Paris/Cell auto
From 2007.igem.org
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The '''DAP is comsume in bacteria G''' <br><br><br> | The '''DAP is comsume in bacteria G''' <br><br><br> | ||
=='''''We have 3 entities in our model'''''== | =='''''We have 3 entities in our model'''''== | ||
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Bact it has a concentration internal of DAP ('''DAPi''') and external ('''DAPe'''). It's a cell in our automaton<br> | Bact it has a concentration internal of DAP ('''DAPi''') and external ('''DAPe'''). It's a cell in our automaton<br> | ||
BactS is a Bact which produce DAPi<br> | BactS is a Bact which produce DAPi<br> | ||
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=='''''We produce this set of rules'''''== | =='''''We produce this set of rules'''''== | ||
<br> | <br> | ||
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For bactS<br> | For bactS<br> | ||
*DAPe = DAPe + DAPe_diffused_in_neighborhood + DAPi_diffused_from_the_BactS<br> | *DAPe = DAPe + DAPe_diffused_in_neighborhood + DAPi_diffused_from_the_BactS<br> | ||
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*DAPe=DAPe + DAPe_diffused_in_neighborhood - DAPi_diffused_from_the_BactG<br> | *DAPe=DAPe + DAPe_diffused_in_neighborhood - DAPi_diffused_from_the_BactG<br> | ||
*DAPi= DAPi -DAPi_consummate + DAPi_diffused_from_the_BactG<br> | *DAPi= DAPi -DAPi_consummate + DAPi_diffused_from_the_BactG<br> | ||
| - | *BactG = if minimal DAPi for differentiation < DAPi < maximal DAPi for differentiation BactS else stay BactG | + | *BactG = if minimal DAPi for differentiation < DAPi < maximal DAPi for differentiation BactS else stay BactG |
| - | + | ||
<br><br><br> | <br><br><br> | ||
=='''''Initial state'''''== | =='''''Initial state'''''== | ||
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*Minimal Dap needed for differentiation<br> | *Minimal Dap needed for differentiation<br> | ||
*Maximal Dap needed for differentiation<br> | *Maximal Dap needed for differentiation<br> | ||
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<br><br><br> | <br><br><br> | ||
=='''''Output'''''== | =='''''Output'''''== | ||
<br> | <br> | ||
The output is two animated pictures one showinf the differntiation the other the diffusion of DAPe | The output is two animated pictures one showinf the differntiation the other the diffusion of DAPe | ||
Revision as of 15:40, 20 October 2007
Contents |
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
