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.

Non linear response of planar asymmetric systems

The seismic behaviour of one-storey asymmetric structures has been studied since 1970s by a number of researches studies which identified the coupled nature of the translational-to-torsional response of those class of systems leading to severe displacement magnifications at the perimeter frames and therefore to significant increase of local peak seismic demand to the structural elements with respect to those of equivalent not-eccentric systems (Kan and Chopra 1987). These studies identified the fundamental parameters (such as the fundamental period TL normalized eccentricity e and the torsional-to-lateral frequency ratio Ωϑ) governing the torsional behavior of in-plan asymmetric structures and trends of behavior. It has been clearly recognized that asymmetric structures characterized by Ωϑ >1, referred to as torsionally-stiff systems, behave quite different form structures with Ωϑ <1, referred to as torsionally-flexible systems. Previous research works by some of the authors proposed a simple closed-form estimation of the maximum torsional response of one-storey elastic systems (Trombetti et al. 2005 and Palermo et al. 2010) leading to the so called “Alpha-method” for the evaluation of the displacement magnification factors at the corner sides. The present paper provides an upgrade of the “Alpha Method” removing the assumption of linear elastic response of the system. The main objective is to evaluate how the excursion of the structural elements in the inelastic field (due to the reaching of yield strength) affects the displacement demand of one-storey in-plan asymmetric structures. The system proposed by Chopra and Goel in 2007, which is claimed to be able to capture the main features of the non-linear response of in-plan asymmetric system, is used to perform a large parametric analysis varying all the fundamental parameters of the system, including the inelastic demand by varying the force reduction factor from 2 to 5. Magnification factors for different force reduction factor are proposed and comparisons with the results obtained from linear analysis are provided.

Studio e realizzazione di un "timing circuit" e "output circuit" per pacemaker

Nell'elaborato è stato svolto uno studio su più livelli degli elementi essenziali del pacemaker asincrono secondo la realizzazione circuitale proposta da Wilson Greatbatch nel 1960. Un primo livello ha riguardato l’analisi teorica del circuito. Un secondo livello ha riguardato un’analisi svolta con LTSPICE. Con questo stesso programma, si è analizzato il segnale di temporizzazione e la forma d’onda sul carico al variare del valore di alcuni componenti chiave del circuito. Infine, si è proceduto alla sua realizzazione su breadboard.

Precise Near-Field Focusing exploiting Bessel Beam Launchers for Wireless Power Transfer at millimeter waves

Wireless Power Transfer has become a promising technology to overcome the limits of wired solutions. Within this framework, the objective of this thesis is to study a WPT link at millimeter waves involving a particular type of antenna working in the radiative near-field, known as Bessel Beam (BB) Launcher. This antenna has been chosen for its peculiarity of generating a Bessel Beam which is by nature non-diffractive, showing good focusing and self-healing capabilities. In particular, a Bull-Eye Leaky Wave Antenna is designed and analysed, fed by a loop antenna and resonating at approximately 30 GHz. The structure excites a Hybrid-TE mode showing zeroth-order Bessel function over the z-component of the magnetic field. The same antenna is designed with two different dimensions, showing good wireless power transport properties. The link budgets obtained for different configurations are reported. With the aim of exploiting BB Launchers in wearable applications, a further analysis on the receiving part is conducted. For WPT wearable or implantable devices a reduced dimension of the receiver system must be considered. Therefore, an electrically large loop antenna in planar technology is modified, inserting phase shifters in order to increase the intensity of the magnetic field in its interrogation zone. This is fundamental when a BB Launcher is involved as transmitter. The loop antenna, in reception, shows a further miniaturization level since it is built such that its interrogation zone corresponds to the main beam dimension of transmitting BB Launcher. The link budget is evaluated with the new receiver showing comparable results with respect to previous configurations, showing an efficient WPT link for near-field focusing. Finally, a matching network and a full-wave rectifying circuit are attached to two of the different receiving systems considered. Further analysis will be carried out about the robustness of the square loop over biological tissues.

Experimental characterization of a planar jet by hot-wire anemometry

The study of turbulence is also nowadays a problem that does not have solution from the mathematical point of view due to the lack of solution to link the mean part of the flow with the fluctuating one. To solve this problem, in the CICLoPE laboratory of Predappio, experiments on different type of jets are performed in order to derive a closure model able to close our mathematical model. One of the most interesting type of jet that could be studied is the planar turbulent free jet which is a two dimensional canonical jet characterized by the self-similarity condition of the velocity profiles. To study this particular jet, a new facility was built. The aim of this project is to characterize the jet at different distances from the nozzle exit, for different values of Reynolds number, to demonstrate that the self-similarity condition is respected. To do that, the evaluation of quantities such as spreading rate, centerline velocity decay and relation between fluctuations and mean part of the flow has to be obtain. All these parameters could be detected thanks to the use of single and X hot-wire anemometry with which it is possible to analyzed the fluctuating behaviour of the flow by associating to an electric signal a physical variable expressed in terms of velocity. To justify the data obtain by the measures, a comparison with results coming from the literature has to be shown.

Development and Automatization of a Planar Jet Wind Tunnel for the X-wire Calibration

The scope of this study is to design an automatic control system and create an automatic x-wire calibrator for a facility named Plane Air Tunnel; whose exit creates planar jet flow. The controlling power state as well as automatic speed adjustment of the inverter has been achieved. Thus, the wind tunnel can be run with respect to any desired speed and the x-wire can automatically be calibrated at that speed. To achieve that, VI programming using the LabView environment was learned, to acquire the pressure and temperature, and to calculate the velocity based on the acquisition data thanks to a pitot-static tube. Furthermore, communication with the inverter to give the commands for power on/off and speed control was also done using the LabView VI coding environment. The connection of the computer to the inverter was achieved by the proper cabling using DAQmx Analog/Digital (A/D) input/output (I/O). Moreover, the pressure profile along the streamwise direction of the plane air tunnel was studied. Pressure tappings and a multichannel pressure scanner were used to acquire the pressure values at different locations. Thanks to that, the aerodynamic efficiency of the contraction ratio was observed, and the pressure behavior was related to the velocity at the exit section. Furthermore, the control of the speed was accomplished by implementing a closed-loop PI controller on the LabView environment with and without using a pitot-static tube thanks to the pressure behavior information. The responses of the two controllers were analyzed and commented on by giving suggestions. In addition, hot wire experiments were performed to calibrate automatically and investigate the velocity profile of a turbulent planar jet. To be able to analyze the results, the physics of turbulent planar jet flow was studied. The fundamental terms, the methods used in the derivation of the equations, velocity profile, shear stress behavior, and the effect of vorticity were reviewed.

Towards the kinetic resolution of mechanically planar chiral rotaxanes

In this work, we reported the synthesis and characterization of two [2]rotaxanes endowed with a central ammonium group and two triazolium recognition stations on either side, acting as complexation sites for a dibenzo-24-crown-8 ether macrocycle. These mechanically interlocked architectures were obtained through the interlocking of a functionalized achiral macrocycle with Cs symmetry (where the symmetry element is a mirror plane corresponding to plane of the ring) and a C∞v symmetric axle (where a mirror plane and a C∞ principal axis are aligned along the axle length). We took advantage of the reversible acid/base triggered molecular shuttling of the ring between two lateral triazolium units to switch the rotaxanes between prochiral and mechanically planar chiral forms, which exists as two rapidly-interconverting co-conformers. We exploited the reactivity of the central amino group to attach an optically pure chiral substituent, with the goal of demonstrating the enantiomeric nature of the co-conformers and to obtain a non-zero diastereomeric excess in the resulting diastereomeric products through a dynamic kinetic resolution. To this end, two enantiopure reagents were chosen that could perform clean and fast reaction with amines: a sulfonyl chloride and an acyl chloride. Only the acyl chloride successfully produced an amide in high yield with the deprotonated rotaxane. The group added to the central amine station acted as a stopper against the shuttling of the macrocycle along the axis, thus preventing the fast interconversion of the two mechanically planar enantiomers. We analysed the results through static and dynamic NMR spectroscopic techniques by varying temperature and solvent used. Indeed, the presence of diastereomers was recorded alongside the configurational isomers resulting from the slow rotation of the CN-CO bond of the amide moiety, thus paving the way for a dynamic kinetic resolution.