NMODL: COMPARTMENT statement in the KINETIC section

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ziemek
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NMODL: COMPARTMENT statement in the KINETIC section

Post by ziemek » Thu Nov 21, 2019 7:47 am

From the Neuron Book, chapter 9.

Ca2+ shells diffusion is defined as follows:

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KINETIC state {
    COMPARTMENT i, diam*diam*vol[ i ] {ca CaBuffer Buffer}
}
  • How does the COMPARTMENT statement work?
  • Why there is diam^2?
  • What is its relation to the volume?
  • if shell_volume=diam*diam*vol[ i ] -> does the rate constant f[ i ] is divided by the shell_volume on each time step?
Also there is:

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PROCEDURE factors() { 
   LOCAL r, dr2 r
   r = 1/2 : starts at edge (half diam)
   : [...]
}
Which stands that r=1/2 which is half of diam. But diam is a param, so it could be specified as any number different than 1. Is it a mistake?

I would be very glad for your help because that part in the book is a little bit confusing for me.

ted
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Re: NMODL: COMPARTMENT statement in the KINETIC section

Post by ted » Thu Nov 21, 2019 1:47 pm

If you actually have a copy of The NEURON Book, see the discussion in 9.10.1 Modeling diffusion with kinetic schemes. Any reader of this thread who does not have the book may download this earlier draft of chapter 9
https://www.neuron.yale.edu/ftp/ted/boo ... xedref.pdf
and read Modeling diffusion with kinetic schemes which starts on page 36 of that pdf.

ziemek
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Re: NMODL: COMPARTMENT statement in the KINETIC section

Post by ziemek » Mon Nov 25, 2019 6:16 am

You're right. After I carefully studied chapters 3 and 9 I got it.

For those who may have similar questions - please read first: Compartment size in the section on Chemical reactions in Chapter 3 and then get back to the Chapter 9.

As to answer my questions (if anyone has similar problems):
1/4. COMPARTMENT statement's volume is computed as mentioned in the Compartment size section of Chapter 3
2/3. diam^2 is pure scaling factor for unit volume

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