From 2007.igem.org

Contents 1 Spacial simulation 2 We make some hypothesis: 3 We have 3 entities in our model 4 We produce this set of rules 5 Initial state 6 Parameters 7 Output

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

We have 3 entities in our model

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
  

Initial state

We use a 30x30 cells automaton. All cells are BactG excepted 4 BactS which are placed randomly on the automaton

Parameters

We have 8 parameters and we can had noise for each of them.
In BactS:

• Dap export
  
• Dap import
  
• Dap production
  

In BactG:

• Dap export
  
• Dap import
  
• Dap consummation
  
• Minimal Dap needed for differentiation
  
• Maximal Dap needed for differentiation
  

Output

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