Search found 43 matches

by bremen
Mon Feb 01, 2021 7:28 am
Forum: Adding new mechanisms and functions to NEURON
Topic: A pump MOD file and no concentration inside
Replies: 3
Views: 330

Re: A pump MOD file and no concentration inside

Hello Ted.

Thank you very much.
I was missing the "mass balance equation".
I have added it to the MOD file and everything is working fine.

Best
Stefano
by bremen
Sat Jan 30, 2021 3:00 am
Forum: Adding new mechanisms and functions to NEURON
Topic: A pump MOD file and no concentration inside
Replies: 3
Views: 330

A pump MOD file and no concentration inside

Hi. My workflow contains the following steps: a substance is generated into a section (MOD file), is pumped out (MOD file) in a cubic ECS (RxD). Than from the ECS it is pumped (MOD file) into another section where there are a series of reactions (RxD). This works fine. Now I'm trying to substitute t...
by bremen
Fri Mar 27, 2020 3:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Syncronized concentrations in and out the membrane
Replies: 1
Views: 1364

Re: Syncronized concentrations in and out the membrane

Never mind. I have found the underlying issue.
by bremen
Thu Mar 26, 2020 11:11 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Syncronized concentrations in and out the membrane
Replies: 1
Views: 1364

Syncronized concentrations in and out the membrane

Hi. I'm trying to define a MOD file capable of reading the internal concentration of a substance and, with a slim to none delay, "transpose" the same concentration in a ecs. The ecs is defined with rxd.Extracellular(). The substance is generated by a MOD file in the inside and as an rxd.sp...
by bremen
Fri Feb 28, 2020 9:13 am
Forum: Reaction-diffusion in NEURON
Topic: Multicomp model, ECS, pumps and strange concentrations
Replies: 3
Views: 938

Re: Multicomp model, ECS, pumps and strange concentrations

Thank you. I have modified your code and i can reproduce the strangeness. from neuron import h, rxd from neuron.units import mV, ms h.load_file('stdrun.hoc') soma = h.Section(name='soma') dend0 = h.Section(name='dend0') dend00 = h.Section(name='dend00') dend00.insert('pump') dend1 = h.Section(name='...
by bremen
Thu Feb 27, 2020 10:17 am
Forum: Reaction-diffusion in NEURON
Topic: Multicomp model, ECS, pumps and strange concentrations
Replies: 3
Views: 938

Multicomp model, ECS, pumps and strange concentrations

Hi. I was checking my RxD code, after implementing it into a multi compartmental model and something very odd came up. I have a substance, produced by a few dendrites and, trough pumps (the same used in the RxD examples) diffused into the ECS. If I cancel the code responsible for the generation of t...
by bremen
Thu Jan 16, 2020 4:10 pm
Forum: NEURON + Python
Topic: different section names, morphology - h.Section
Replies: 2
Views: 961

Re: different section names, morphology - h.Section

Hi.

Thank you very much, it solved my Netcon issue.

Best
Stefano
by bremen
Fri Jan 10, 2020 4:53 pm
Forum: NEURON + Python
Topic: different section names, morphology - h.Section
Replies: 2
Views: 961

different section names, morphology - h.Section

Hi. I was looking at a h.topology() of one of my Python/NEURON models and sow something "odd" in the names of the sections. Part of the cell uses a neurolucida morphology, which i load with: cell = h.Import3d_Neurolucida3() cell.input('morphology.asc') In this case the sections are called ...
by bremen
Mon Oct 07, 2019 2:52 pm
Forum: Reaction-diffusion in NEURON
Topic: NEURON 7.7.1 RxD issue
Replies: 2
Views: 1679

Re: NEURON 7.7.1 RxD issue

Hi.

The fix solved the issue.
Thank you.

Best
Stefano
by bremen
Thu Oct 03, 2019 8:45 am
Forum: Reaction-diffusion in NEURON
Topic: NEURON 7.7.1 RxD issue
Replies: 2
Views: 1679

NEURON 7.7.1 RxD issue

Hello. I haven't worked on my RxD model for months and now, after installing the latest NEURON version from git (3 october 2019) to be up to date, my code give rise to an error. The issue is generated by reactions with species placed across different locations, in this case, the soma of two distinct...
by bremen
Sat Mar 16, 2019 12:06 pm
Forum: Reaction-diffusion in NEURON
Topic: Reactions only when concentration above a certain limit?
Replies: 1
Views: 2612

Reactions only when concentration above a certain limit?

Hi. Is there a way to know the concentration of a species, during the simulation, so that it can be used to automatically start specific reactions? I have found this command in the help: https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/rxd.html#neuron.rxd.species.SpeciesOnRegi...
by bremen
Sun Mar 03, 2019 8:17 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2858

Re: diffusion intracellular->extracellular->intracellular

Hi. I will soon start working on a particular reaction and, before doing it with a mod file, i tried MultiCompartmentReaction with the lastest code (compiled today). ecs_cell2_membrane = rxd.Region([cell2.soma], name='mem', geometry = rxd.ScalableBorder(1, on_cell_surface=False)) pump_ecs_cell2 = rx...
by bremen
Sat Feb 23, 2019 6:43 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2858

Re: diffusion intracellular->extracellular->intracellular

Hi.
Thank you very much.

Best regards
Stefano
by bremen
Sat Feb 16, 2019 5:01 pm
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2858

Re: diffusion intracellular->extracellular->intracellular

Hi. After some more testing i have some questions: 1) I have recorded a vector, pointed to the outside name of the substance "self.soma(0.5)._ref_xo", to record the concentration in the ecs. The resulting graph is congruent with my expectation since it records only a part of the entire dif...
by bremen
Tue Feb 12, 2019 8:22 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2858

Re: diffusion intracellular->extracellular->intracellular

Hi.
Thank you.
Currently the easiest way to do this is with mod files describing pump mechanism.
I'll try this approach.