Search found 43 matches

by adamjhn
Mon Nov 16, 2020 10:18 am
Forum: Reaction-diffusion in NEURON
Topic: Issue with larger and more equations in Reaction
Replies: 1
Views: 101

Re: Issue with larger and more equations in Reaction

Sorry for the late reply. 1. This is a great question, your workaround sounds reasonable. I don’t think it’s necessary to split the axon into multiple sections, just set nseg as required. An alternative solution is to use node.include_flux, here is a toy example using an nmodl mechanism to allow a l...
by adamjhn
Mon Oct 12, 2020 10:01 pm
Forum: Reaction-diffusion in NEURON
Topic: Help measuring/plotting the cytoplasmic Ca flux (nM/s) as function of Ca concentration
Replies: 2
Views: 165

Re: Help measuring/plotting the cytoplasmic Ca flux (nM/s) as function of Ca concentration

If `pmp_thr` is the only rxd mechanism producing a membrane flux for calcium then simply recording the calcium current (as you have `ca_cur`) is sufficient. Unfortunately if this is not the case the contribution of the current resulting from a particular MulticompartmentReaction is not directly acce...
by adamjhn
Tue Jul 14, 2020 9:12 am
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 770

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

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...
by adamjhn
Tue Jun 30, 2020 10:56 pm
Forum: Reaction-diffusion in NEURON
Topic: Using NEURON to model a system of endocrine cells
Replies: 2
Views: 404

Re: Using NEURON to model a system of endocrine cells

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...
by adamjhn
Wed Apr 22, 2020 11:20 pm
Forum: Reaction-diffusion in NEURON
Topic: Problem initializing with rxd.Rate
Replies: 2
Views: 875

Re: Problem initializing with rxd.Rate

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 ...
by adamjhn
Mon Apr 13, 2020 12:57 pm
Forum: Reaction-diffusion in NEURON
Topic: MultiCompartmentReaction Section List Mismatch
Replies: 1
Views: 572

Re: MultiCompartmentReaction Section List Mismatch

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...
by adamjhn
Fri Mar 06, 2020 12:24 pm
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 3
Views: 898

Re: Cell membrane with PMCA pump

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...
by adamjhn
Tue Feb 25, 2020 10:25 am
Forum: Reaction-diffusion in NEURON
Topic: Making a Nucleus
Replies: 1
Views: 724

Re: Making a Nucleus

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...
by adamjhn
Fri Jan 03, 2020 9:49 am
Forum: Reaction-diffusion in NEURON
Topic: Checking the units
Replies: 2
Views: 575

Re: Checking the units

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.
by adamjhn
Fri Jan 03, 2020 9:45 am
Forum: Reaction-diffusion in NEURON
Topic: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model
Replies: 3
Views: 756

Re: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model

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...
by adamjhn
Wed Dec 18, 2019 1:12 pm
Forum: Reaction-diffusion in NEURON
Topic: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model
Replies: 3
Views: 756

Re: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model

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...
by adamjhn
Tue Dec 10, 2019 4:47 pm
Forum: Reaction-diffusion in NEURON
Topic: rxd, crxd and dx
Replies: 2
Views: 1087

Re: rxd, crxd and dx

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...
by adamjhn
Mon Dec 02, 2019 3:12 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 1192

Re: using diam and L params inside MODL file

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...
by adamjhn
Mon Nov 18, 2019 2:58 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 20
Views: 3229

Re: The equilibrium between the FS and external

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 ...
by adamjhn
Wed Nov 06, 2019 5:15 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 20
Views: 3229

Re: The equilibrium between the FS and external

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 ...