Team:Paris Bettencourt/Modeling/Diffusion

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Team IGEM Paris 2011

model description

we wanted to know if nanotubes are active or passive medium, so we define a model for passive diffusion. So we modelise each bacteria as a 3D M*M*L matrix.
The nanotube are also modelised as a 3D M'*M'*L' matrix.
We adapte each cell to the molecule we want to modelise, so the molecul have a size of 1*1*1. so the matrix is divided in site of the size of a molecule.
For example : for the glucose, if we want to have a size of 1*1*1 the matrix representing the cell need to be 1000*1000*4000 and the nanotube 100*100*600.
All the 100 molecules of the simulation will start in one cell and move randomly until at least 10 molecule pass throw the nanotube to the other cell.
We use a synchronous modelisation so all the 100 molecules move simultaneously. at each row (step of execution), all the molecule move randomly from there site to one of the 26 other possible position.
We take acount of :

  • Brownian movment of particle : each particle have a random movment at each row.
  • colision : we have 2 model of colision :
    • if a molecule colide another object, it will reset to is start point.
    • if a molecule colide another object, it will stay at it's position for this row.
  • colision with cell membrane, nanotube and self colision
for each type of molecule, we do 10 simulation and we take the average time of those 10.

How do we calculate the real time ?


A row correspond to the movment frome one site to an other, so in reality it take So we optain the realtime of diffusion ofr ten molecules throw the nanotube with : Rtime=*(number of row).
finaly we obtain th time for diffusion from a cell to an other with : Rtime/10.
this model is mapped in Maya for a user friendly aspect.

results

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