Search found 37 matches

by adamjhn
Fri Mar 06, 2020 12:24 pm
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 3
Views: 268

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: 294

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: 114

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: 215

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: 215

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: 237

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: 611

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: 1362

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: 1362

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 ...
by adamjhn
Wed Nov 06, 2019 10:02 am
Forum: Reaction-diffusion in NEURON
Topic: Tracking External and Internal Na & K concentration
Replies: 2
Views: 291

Re: Tracking External and Internal Na & K concentration

I've replied here, let me know if you have any problems.
by adamjhn
Wed Nov 06, 2019 9:57 am
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 20
Views: 1362

Re: The equilibrium between the FS and external

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 ...
by adamjhn
Thu Oct 03, 2019 3:21 pm
Forum: Reaction-diffusion in NEURON
Topic: NEURON 7.7.1 RxD issue
Replies: 2
Views: 890

Re: NEURON 7.7.1 RxD issue

Thanks for getting in touch, this is a bug where the reaction tries to find rate strings for all regions the species are defined on rather than the just the region specified in the constructor. A fix has just been pushed to the github; https://github.com/neuronsimulator/nrn Alternatively, a possible...
by adamjhn
Tue Aug 27, 2019 11:48 am
Forum: Reaction-diffusion in NEURON
Topic: Using setpointer() and RXD concentrations
Replies: 1
Views: 622

Re: Using setpointer() and RXD concentrations

The rxd Species, State and Parameter can be accessed in density mechanisms by their name. For example in the extracellular diffusion example ; The species has name='k', charge=1 which is accessed in steady_k.mod with USEION k WRITE ik CHARGE 1 Note the names have to match and the charge must equal t...
by adamjhn
Wed Aug 21, 2019 4:43 pm
Forum: Reaction-diffusion in NEURON
Topic: Using include_flux() properly
Replies: 1
Views: 1471

Re: Using include_flux() properly

Thanks for bringing this oversight to our attention; support for node.include_flux was accidentally broken with the release of NEURON 7.7. (It works in 7.6.x). This will be remedied in 7.7.3. In the meantime it is possible to achieve the outcome of include flux using a Parameter and a Rate. For exam...
by adamjhn
Thu Aug 15, 2019 5:25 pm
Forum: Reaction-diffusion in NEURON
Topic: Parameter and MultiCompartmentReaction Error
Replies: 1
Views: 540

Re: Parameter and MultiCompartmentReaction Error

Thanks for letting us know about this bug, it will be fixed in the next release. As you have identified, one workaround is to use a float instead of a Parameter. Alternatively, like the calcium wave example , you could define the Parameter on the membrane instead of the cytosol; g_ip3r = rxd.Paramet...