Title
Simulating multicell populations with an accelerated gro simulator
Authors
Martín Gutiérrez, Alfonso Rodriguez-Paton
Schedule
Date: Friday 8 Sept
Talk Time: TBA
Session: Artificial chemistries and models of cellular dynamics 2 10:30
Keywords
Individual-based Model, Agent-based Model, Synthetic biology, gro, Systems biology, Genetic circuit, Multicell modelling, Microbial colony, Cell-cell communication, Cell shoving algorithm
Abstract
Synthetic Biology follows a Design-Build-Test cycle for the construction of novel circuits. Recently, simulation of circuits has also entered this cycle for accelerating it through early detection and correction of fundamental flaws in the design. One of these simulators is gro, a 2D Individual based Model (IbM). The objectives of this work are to: Implement an IbM platform that can quickly simulate a large amount of E. Coli cells and to extend the array of functions that a cell executes. Our goal is to provide a fast and easy to use IbM simulator for synthetic circuits. We developed multiple extensions for gro as external modules programmed in C/C++. We improved the speed of the simulator through a new physics engine called CellEngine. It implements a ring-based algorithm for cell shoving. A digital protein module that directs the intracellular regulation along with a new language specification layer were added to the simulator as well. We also improved the existing signal capabilities in the simulator. Finally, bacterial conjugation was implemented in the simulator as a new intercellular communication mechanism. Our new gro version enables the simulation of colonies having 10^5 bacteria in minutes; while the previous version took over five days to do the same. The new specification layer and the underlying regulatory module offer a new structure- oriented paradigm where the cell behavior emerges from the specification. All of the new features extend gro to be a fast and versatile tool for prototyping in Synthetic Biology.
