Consider an axon of length $L$ with the soma located at $x=0$ and the tip located at $x=L$.

We assume that there is a constant input of Kinesin motors to location $x=0$ coming in from $x \le 0$.

Assuming that all Kinesin motors travel at the same speed $v$, the proteins reach the location $x=L$ after a time $\tau = \frac{L}{v}$.

At $x=L$, incoming Kinesin motors induce Dynein motors to travel from $x=L$ to $x=0$.

Assuming that all Dynein motors travel also at the same speed $v$, they reach the Location $x=0$ after a time $\tau = \frac{L}{v}$.

At $x=0$, incoming Dynein motors inhibit Kinesin motors from travelling to $x=L$.

Thus, we get a negative feedback.

My question:

Can this system of mutual promoting and repressing preoteins be simulated using Gillespie algorithm?

I already simulated it with a mathematical model of delay-differential equations, but as this model doesn' t show all effects, I would like to try using Gillespie algorithm.

  • $\begingroup$ Why don't you just try it and find out? $\endgroup$ – MattDMo Sep 4 '16 at 18:21
  • $\begingroup$ Yes Gillespie's algorithm has been used to study such feedbacks. Are you also modelling diffusion? In that case you should also incorporate Brownian motion. $\endgroup$ – WYSIWYG Sep 5 '16 at 6:01
  • $\begingroup$ Yes, I' m also modelling diffusion. Thank you for your help! $\endgroup$ – Peter123 Sep 5 '16 at 13:16

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