Search found 41 matches

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: 1004

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: 1004

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.species on t...
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: 407

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: 407

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: 493

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: 493

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 like this:...
by bremen
Mon Oct 07, 2019 2:52 pm
Forum: Reaction-diffusion in NEURON
Topic: NEURON 7.7.1 RxD issue
Replies: 2
Views: 1217

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: 1217

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: 2245

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: 2062

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: 2062

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: 2062

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 diffusion. ht...
by bremen
Tue Feb 12, 2019 8:22 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2062

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.
by bremen
Sun Feb 10, 2019 10:32 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2062

Re: diffusion intracellular->extracellular->intracellular

Hi. I was able to solve most of the workflow but I'm missing something in the "MultiCompartmentReaction". I'm trying to release the substance X, correctly generated in the internal region of cell_1, to the ecs. With the MultiCompartmentReaction wrote in this way: rxd.MultiCompartmentReaction(sub_x[i...
by bremen
Thu Feb 07, 2019 11:25 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 2062

diffusion intracellular->extracellular->intracellular

Hi. After reading the 2018 paper, i was wondering if is feasible, with rxd.extracellular, to reproduce the following situation: A substance X is internally produced by cell_1. It is pumped outside the membrane into the extracellular space. Here it diffuses until it reaches cell_2. It is then uptake ...