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.

Impatto della propagazione elettromagnetica sulle prestazioni delle reti M3N

Con il termine Smart Grid si intende una rete urbana capillare che trasporta energia, informazione e controllo, composta da dispositivi e sistemi altamente distribuiti e cooperanti. Essa deve essere in grado di orchestrare in modo intelligente le azioni di tutti gli utenti e dispositivi connessi al fine di distribuire energia in modo sicuro, efficiente e sostenibile. Questo connubio fra ICT ed Energia viene comunemente identificato anche con il termine Smart Metering, o Internet of Energy. La crescente domanda di energia e l’assoluta necessità di ridurre gli impatti ambientali (pacchetto clima energia 20-20-20 [9]), ha creato una convergenza di interessi scientifici, industriali e politici sul tema di come le tecnologie ICT possano abilitare un processo di trasformazione strutturale di ogni fase del ciclo energetico: dalla generazione fino all’accumulo, al trasporto, alla distribuzione, alla vendita e, non ultimo, il consumo intelligente di energia. Tutti i dispositivi connessi, diventeranno parte attiva di un ciclo di controllo esteso alle grandi centrali di generazione così come ai comportamenti dei singoli utenti, agli elettrodomestici di casa, alle auto elettriche e ai sistemi di micro-generazione diffusa. La Smart Grid dovrà quindi appoggiarsi su una rete capillare di comunicazione che fornisca non solo la connettività fra i dispositivi, ma anche l’abilitazione di nuovi servizi energetici a valore aggiunto. In questo scenario, la strategia di comunicazione sviluppata per lo Smart Metering dell’energia elettrica, può essere estesa anche a tutte le applicazioni di telerilevamento e gestione, come nuovi contatori dell’acqua e del gas intelligenti, gestione dei rifiuti, monitoraggio dell’inquinamento dell’aria, monitoraggio del rumore acustico stradale, controllo continuo del sistema di illuminazione pubblico, sistemi di gestione dei parcheggi cittadini, monitoraggio del servizio di noleggio delle biciclette, ecc. Tutto ciò si prevede possa contribuire alla progettazione di un unico sistema connesso, dove differenti dispositivi eterogenei saranno collegati per mettere a disposizione un’adeguata struttura a basso costo e bassa potenza, chiamata Metropolitan Mesh Machine Network (M3N) o ancora meglio Smart City. Le Smart Cities dovranno a loro volta diventare reti attive, in grado di reagire agli eventi esterni e perseguire obiettivi di efficienza in modo autonomo e in tempo reale. Anche per esse è richiesta l’introduzione di smart meter, connessi ad una rete di comunicazione broadband e in grado di gestire un flusso di monitoraggio e controllo bi-direzionale esteso a tutti gli apparati connessi alla rete elettrica (ma anche del gas, acqua, ecc). La M3N, è un’estensione delle wireless mesh network (WMN). Esse rappresentano una tecnologia fortemente attesa che giocherà un ruolo molto importante nelle futura generazione di reti wireless. Una WMN è una rete di telecomunicazione basata su nodi radio in cui ci sono minimo due percorsi che mettono in comunicazione due nodi. E’ un tipo di rete robusta e che offre ridondanza. Quando un nodo non è più attivo, tutti i rimanenti possono ancora comunicare tra di loro, direttamente o passando da uno o più nodi intermedi. Le WMN rappresentano una tipologia di rete fondamentale nel continuo sviluppo delle reti radio che denota la divergenza dalle tradizionali reti wireless basate su un sistema centralizzato come le reti cellulari e le WLAN (Wireless Local Area Network). Analogamente a quanto successo per le reti di telecomunicazione fisse, in cui si è passati, dalla fine degli anni ’60 ai primi anni ’70, ad introdurre schemi di rete distribuite che si sono evolute e man mano preso campo come Internet, le M3N promettono di essere il futuro delle reti wireless “smart”. Il primo vantaggio che una WMN presenta è inerente alla tolleranza alla caduta di nodi della rete stessa. Diversamente da quanto accade per una rete cellulare, in cui la caduta di una Base Station significa la perdita di servizio per una vasta area geografica, le WMN sono provviste di un’alta tolleranza alle cadute, anche quando i nodi a cadere sono più di uno. L'obbiettivo di questa tesi è quello di valutare le prestazioni, in termini di connettività e throughput, di una M3N al variare di alcuni parametri, quali l’architettura di rete, le tecnologie utilizzabili (quindi al variare della potenza, frequenza, Building Penetration Loss…ecc) e per diverse condizioni di connettività (cioè per diversi casi di propagazione e densità abitativa). Attraverso l’uso di Matlab, è stato quindi progettato e sviluppato un simulatore, che riproduce le caratteristiche di una generica M3N e funge da strumento di valutazione delle performance della stessa. Il lavoro è stato svolto presso i laboratori del DEIS di Villa Grifone in collaborazione con la FUB (Fondazione Ugo Bordoni).

Ex situ X-­Ray absorption study of Li-­rich layered cathode material Li[Li0.2Mn0.56Ni0.16Co0.08]O2

The Li-rich layered transition metal oxides (LLOs) Li2MnO3-LiMO2 (M=Mn, Co, Ni, etc.) have drawn considerable attention as cathode materials for rechargeable lithium batteries. They generate large reversible capacities but the fundamental reaction mechanism and structural perturbations during cycling remain controversial. In the present thesis, ex situ X-ray absorption spectroscopy (XAS) measurements were performed on Li[Li0.2Mn0.56Ni0.16Co0.08]O2 at different stage of charge during electrochemical oxidation/reduction. K-edge spectra of Co, Mn and Ni were recorded through a voltage range of 3.7-4.8V vs. Li/Li+, which consist of X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). Oxidation states during initial charge were discussed based on values from literature as well as XANES analysis. Information about bond distance, coordination number as well as corresponding Debye-Waller factor were extracted from Gnxas analysis of raw data in the EXAFS region. The possibility of oxygen participation in the initial charge was discussed. Co and Ni prove to take part in the oxidation/reduction process while Mn remain in the tetravalent state. The cathode material appears to retain good structural short-range order during charge-discharge. A resemblance of the pristine sample and sample 4 was discovered which was firstly reported for similar compounds.

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.