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.

Influence of microstructure variability on short crack growth behavior

Fatigue life in metals is predicted utilizing regression analysis of large sets of experimental data, thus representing the material’s macroscopic response. Furthermore, a high variability in the short crack growth (SCG) rate has been observed in polycrystalline materials, in which the evolution and distributionof local plasticity is strongly influenced by the microstructure features. The present work serves to (a) identify the relationship between the crack driving force based on the local microstructure in the proximity of the crack-tip and (b) defines the correlation between scatter observed in the SCG rates to variability in the microstructure. A crystal plasticity model based on the fast Fourier transform formulation of the elasto-viscoplastic problem (CP-EVP-FFT) is used, since the ability to account for the both elastic and plastic regime is critical in fatigue. Fatigue is governed by slip irreversibility, resulting in crack growth, which starts to occur during local elasto-plastic transition. To investigate the effects of microstructure variability on the SCG rate, sets of different microstructure realizations are constructed, in which cracks of different length are introduced to mimic quasi-static SCG in engineering alloys. From these results, the behavior of the characteristic variables of different length scale are analyzed: (i) Von Mises stress fields (ii) resolved shear stress/strain in the pertinent slip systems, and (iii) slip accumulation/irreversibilities. Through fatigue indicator parameters (FIP), scatter within the SCG rates is related to variability in the microstructural features; the results demonstrate that this relationship between microstructure variability and uncertainty in fatigue behavior is critical for accurate fatigue life prediction.

Progetto di un sistema a microcontrollore per modulazione back-scattering uwb

La tesi tratta il progetto di una piattaforma di simulazione per modulazioni back-scatter UWB su un sistema a microcontrollore PIC. Il sistema utilizza uno switch a UWB per eseguire la modulazione, modificando le condizioni di carico d'antenna; il software implementa la modulazione attraverso la variazione del segnale di controllo dello switch e si interfaccia con l'utente attraverso l'uso di una periferica USB, permettendo la modifica runtime della configurazione. Si interfaccia inoltre con strumenti esterni attraverso segnali di sincronizzazione.

High precision radial velocities with giano spectra

Radial velocities measured from near-infrared (NIR) spectra are a potential tool to search for extrasolar planets around cool stars. High resolution infrared spectrographs now available reach the high precision of visible instruments, with a constant improvement over time. GIANO is an infrared echelle spectrograph and it is a powerful tool to provide high resolution spectra for accurate radial velocity measurements of exo-planets and for chemical and dynamical studies of stellar or extragalactic objects. No other IR instruments have the GIANO's capability to cover the entire NIR wavelength range. In this work we develop an ensemble of IDL procedures to measure high precision radial velocities on a few GIANO spectra acquired during the commissioning run, using the telluric lines as wevelength reference. In Section 1.1 various exoplanet search methods are described. They exploit different properties of the planetary system. In Section 1.2 we describe the exoplanet population discovered trough the different methods. In Section 1.3 we explain motivations for NIR radial velocities and the challenges related the main issue that has limited the pursuit of high-precision NIR radial velocity, that is, the lack of a suitable calibration method. We briefly describe calibration methods in the visible and the solutions for IR calibration, for instance, the use of telluric lines. The latter has advantages and problems, described in detail. In this work we use telluric lines as wavelength reference. In Section 1.4 the Cross Correlation Function (CCF) method is described. This method is widely used to measure the radial velocities.In Section 1.5 we describe GIANO and its main science targets. In Chapter 2 observational data obtained with GIANO spectrograph are presented and the choice criteria are reported. In Chapter 3 we describe the detail of the analysis and examine in depth the flow chart reported in Section 3.1. In Chapter 4 we give the radial velocities measured with our IDL procedure for all available targets. We obtain an rms scatter in radial velocities of about 7 m/s. Finally, we conclude that GIANO can be used to measure radial velocities of late type stars with an accuracy close to or better than 10 m/s, using telluric lines as wevelength reference. In 2014 September GIANO is being operative at TNG for Science Verification and more observational data will allow to further refine this analysis.

From the traditional verification approach to the spatial methods: a study of applicability of the SAL metric in the framework of the WMO project MesoVICT

Increasing in resolution of numerical weather prediction models has allowed more and more realistic forecasts of atmospheric parameters. Due to the growing variability into predicted fields the traditional verification methods are not always able to describe the model ability because they are based on a grid-point-by-grid-point matching between observation and prediction. Recently, new spatial verification methods have been developed with the aim of show the benefit associated to the high resolution forecast. Nested in among of the MesoVICT international project, the initially aim of this work is to compare the newly tecniques remarking advantages and disadvantages. First of all, the MesoVICT basic examples, represented by synthetic precipitation fields, have been examined. Giving an error evaluation in terms of structure, amplitude and localization of the precipitation fields, the SAL method has been studied more thoroughly respect to the others approaches with its implementation in the core cases of the project. The verification procedure has concerned precipitation fields over central Europe: comparisons between the forecasts performed by the 00z COSMO-2 model and the VERA (Vienna Enhanced Resolution Analysis) have been done. The study of these cases has shown some weaknesses of the methodology examined; in particular has been highlighted the presence of a correlation between the optimal domain size and the extention of the precipitation systems. In order to increase ability of SAL, a subdivision of the original domain in three subdomains has been done and the method has been applied again. Some limits have been found in cases in which at least one of the two domains does not show precipitation. The overall results for the subdomains have been summarized on scatter plots. With the aim to identify systematic errors of the model the variability of the three parameters has been studied for each subdomain.