# Paris/Cell auto

### From 2007.igem.org

(→'''''We make some hypothesis:''''') |
(→'''''We make some hypothesis:''''') |
||

Line 8: | Line 8: | ||

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.<br> | 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.<br> | ||

- | '''Without DAP a cell can't do anything | + | '''Without DAP a cell can't do anything''', so it seems that DAP ''wake up'' bacteria but it's just an artifact.<br> |

The differentiation is '''DAP dependent''', it's append when the cell as enough DAP to evolve but not enough to divide.<br> | The differentiation is '''DAP dependent''', it's append when the cell as enough DAP to evolve but not enough to divide.<br> | ||

The '''DAP is made in bacteria S''', the production rate is the difference between the total production and self consummation<br> | The '''DAP is made in bacteria S''', the production rate is the difference between the total production and self consummation<br> |

## Revision as of 08:04, 25 October 2007

## Contents |

## Spatial simulation

We try with this work to characterize the diffusion of the DAP and the effect on the cells. We have a lawn of bacterias with germinal cells and some somatic cells, we also introduce a spatial localisation for the cells.

## **We make some hypothesis:**

**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.

**Without DAP a cell can't do anything**, so it seems that DAP *wake up* bacteria but it's just an artifact.

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 bags and 2 entities in our model**

**We have 3 bags and 2 entities in our model**

- bag

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

- entity

DAPi internal value of DAP

DAPe external value of DAP

## **We produce this set of rules**

**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**

**Initial state**

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

## **Parameters**

**Parameters**

We have 8 parameters and we can add 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**

**Output**

*We use gbview to generate those pictures*

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.

## **Sources**

**Sources**