Gap junction depends on the pre- and postsynaptic intracellular concentrations

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Dec 2, 2019, 11:21:24 AM12/2/19
to DynaSim Users
Hi all,

We have encountered a difficulty while implementing a network with gap junctions, when the gap junction current is given by the Goldman-Hodgkin-Katz equation (this is useful, when investigating spreading depression waves in a computational network).
For the membrane potential the "V_pre" and "V_post" reserved variables are very useful in a connection mechanism, allowing access to the pre- and postsynaptic cells. However, because the connection mechanism here also depends on the post/pre gap junction (sodium and potassium) concentrations, we were wondering if a similar approach exists in Dynasim for the concentrations (e.g. Na_post and Na_pre for post- and presynaptic sodium). 

Is there an efficient and clean way to implement this type of mechanism in Dynasim?

Kind regards,

Ardid, Salva

Dec 2, 2019, 11:34:31 AM12/2/19
Hi Thomas,

You should be able to access any state variable that way. Did you try and didn't work?


El dilluns, 2 de desembre de 2019, a les 11:21:24 EST, va escriure:

Thomas Tarnaud (UGent-imec)

Dec 4, 2019, 6:13:05 AM12/4/19
to Ardid, Salva,
Dear Salva,

Thank you for the response.
We tried to access the concentration state variables this way: we now notice that this works, only if the state variable is defined in the equations cell.
If the state variable is defined in a .mech file, the _pre and _post method doesn't seem to be recognized by Dynasim (although Dynasim labels the concentrations as state variables in the name_map, that is generated by dsGenerateModel).

We were wondering if it is possible in Dynasim to use the _pre and _post syntax, together with state variables that are defined in .mech-files: this would allow a more elegant implementation of our model.

Thank you and with kind regards,
Van: Ardid, Salva <>
Verzonden: maandag 2 december 2019 17:34
CC: Thomas Tarnaud (UGent-imec)
Onderwerp: Re: [DS] Gap junction depends on the pre- and postsynaptic intracellular concentrations

Ardid, Salva

Dec 4, 2019, 6:53:37 AM12/4/19
to Thomas Tarnaud (UGent-imec),
Yes, that seems right. Perhaps it is different in the Dev branch, but I'm not sure. What Dynasim version are you using?

Anyway, this seems a proper request. I invite you to submit this issue in github at

In order to reproduce and debug or help implementing, submitting a minimal code that reproduces the issue in your system helps us a lot. In your case this means a minimal main script with main equations and two minimal mechanisms, a first one creating a state variable, and a second one using the pre/post version of the state variable of the first mechanism. Please test that this minimal code works fine when you define the state variable in the main script but it doesn't when created within a mechanism, and that this still happens when using the Dev branch of Dynasim.

Thanks and best,

El dimecres, 4 de desembre de 2019, a les 6:13:02 EST, Thomas Tarnaud (UGent-imec) va escriure:
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