From 2007.igem.org

Spacial simulation

We try with this work to characterize the diffusion of the DAP and the effect on the cells. We have a "tapis bactériens" with germinal cells and some somatic cells.

We make some hypothesis:

We work with a constant population (no death and no division), we can imagine that we are a stationary phase or between to division cycle.
The differentiation is DAP dependent, it's append when the cell as enough DAP to evolve but not enough to divide.
The DAP is made in bacteria S, the production rate is the difference between the total production and self consummation
The DAP can be under two types intra/extra cellular (DAPi/DAPe)
The DAP is comsume in bacteria G

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We have 3 entities in our model </b></u>

Bact it has a concentration internal of DAP DAPi and external DAPe. It's a cell in our automaton BactS is a Bact which produce DAPi BactG is a Bact which consume DAPi

We produce this set of rules: For bactS -DAPe = DAPe + DAPe_diffused_in_neighborhood + DAPi_diffused_from_the_BactS -DAPi= DAPi +DAPi_produced - DAPi<_diffused_from_the_BactS

For BactG -DAPe=DAPe + DAPe_diffused_in_neighborhood - DAPi_diffused_from_the_BactG -DAPi= DAPi -DAPi_consummate + DAPi_diffused_from_the_BactG -BactG = if minimal DAPi for differentiation < DAPi < maximal DAPi for differentiation BactS else stay BactG

The output is two animated pictures one showinf the differntiation the other the diffusion of DAPe