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.

Riorganizzazione di un distribution center mediante le tecniche di lean production: il caso Gambro Dasco spa

La Lean Production è un tema di estrema attualità per tutte le aziende che abbiano compreso l’importanza di produrre di più, con le risorse che si hanno a disposizione, eliminando sistematicamente tutte le attività che non creano valore aggiunto. La Produzione Snella è diventato un metodo per incrementare la competitività, riducendo l’incertezza e aumentando il servizio fornito al cliente. Nella realtà attuale vi è ancora una scarsa diffusione dei concetti Lean. Le cause di questo problema sono imputabili soprattutto alla cultura del management aziendale, alla mancanza di efficaci strumenti tecnologici a supporto, e in alcuni casi, la scarsa disponibilità delle imprese ad abbracciare la filosofica “snella”. La presente tesi, dopo una panoramica introduttiva su l’origine e l’evoluzione del Pensiero Snello e l’analisi di tutti i tools disponibili per combattere lo spreco; si propone di analizzare l’applicazione degli stessi in Gambro Dasco, multinazionale biomedicale leader nella vendita delle sue apparecchiature per dialisi.

Modelling, simulation and optimization of maintenance considerations on condition based maintenance

Globalization has increased the pressure on organizations and companies to operate in the most efficient and economic way. This tendency promotes that companies concentrate more and more on their core businesses, outsource less profitable departments and services to reduce costs. By contrast to earlier times, companies are highly specialized and have a low real net output ratio. For being able to provide the consumers with the right products, those companies have to collaborate with other suppliers and form large supply chains. An effect of large supply chains is the deficiency of high stocks and stockholding costs. This fact has lead to the rapid spread of Just-in-Time logistic concepts aimed minimizing stock by simultaneous high availability of products. Those concurring goals, minimizing stock by simultaneous high product availability, claim for high availability of the production systems in the way that an incoming order can immediately processed. Besides of design aspects and the quality of the production system, maintenance has a strong impact on production system availability. In the last decades, there has been many attempts to create maintenance models for availability optimization. Most of them concentrated on the availability aspect only without incorporating further aspects as logistics and profitability of the overall system. However, production system operator’s main intention is to optimize the profitability of the production system and not the availability of the production system. Thus, classic models, limited to represent and optimize maintenance strategies under the light of availability, fail. A novel approach, incorporating all financial impacting processes of and around a production system, is needed. The proposed model is subdivided into three parts, maintenance module, production module and connection module. This subdivision provides easy maintainability and simple extendability. Within those modules, all aspect of production process are modeled. Main part of the work lies in the extended maintenance and failure module that offers a representation of different maintenance strategies but also incorporates the effect of over-maintaining and failed maintenance (maintenance induced failures). Order release and seizing of the production system are modeled in the production part. Due to computational power limitation, it was not possible to run the simulation and the optimization with the fully developed production model. Thus, the production model was reduced to a black-box without higher degree of details.

Dynamic characterisation of four nine-story large-panel R.C. buildings in Bishkek (Kyrgyzstan): A comparison between experimental ambient vibration analysis and numerical finite element modeling

With the outlook of improving seismic vulnerability assessment for the city of Bishkek (Kyrgyzstan), the global dynamic behaviour of four nine-storey r.c. large-panel buildings in elastic regime is studied. The four buildings were built during the Soviet era within a serial production system. Since they all belong to the same series, they have very similar geometries both in plan and in height. Firstly, ambient vibration measurements are performed in the four buildings. The data analysis composed of discrete Fourier transform, modal analysis (frequency domain decomposition) and deconvolution interferometry, yields the modal characteristics and an estimate of the linear impulse response function for the structures of the four buildings. Then, finite element models are set up for all four buildings and the results of the numerical modal analysis are compared with the experimental ones. The numerical models are finally calibrated considering the first three global modes and their results match the experimental ones with an error of less then 20%.

Manutenzione preventiva della Rail Line tramite il metodo MAGEC

L'elaborato è il risultato del progetto di tesi svolto presso l’azienda Lift Truck Equipment L.T.E. di Ostellato (Ferrara) che opera nell’ambito della progettazione e produzione di gruppi di sollevamento ed attrezzature per carrelli elevatori all’interno del gruppo Toyota Material Handling. Il progetto è stato svolto nel periodo da gennaio a marzo 2016 in collaborazione con l’ufficio di Ingegneria di processo di L.T.E. e riguarda l’applicazione del metodo MAGEC (Modi e Analisi dei Guasti e delle Criticità) per l’analisi dei guasti di una linea produttiva dell’azienda, la Rail Line. Nel primo capitolo viene inquadrato il sistema produttivo dell’azienda in aderenza con la filosofia del TPS (Toyota Production System) per chiarire l’ambito in cui è nato il progetto, le motivazioni che hanno portato al suo sviluppo e l’ottica secondo cui è stato svolto. Nel secondo capitolo è fornita una descrizione dell’approccio utilizzato, che consiste in una variante della FMECA, il metodo più utilizzato per le analisi in ambito affidabilistico. Inoltre sono riportate le attività di pianificazione che sono state svolte preliminarmente all’inizio del progetto. Successivamente nel terzo capitolo sono illustrati in modo dettagliato i vari step dell’implementazione del metodo, dalla raccolta dati, effettuata presso l’azienda, all’elaborazione. L’ultimo capitolo è dedicato ai risultati dell’analisi e a una breve descrizione di come tali risultati sono stati utilizzati nelle attività di manutenzione preventiva.