www.neuron.yale.edu

Hello all,

Sorry in advance, I am new to NEURON.

For my thesis I am investigating the phenomenon of nerve conduction block. I am required to build a model of an axon and expose it to high frequency biphasic extracellular stimulation via a (monopolar) block electrode at one end of the axon. I will then have a test electrode at the other end delivering a single pulse in order to evoke an AP which may or may not propagate through the site of the block electrode.

To begin with I am attempting to build a simple model of an unmyelinated axon with hodgkin huxley mechanisms implemented in all segments. Then later I plan to move onto McIntyre and Grills (2001) MRG model of a myelinated nerve.

So far I have built the basic model of the nerve along with the test electrode which seems to be working fine, however I am having some troubles in modelling the block electrode. I have spent some time looking on these forums and I understand there are multiple ways to approach this. I have inserted the extracellular mechanism and was thinking about using xtra and Fsin to implement the sinusoidally fluctuating field, however I am confused about how to practically go about doing this and keep on getting errors when I try. I understand that another popular method is to model the extracellular current stimulus on MATLAB or COMSOL then use the vector play method to read it into NEURON via the extracellular mechanism, but once again I don't know how to go about doing this and would greatly appreciate it if someone could explain the process to me or at least point me to somewhere that I could find out.

So essentially my question is what would be the best approach for me to go for? Bearing in mind that I am new to NEURON and fairly new to programming in general, despite some experience with MATLAB.

Thanks a bunch,

Theo

Are you familiar with this reference and others cited by it?
@Article{Pelot2017,
author = {Pelot, N A and Behrend, C E and Grill, W M},
title = {Modeling the response of small myelinated axons in a compound nerve to kilohertz frequency signals},
journal = {Journal of Neural Engineering},
year = {2017},
volume = {14},
issue = {4},
month = mar,
pages = {046022},
pmid = {28361793},
}

Hi ted,
Thanks for getting back to me so quickly. I was not familiar with this paper in particular, I am however familiar with many cited by it.

I should have pointed out that I do not have access to COMSOL currently so I was going to start off with simply modelling the block electrode as a point source, as has been done by many previously that are cited in this paper (Ackermann et al 2011, Bhadra et al 2007 etc.). This is primarily what I want and am struggling to do, however looking on these forums I read that some people were modelling the extracellular current source through MATLAB so I wasn't sure if that was another option.

Later I may have access to SIM4LIFE so I might try my hand at FEM at some point.

You might find some helpful code examples in ModelDB entry 239006. It uses xstim (basically xtra sans the "extracellular recording" stuff). Be sure to read the comments and readme.html, as well as Reilly 2016. In particular note that the "point source" simulations assume that the electrode is located at the surface of a semi-infinite conductive medium.

Thanks so much ted, seems promising ill take a look!