Search found 41 matches
- 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: 1234
Re: Syncronized concentrations in and out the membrane
Never mind. I have found the underlying issue.
- 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: 1234
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...
- Fri Feb 28, 2020 9:13 am
- Forum: Reaction-diffusion in NEURON
- Topic: Multicomp model, ECS, pumps and strange concentrations
- Replies: 3
- Views: 755
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='...
- Thu Feb 27, 2020 10:17 am
- Forum: Reaction-diffusion in NEURON
- Topic: Multicomp model, ECS, pumps and strange concentrations
- Replies: 3
- Views: 755
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...
- Thu Jan 16, 2020 4:10 pm
- Forum: NEURON + Python
- Topic: different section names, morphology - h.Section
- Replies: 2
- Views: 792
Re: different section names, morphology - h.Section
Hi.
Thank you very much, it solved my Netcon issue.
Best
Stefano
Thank you very much, it solved my Netcon issue.
Best
Stefano
- Fri Jan 10, 2020 4:53 pm
- Forum: NEURON + Python
- Topic: different section names, morphology - h.Section
- Replies: 2
- Views: 792
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 ...
- Mon Oct 07, 2019 2:52 pm
- Forum: Reaction-diffusion in NEURON
- Topic: NEURON 7.7.1 RxD issue
- Replies: 2
- Views: 1504
Re: NEURON 7.7.1 RxD issue
Hi.
The fix solved the issue.
Thank you.
Best
Stefano
The fix solved the issue.
Thank you.
Best
Stefano
- Thu Oct 03, 2019 8:45 am
- Forum: Reaction-diffusion in NEURON
- Topic: NEURON 7.7.1 RxD issue
- Replies: 2
- Views: 1504
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...
- Sat Mar 16, 2019 12:06 pm
- Forum: Reaction-diffusion in NEURON
- Topic: Reactions only when concentration above a certain limit?
- Replies: 1
- Views: 2474
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...
- Sun Mar 03, 2019 8:17 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 2596
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...
- Sat Feb 23, 2019 6:43 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 2596
Re: diffusion intracellular->extracellular->intracellular
Hi.
Thank you very much.
Best regards
Stefano
Thank you very much.
Best regards
Stefano
- Sat Feb 16, 2019 5:01 pm
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 2596
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...
- Tue Feb 12, 2019 8:22 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 2596
Re: diffusion intracellular->extracellular->intracellular
Hi.
Thank you.
Thank you.
I'll try this approach.Currently the easiest way to do this is with mod files describing pump mechanism.
- Sun Feb 10, 2019 10:32 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 2596
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.MultiCompartmentReacti...
- Thu Feb 07, 2019 11:25 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 2596
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 ...