Search found 13 matches

by Tuoma
Thu Oct 13, 2022 2:16 am
Forum: Reaction-diffusion in NEURON
Topic: parameter controlling the rate of influx of a species in multiple compartments
Replies: 1
Views: 297

Re: parameter controlling the rate of influx of a species in multiple compartments

I think I resolved the issue. The problem seems to be that I first defined a "master" RxD region 'cyt' and then for each of the sections (already included in 'cyt') a separate miniregion cyts , and maybe that's what caused the error message "Rates and Reactions with species defined on...
by Tuoma
Wed Oct 05, 2022 11:09 am
Forum: Reaction-diffusion in NEURON
Topic: parameter controlling the rate of influx of a species in multiple compartments
Replies: 1
Views: 297

parameter controlling the rate of influx of a species in multiple compartments

I'm trying to introduce RxD species and reactions into a set of compartments in a multicompartmental neuron model and give inputs to some of the species. I have a list of sections for which I'm creating the Rxd Region (after defining a cell model L5PC, in this case a regular Hay model) as seclist = ...
by Tuoma
Mon Sep 19, 2022 7:33 am
Forum: Reaction-diffusion in NEURON
Topic: Reading species concentration in a MOD file using a list of species
Replies: 1
Views: 135

Reading species concentration in a MOD file using a list of species

I'm trying to make a .mod ion-channel mechanism file where the maximal conductance of the channel would depend on the concentration of a certain species. Currently all my molecular species are part of a list, meaning that they are called 'specs[0]' ... 'specs[19]' and I define my reactions as e.g. r...
by Tuoma
Mon Mar 01, 2021 4:18 am
Forum: Reaction-diffusion in NEURON
Topic: Running pde solver more than once
Replies: 6
Views: 12764

Re: Running pde solver more than once

I've got another issue related to this topic. I used to run my simulator from the command line (even inside a python script) to make sure there are no issues with reinitialization of the RxD model. Now I'm trying to rewrite the code to be run as a normal python function to avoid i/o overload on the ...
by Tuoma
Wed Aug 14, 2019 5:14 am
Forum: Reaction-diffusion in NEURON
Topic: decay reactions
Replies: 1
Views: 1374

decay reactions

How to implement a decay reaction (a reaction with no products)?

In an earlier NEURON version it was possible to write

Code: Select all

reaction_decay = rxd.Reaction(Ca > 0*Ca, 1e-8)
but now (v. 7.7) I get an error "AttributeError: 'Reaction' object has no attribute '_react_regions'"
by Tuoma
Fri Nov 16, 2018 6:07 am
Forum: Reaction-diffusion in NEURON
Topic: maximum length for the name of a species?
Replies: 2
Views: 2456

Re: maximum length for the name of a species?

Thanks for the reply. However, the problem persists even if I remove "nrn_region='i'", or change it to None or 'o'.
by Tuoma
Wed Nov 14, 2018 10:59 am
Forum: Reaction-diffusion in NEURON
Topic: maximum length for the name of a species?
Replies: 2
Views: 2456

maximum length for the name of a species?

I get a weird "Abort trap: 6" error that seems to depend on the length of the names of my species. MWE: from neuron import h, rxd from pylab import * h.load_file('stdrun.hoc') dend = h.Section(name='dend') cyt = rxd.Region([dend], name='cyt', nrn_region='i') specNameLen=21 specs = [] vecs ...
by Tuoma
Tue Jul 31, 2018 3:22 am
Forum: Anatomically detailed models
Topic: Changing diameters of reconstructed neurons
Replies: 5
Views: 3634

Re: Changing diameters of reconstructed neurons

I'm getting a syntax error with NEURON 7.5 whenever I try to assign something to diam3d(j), e.g.
forall {
for (j = 0; j < n3d(); j+=1) {
diam3d(j)=1.0
}
}
by Tuoma
Mon Jul 30, 2018 3:47 am
Forum: Anatomically detailed models
Topic: Changing diameters of reconstructed neurons
Replies: 5
Views: 3634

Changing diameters of reconstructed neurons

I have a reconstructed morphology (loaded from an .asc file), where I would like to change the diameters of the sections by some factor. Is there a neat way of doing it? For a starter, I tried forall { for (j = 0; j < nseg+1; j+=1 ) { diam(j/nseg) = diam(j/nseg)*1.0 } } but it changed the diameter a...
by Tuoma
Mon Jun 11, 2018 11:25 am
Forum: Reaction-diffusion in NEURON
Topic: Custom reaction rates
Replies: 1
Views: 3049

Custom reaction rates

How can I customize the reaction rates? (Do you have a tutorial on it somewhere?) To be more concrete, I thought I could replace reaction = rxd.Reaction(2 * hydrogen + oxygen > water, 1.0) by reac_speed = 1.0*hydrogen**2*oxygen reaction = rxd.Reaction(2 * hydrogen + oxygen > water, reac_speed) It ru...
by Tuoma
Tue May 08, 2018 5:02 am
Forum: Reaction-diffusion in NEURON
Topic: Negative concentrations
Replies: 5
Views: 5290

Re: Negative concentrations

Thanks for the reply. The system was a mass-action reaction system, and the rates of all injected species were positive. But I finally managed to solve the problem by making the tolerance way smaller (down to 3e-9) than it used to be. The downside is of course that now my simulations are much slower...
by Tuoma
Mon May 07, 2018 10:36 am
Forum: Reaction-diffusion in NEURON
Topic: Negative concentrations
Replies: 5
Views: 5290

Negative concentrations

Is there a way to force the concentrations to be non-negative? I'm using CVode and adaptive time step in a system of >100 reactions, and very often end up with negative concentrations for some of the species, although initial concentrations are all non-negative. Consequently (at least so it seems), ...
by Tuoma
Tue Apr 24, 2018 10:10 am
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 6170

basic questions on RxD

I have some questions to which I didn't find answers in the tutorial. 1) How can I record concentrations? Say, I would like to record the hydrogen concentration at location dend(0.5) into a vector in the example of https://neuron.yale.edu/neuron/static/docs/rxd/tut_main.html#simple-reaction-with-abr...