www.neuron.yale.edu

Sorry for the delay, you're right about not using charge=0. Rxd reads the currents and then (if they have a charge or valence) divides it by the charge and scale it appropriately to determine the change in concentration. Unfortunately this does not work with charge=0. As you have found, to work arou...

Here is a simple example of two cells connected by diffusion through the extracellular space. from neuron import h, rxd from neuron.rxd import v from neuron.units import mV, s from matplotlib import pyplot h.load_file('stdrun.hoc') # create a couple of cells cell1 = h.Section('cell1') cell1.pt3dclea...

Thanks for getting in touch. Unfortunately I cannot reproduce the error on my machine. It looks like there is a mismatch between the directory where the compiled reactions are stored and the directory we try to load them from. Could you try running the simulation directly, e.g. python -i runCell.py ...

The current work around is to create the regions everywhere as you had before, then alter the diffusion coefficient and use parameters to exclude the unwanted region. Unfortunately, this approach does not allow the volume fraction to vary; that is, if there is no ER in the spine, you might expect cy...

Sorry for the late reply. You’re right that rxd.Extracellular may be more expensive but you could easily include an outside region paralleling the cell (nrn_region=’o’) with minimal overhead cost. Additionally you can use a Parameter, so its value won’t be updated. With a recent improvement on the d...

Sorry for the late response. A feature that was present for extracellular 3d (allowing voxels to have independent diffusion coefficients) was initially omitted form intracellular 3d. It has now been added (in the development branch; https://github.com/neuronsimulator/nrn ). Using that it is possible...

There are no automated unit checks (like modlunit for mod file) in rxd, however you can import constants from neuron.units to scale parameters appropriately, as noted in the circadian rhythm example.

Yes, the diffusion coefficient has units of μm²/ms.

1] Yes, the shell in the mod file is independent of the shells in your rxd model. For your model to make sense you should make sure they are the same. The nmodl current are applied to the rxd region defined with nrn_region='i'. 2] There are race conditions, rxd has a copy of states e.g. cai, which i...

That's a good question, both rxd and nmodl can be used to produce the same results e.g. Hodgkin Huxley model. The advantage of rxd is the code for the calcium dynamics will be all in one place and using the same syntax. The advantage of nmodl is that it allows you to record currents for the specific...

In previous versions of NEURON crxd was a faster implementation of rxd using a C/C++ backend. In the current release (7.7.2) there is no difference as crxd has become rxd. When using the 3D solver, dx is set when creating a region, by default it is 0.25μm. e.g. cyt = rxd.Region(h.allsec(), nrn_regio...

1] The default geometry is rxd.geometry.inside. This is effectively a single shell for the segment. 2] Specifying a geometry changes the way rxd handle the same space, e.g. A region with rxd.Shell(lo, hi) is treated as a hollow cylinder extending from lo multiplied by the segments diameter, to hi mu...

How are you trying to run the example and what errors are you getting? The recommended way is to use the Python interpreter, if you save the example as a file e.g. "example.py", you can execute it with; python -i example.py You can also run it with nrniv or nrngui e.g; nrniv -python example.py More ...

These changes to concentrations in the Frankenhaeuser–Hodgkin would not directly alter the membrane potential, but may influence the currents for mechanisms you choose to put in the axon, via the Nernst potentials. This code above is written with NEURON. Python is the standard interface for NEURON ...

I've replied here, let me know if you have any problems.

The rates you’ve given are in ms, so the rate of change “((Kbath-Ko)/tau)*volume/area surface” is mM μm per ms (assuming the default mM for concentrations and μm for lengths). It looks like you are missing a distance? We can use your time constants to specify the rate at which concentrations in the ...