From aba2a35010e9f856081c0b81b6f586241e36e899 Mon Sep 17 00:00:00 2001 From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com> Date: Thu, 10 Oct 2024 20:34:02 +0200 Subject: [PATCH] Apply suggestions from code review Review suggestions Co-authored-by: Jannik Luboeinski <33398515+jlubo@users.noreply.github.com> --- doc/tutorial/full-feature-diffusion.rst | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/tutorial/full-feature-diffusion.rst b/doc/tutorial/full-feature-diffusion.rst index c85681de50..998ff7a534 100644 --- a/doc/tutorial/full-feature-diffusion.rst +++ b/doc/tutorial/full-feature-diffusion.rst @@ -16,7 +16,7 @@ Theory ------ In order to build a complete model, we will need to review the foundational -equations as implemented in Arbor. We assume a single ion species :math:`s` with +equations as implemented in Arbor. We assume a single ion (in general: particle) species :math:`s` with valence :math:`q_s` and no leak currents such that :math:`I_m = I_s`. More ion species can be added, but do not change the fundamental mechanisms. First, the cable equation @@ -71,7 +71,7 @@ amount, in conjunction with the charge per ion :math:`q_s`, which we scale again by the volume :math:`V` to arrive at a change in concentration. We implement this as an NMODL file intended to be added to the full cell that -should look like this +should look like this (cf. :ref:`here `): .. code-block:: @@ -84,7 +84,7 @@ should look like this PARAMETER { F = 96485.3321233100184 (coulomb/mole) : Faraday's constant - diam + diam : compartment diameter xi0 : initial concentration } @@ -112,9 +112,9 @@ Note that this requires explicit intialisation of both ``xi`` and ``xd``. Setting up a Simulation ----------------------- -Having layed the foundation, adding this to a simulation is pretty simple. Save +Having laid the foundation, adding this to a simulation is pretty simple. Save the NMODL file, add it to your local catalogue, and compile & load that via the -usual method. +usual method (cf. :ref:`here `). First, declare the ion -- we'll use a new species ``X`` here, but any name will do -- by calling ``set_ion("X", valence=1)`` on your global properties object. @@ -148,13 +148,13 @@ While simple, note some subtleties around our custom concentration mechanism: ``xi``. If that is not your intention, you will have to provide a modified version of ``nernst`` in which ``xi`` is replaced with ``xd``. -Conclusion ----------- +Final notes +----------- -Apart from some theory, adding an ion with diffusion and full feedback via the -transmembrane current to a simulation is actually quite straightforward. You -might also consider changing the external concentration ``Xo`` according to the -ion current ``iX``. This was not shown above for two reasons. First, Arbor does +Although the related theory is somewhat intricate, as this tutorial has shown, adding an ion (or another particle) with diffusion and full +transmembrane current dynamics to a simulation is quite straightforward. You +might also want to consider changing the external concentration ``Xo`` according to the +ion current ``iX``. This was not shown here for two reasons. First, Arbor does not handle extra-cellular dynamics and thus has no extra-cellular diffusion. Second, the method for handling this is identical to what we have done for ``xi``, so including it doesn't add any insight.