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Computational Simulation of Gene Regulatory Networks Implementing an Extendable Synchronous Single-Input Delay Flip-Flop and State Machine


Computational Simulation of Gene Regulatory Networks Implementing an Extendable Synchronous Single-Input Delay Flip-Flop and State Machine

Hoteit, Imad (2011) Computational Simulation of Gene Regulatory Networks Implementing an Extendable Synchronous Single-Input Delay Flip-Flop and State Machine. Masters thesis, Concordia University.

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We present a detailed and extendable design of the first synchronous single-input delay flip-flop implemented as a gene regulatory network in Escherichia coli (E. coli). The device, which we call the BioD, has one data input (trans-acting RNA), one clock input (far-red light) and an output that reports the state of the device using green fluorescent protein (GFP). The proposed design builds on Gardner’s toggle switch, to provide a more sophisticated device that can be synchronized with other devices within or without the same cell, and which requires only one data input. We provide a mathematical model of the system and simulation results. The results show that the device behaves in line with desired functionality. Further, we discuss the constraints of the design, which pertain to ranges of parameter values. The BioD is extended via the addition of an update function and input and output interfaces. The result is the BioFSM, which constitutes a synchronous and modular finite state machine, which uses an update function to change its state, stored in the BioD. The BioFSM uses its input and output interfaces for inter-cellular communications. This opens the door to the design of a circular cellular automata (the BioCell), which is envisioned as a number of communicating E. coli colonies, each made of clones of one BioFSM.

Divisions:Concordia University > Gina Cody School of Engineering and Computer Science > Electrical and Computer Engineering
Item Type:Thesis (Masters)
Authors:Hoteit, Imad
Institution:Concordia University
Degree Name:M.A. Sc.
Program:Electrical and Computer Engineering
Date:4 October 2011
Thesis Supervisor(s):Kharma, Nawwaf
Keywords:Escherichia coli, logic gates, synthetic biology, delay flip flop, finite state machine, cellular automata.
ID Code:35979
Deposited By: IMAD HOTEIT
Deposited On:17 Nov 2011 16:59
Last Modified:18 Jan 2018 17:36


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