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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
Computational simulation of a gene regulatory network implementing an extendable synchronous single-input delay
Imad Hoteit1, Nawwaf Kharma, Luc Varin
1ECE Department, Concordia University, Montreal, QC, Canada. i_hoteit@ece.concordia.ca
Bio Systems
|February 14, 2012
Summary
We engineered the first synchronous gene circuit flip-flop (BioD) in E. coli, using RNA input and light signals. This design enables complex cellular computation and communication networks.
Area of Science:
- Synthetic Biology
- Genetic Engineering
- Systems Biology
Background:
- Developing reliable biological components for computation is crucial.
- Existing genetic toggle switches lack sophisticated synchronization and single-input capabilities.
Purpose of the Study:
- To design and model the first synchronous single-input delay flip-flop gene circuit (BioD) in E. coli.
- To extend the BioD into a synchronous finite state machine (BioFSM) for modular cellular computation.
- To lay the groundwork for cellular automata using communicating bacterial colonies.
Main Methods:
- Design of a gene regulatory network based on Gardner's toggle switch.
- Mathematical modeling and computer simulations to validate functionality.
- Incorporation of update functions and input/output interfaces for advanced capabilities.
Main Results:
- The BioD gene circuit successfully functions as a synchronous delay flip-flop.
- Simulations confirm the device's desired behavior and performance.
- The extended BioFSM demonstrates modularity and potential for inter-cellular communication.
Conclusions:
- The BioD represents a novel, synchronized biological memory element.
- The BioFSM provides a foundation for building complex, programmable biological systems.
- This work facilitates the development of bacterial communication networks and cellular automata.
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