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Post by Xin on Jun 22, 2021 6:32:20 GMT
Hello,
Is the interaction radius only applied for volume molecules? (Or it can also be applied for surface molecules.)
Best regards,
Xin
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Post by Adam on Jun 22, 2021 13:37:54 GMT
Hello Xin,
thank you for your question.
The interaction radius is only for volume-volume molecule reactions.
Volume-surface reactions interaction radius is given by surface grid density - the tile that was hit by a diffusing volume molecule is checked whethere there is a molecule.
And for surface-surface reactions, the surface molecule first diffuses and ends on a destination tile, its 12 neighbors are then checked for a possible reaction.
Each of this type's reaction probabillity is computed differently so that MCell gives the correct result in the end.
Best regards,
Adam
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Post by Xin on Jun 23, 2021 11:23:24 GMT
Hello Adam,
thank you for your prompt reply. What you mean is the reaction between a volume molecule and a surface. Is it possible to set the reaction radius between volume molecules and surface molecules. I tried a lot of different interaction radii, but the plotted results are all the same. It seems, that the reaction radius does not affect the reaction.
Thank you,
Xin
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Post by Adam on Jun 23, 2021 16:38:49 GMT
Hello Xin,
> What you mean is the reaction between a volume molecule and a surface.
This is a case when a volume molecule freely fiffuses (e.g. in cytoplasm) and then hits a surface molecule located in a membrane. There is a certain probability computed from the reaction rate that these two moleculees will reaction when the volume molecule hits the surface molecu.e
> Is it possible to set the reaction radius between volume molecules and surface molecules.
No, these are fixed.
> I tried a lot of different interaction radii, but the plotted results are all the same. It seems, that the reaction radius does not affect the reaction.
One should see some differences when the copy numbers of molecules are low and the diffusion constants are low as well.
For instance what I tried is to have 100 of 'a' and 100 of 'b' in a cube (1um^3) both with diffusion constants 1e-8, reaction a+b->c with fwd rate 1e8, 100000 iterations. When I set the reaction radius to 0.5 um then there were more reactions (less 'a') that for the default value.
When the molecules have fast diffusion constants and there is sufficient concentration of them, the reaction radius has no effect.
I hope this helps,
Adam
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