamento viscoso è stato valutato considerando la loss tangent e la viscosità ricavata dai modelli di Voigt e Maxwell. Il passaggio da un comportamento più viscoso ad uno più elastico è stato trovato a 40 Hz (~1.1•10-2 s-1). Il maggior contributo alla dissipazione è nel range 1-10 Hz. Infine, le simulazioni numeriche del modulo di Young sono state ottenute nello stesso modo di Reuter et al.. La differenza tra le simulazioni ed i valori sperimentali di E' sono, al massimo, di un fattore 5; invece, in Reuter et al.⁠, era di 3 ordini di grandezza. Pertanto, i nostri valori sperimentali e numerici corrispondono meglio, indicando che il metodo qui utilizzato ha portato ad un miglioramento significativo.

Impact of irrigation in the Po valley (Italy) on meteorological parameters through numerical simulation

Recent studies found that soil-atmosphere coupling features, through soil moisture, have been crucial to simulate well heat waves amplitude, duration and intensity. Moreover, it was found that soil moisture depletion both in Winter and Spring anticipates strong heat waves during the Summer. Irrigation in geophysical studies can be intended as an anthropogenic forcing to the soil-moisture, besides changes in land proprieties. In this study, the irrigation was add to a LAM hydrostatic model (BOLAM) and coupled with the soil. The response of the model to irrigation perturbation is analyzed during a dry Summer season. To identify a dry Summer, with overall positive temperature anomalies, an extensive climatological characterization of 2015 was done. The method included a statistical validation on the reference period distribution used to calculate the anomalies. Drought conditions were observed during Summer 2015 and previous seasons, both on the analyzed region and the Alps. Moreover July was characterized as an extreme event for the referred distribution. The numerical simulation consisted on the summer season of 2015 and two run: a control run (CTR), with the soil coupling and a perturbed run (IPR). The perturbation consists on a mask of land use created from the Cropland FAO dataset, where an irrigation water flux of 3 mm/day was applied from 6 A.M. to 9 A.M. every day. The results show that differences between CTR and IPR has a strong daily cycle. The main modifications are on the air masses proprieties, not on to the dynamics. However, changes in the circulation at the boundaries of the Po Valley are observed, and a diagnostic spatial correlation of variable differences shows that soil moisture perturbation explains well the variation observed in the 2 meters height temperature and in the latent heat fluxes.On the other hand, does not explain the spatial shift up and downslope observed during different periods of the day. Given the results, irrigation process affects the atmospheric proprieties on a larger scale than the irrigation, therefore it is important in daily forecast, particularly during hot and dry periods.

Development of the Simulation Model for the CoSES Laboratory Test Microgrid in Modelica

Evolution of the traditional consumer in a power system to a prosumer has posed many problems in the traditional uni-directional grid. This evolution in the grid model has made it important to study the behaviour of microgrids. This thesis deals with the laboratory microgrid setup at the Munich School of Engineering, built to assist researchers in studying microgrids. The model is built in Dymola which is a tool for the OpenModelica language. Models for the different components were derived, suiting the purpose of this study. The equivalent parameters were derived from data sheets and other simulation programs such as PSCAD. The parameters were entered into the model grid and tested at steady state, firstly. This yielded satisfactory results that were similar to the reference results from MATPOWER power flow. Furthermore, fault conditions at several buses were simulated to observe the behaviour of the grid under these conditions. Recommendations for further developing this model to include more detailed models for components, such as power electronic converters, were made at the end of the thesis.

Development of iodine and air chemistry models for the simulation of plasma in Helicon Plasma Thrusters

The aim of this work is to analyse the chemistry models of low pressure Helicon discharges fed with iodine and air. In particular the focus of this research is to understand the plasma dynamics in order to predict propulsive performances of iodine and air-breathing Helicon Plasma Thrusters. The two systems have been simulated and analysed with the use of global models, i.e. a 0 dimensional tool to solve the set of governing equations by assuming that all quantities are volume averaged. Furthermore, some strategies have been implemented to improve the accuracy of this approach. A verification have been accomplished on the global models for both iodine and air, comparing results against simulations taken from literature. Moreover, the iodine global model has been validated against the experimental measurements of REGULUS, an helicon plasma thruster developed by the Italian company T4i, with a good agreement. From the analysis of iodine model, it has been found a significantly higher density for atomic positive ions with respect to molecular ions. Negative ions, instead, have shown to have negligible effect on the propulsive results. Also, the influence of reactions between heavy particles has been analysed with the global model. Results have demonstrated that, in the iodine case, chemistry is almost entirely affected by electronic collisions. For what concerns air-breathing results, it has been investigated the effects of the orbital height on propulsive performances. In particular, the global model has shown that at lower height, the values of thrust and specific impulse are lower due a change in atmosphere concentration. Finally, the iodine chemistry model has been introduced in the fluid code 3D-VIRTUS in order to preliminary assess the plasma properties of a Helicon discharge chamber for electric propulsion.

Simulation of URLLC slicing with resource reconfiguration in 5G networks

This thesis seeks to analyse the performance of dynamic slice provisioning in a 5G metro network with the low latency and reliability guaranties. This elaborate highlight the comparison in terms of performance of two versions of a simulator developed in Python based on different models: the Exhaustive research model and Shortest Path First Fit (SPFF) model. It further presents the differences between the dedicated path protection and the shared path protection. This analysis is made through several simulations at different network conditions by varying networks resources and observing the network performances while comparing the 2 models mentioned above. A reconfiguration procedure was implemented on backup resources in the shortest path first fit in order to improve its performance with respect to the exhaustive research which is more optimised. Subsequently, several triggering events was implemented, for the reconfiguration. And a comparison is made between these different triggering events in terms blocking probability, bandwidth at link, capacity at each node, primary and backup bandwidth per slice and backup capacity per slice.