How to implement ion diffusion

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How to implement ion diffusion#

Jaxley allows you to:

  • define ion pumps,

  • update the reversal potential via the Nernst equation, and

  • diffuse ions within a cell.

Here is a small code snippet that shows this (this snippet requires pip install jaxley-mech):

from jaxley.pumps import CaPump, CaNernstReversal
from jaxley_mech.channels.l5pc import CaHVA


branch = jx.Branch()
cell = jx.Cell(branch, parents=[-1, 0, 0])

# Insert a voltage-gated calcium channel.
cell.insert(CaHVA())

# Insert an ion pump which modifies the intracellular calcium based on the calcium current.
cell.insert(CaPump())

# Insert a mechanism that updates the calcium reversal potential based on the intracellular calcium level.
cell.insert(CaNernstReversal())

# Let the intracellular calcium diffuse within the cell.
cell.diffuse("CaCon_i")
cell.set("axial_resistivity_CaCon_i", 1_000.0)

Jaxley does not yet provide functionality for diffusing ions extracellularly. In addition, intracellular ion diffusion in Jaxley currently has the following limitations:

  • we only allow to diffuse ions within the entire cell (not in just a few branches),

  • if enabled, ion diffusion occurs within every cell of a network.

Finally, note that, even when ion diffusion is enabled, Jaxley uses a cylindrical approximation for the compartment area (which is unlike NEURON, which uses a conic approximation when ion diffusion is enabled).

More explanation#

See this tutorial for more information.

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