Search found 14 matches

by mcapllonchj
Wed Jul 25, 2018 10:12 am
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 7
Views: 1981

Re: Parallel simulations of ephaptic connections

The answers to the questions are: 1. No. Radial spread happens through the transverse resistors. And the walls of the bundle have a current path to a 'distant' ground. 2. Yes. Only nearest neighbours are connected using resistors. This doesn't mean, however, that non-nearest neighbours are electrica...
by mcapllonchj
Thu Jun 21, 2018 6:05 am
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 7
Views: 1981

Re: Parallel simulations of ephaptic connections

Are you representing the extracellular medium as a 3D resistive mesh? Yes. The xraxial of every axon accounts for the extracellular space in the longitudinal direction (z-axis, parallel to the axons), while the connections are between the xraxial of neighboring axons, and they are on the x-y plane....
by mcapllonchj
Wed Jun 20, 2018 12:30 pm
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 7
Views: 1981

Re: Parallel simulations of ephaptic connections

which is why two source_var - target_var pairs are used to parallelize gap junction coupling--one pair for each direction. Thanks for that. It was so obvious and still I didn't see it. There is a point that I'm still not sure if I understand. Is copying the value of a variable, say, vext, from sour...
by mcapllonchj
Fri Jun 15, 2018 12:01 pm
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 7
Views: 1981

Re: Parallel simulations of ephaptic connections

Hello, I would like to rephrase this question in much simpler terms to make things easier. It would be very helpful if someone could provide some hints. So I have a large resistor network implemented with LinearMechanism (which models the 3D extracellular space of a bundle of axons). For a simulatio...
by mcapllonchj
Tue Mar 13, 2018 1:55 pm
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 7
Views: 1981

Parallel simulations of ephaptic connections

Hello, I am using a model that connects axons ephaptically using LinearMechanism. The ephaptic connections are modelled as "transverse" resistors connecting the opposite nodes of two interacting cells (so it's more like a network, not at all using a mean-field model; the longitudinal extracellular r...
by mcapllonchj
Fri Oct 20, 2017 7:25 am
Forum: Specific models
Topic: Stimulation in ephaptic example
Replies: 4
Views: 16126

Re: Stimulation in ephaptic example

Hi Ted, Yes, I did. Actually, that's how I realised I could create the code from the LinearCircuit builder. My question was more in the line of figuring out how the code you made in ephapx.ses translated into Python. Although that's sorted. I needed to add a label to one of the nodes of the circuit....
by mcapllonchj
Mon Oct 16, 2017 2:52 pm
Forum: Specific models
Topic: Stimulation in ephaptic example
Replies: 4
Views: 16126

Re: Stimulation in ephaptic example

Hi Ted, Thanks for your quick response. I see, as you say, that this is a GUI tool. I have been practising today and I have managed to create and simulate a simple RC circuit, and I have saved it into a hoc file with the Create Class button. However, I am not sure how this can be implemented program...
by mcapllonchj
Fri Oct 13, 2017 11:28 am
Forum: Specific models
Topic: Stimulation in ephaptic example
Replies: 4
Views: 16126

Stimulation in ephaptic example

Hello, I have been going over your example for Bokil & al. (2001): https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=3676&file=/ephaptic/ephap.hoc#tabs-1 and I was wondering, where do you define the stimulation of the axons? I haven't seen any "IClamp" in the entire folder. Is there anoth...
by mcapllonchj
Mon Aug 07, 2017 11:45 am
Forum: Modeling networks
Topic: Error at implementing the ephap.zip example in Python
Replies: 0
Views: 11149

Error at implementing the ephap.zip example in Python

Hello, I have translated part of the code from ephap.zip into Python. If I create a class ephap like: h.load_file("ephap.hoc") ephap = h.Ephap() , everything works fine, of course, but I wanted to have as much code as I could in Python, ideally all of it, so I have tried to create a Python class equ...
by mcapllonchj
Wed May 31, 2017 8:11 am
Forum: Modeling networks
Topic: Instabilities in ephaptic coupling
Replies: 0
Views: 10311

Instabilities in ephaptic coupling

Dear all, I am simulating ephaptic coupling between two unmyelinated axons (the simplest case I could use) by calculating the external potential from the membrane currents at each time step, with phi(x) = (1/4*pi*sigma) * sum[over the nodes](I(node) / dist(x, node)), (so, the typical for LFPs if I a...
by mcapllonchj
Tue Mar 28, 2017 6:59 am
Forum: Modeling networks
Topic: Convergence of e_extracellular and membrane currents
Replies: 6
Views: 7218

Re: Convergence of e_extracellular and membrane currents

Dear Ted, many thanks for that reply (and sorry for this late reply). I see your point. I will come back to this question at some point later on and let you know if I am successful implementing the convergence process.
by mcapllonchj
Mon Feb 27, 2017 3:18 pm
Forum: Modeling networks
Topic: Convergence of e_extracellular and membrane currents
Replies: 6
Views: 7218

Re: Convergence of e_extracellular and membrane currents

Many thanks for this. I will have a think to fully understand it and then implement it to try. Just in case and for the various experiments I am going to do both with keeping time constant and using fadvance (specifically for the former, actually), is there a way in NEURON to force variables like th...
by mcapllonchj
Mon Feb 27, 2017 9:36 am
Forum: Modeling networks
Topic: Convergence of e_extracellular and membrane currents
Replies: 6
Views: 7218

Re: Convergence of e_extracellular and membrane currents

Dear Hines,   Thank you very much for your response. Actually I had not discovered PtrVector before. So far I was using: for j, seg in enumerate(seglist): phi[j].play(seg._ref_e_extracellular, h.dt) I have used PtrVector together with pv.scatter in my code now and simulations are so much faster. Tha...
by mcapllonchj
Thu Feb 16, 2017 10:38 am
Forum: Modeling networks
Topic: Convergence of e_extracellular and membrane currents
Replies: 6
Views: 7218

Convergence of e_extracellular and membrane currents

Dear all, I am using NEURON to model ephaptic coupling between axons in a nerve. My model necessarily requires coupling NEURON to a Poisson solver (FEM, although for minimal working examples, I just use phi = 1/(4*pi*sigma) * sum(membr.currents/distance) for calculating the extracellular potential f...