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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...

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....

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...

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...

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...

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....

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...

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...

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...

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...

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.

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...

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...

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...