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Kappa Modelling - Introduction
Part of EdiGEM's project is to implement the MtrCAB electron transfer system from Shewanella oneidensis in Escherichia coli. Refer to Bioelectric Interface for more information.
We attempt to model this system by using the stochastic, agent-based language Kappa and its implementation KaSim 3.0 which can be downloaded from here. Our kappa code can be found at EdiGEM’s github repository together with a detailed description of all made assumptions and used rates.
The whole process is divided into sub-processes which we try to model separately at first and combine at the end.
Biosensors
Our MATLAB modellers decided to take on the task of modelling the bioelectric interface as a biosensor similar to the one created by the Edinburgh iGEM team in 2006. While the KAPPA modellers were looking at the electron transport going on inside the cell between molecules, the MATLAB modellers wanted to look at how the cell becomes an electric interface and if this can become a useful model.
As described in the video abstract, an inducer molecule starts the process by interacting with the mtrCAB gene which will then lead to the production of the mtrCAB proteins required to make an ordinary cell into a bioelectric interface. If we are to use the bioelectric interface as an arsenic biosensor, the inducer molecule will be the arsenic molecule being detected and the protein being expressed will be the mtrCAB proteins.
