From 2007.igem.org

Contents 1 Spatial 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

Spatial 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 consumed 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 show the differentiation the other the diffusion of DAPe

• The first picture show the diffusion of DAP

We can see a front wave in light blue after that there is a dark blue area in which the systeme is stable the concentration doesn't evolve.

• The second picture show the differentiation

Red BactG

Green BactS

The differentiation follow the wave front

After playing with the parameters, we can deduct 2 important things:

• The inhibition most be strong and effective (we play with the minimal and maximal value of DAP for differentiation)

if it isn't the case the system collapse all the bactG stay BactG if the inhibition is too strong or switch to BactS if the inhibition is not enough strong.

• The production and diffusion of DAP will be a critical factor

The DAP has to be produce then he will be exported, it will diffuse in the medium and will be imported

There is no proof of a special system to import or export DAP, so for each step there is a large amount of DAP lost.