You need what is often called a "space plot." See How to plot a variable vs. distance in the Hot tips area of the Forum. You might find it useful to turn on the space plot's "Keep lines" (click on its menu box--in the upper left corner of the graph's canvas--and select the "Keep Lines" item so that a check mark appears next to it), and to reduce "Points plotted /ms" in the RunControl panel from its default 40 to 4, 2, 1, or even 0.5 or less (this will generate a sequence of "snapshots" of v along the axon). You may find it useful to erase traces (Graph menu / Erase) before running a simulation with a different value for "Points plotted/ms".dsengupta wrote:I want to model a simple axon model with myelin and without myelin to show how the action potential changes as a signal propagates down the axon. My question is, is there a way to graph voltage vs length? My goal is to show how the action potential degenerates as it travels through a section of myelin and then how it regenerates itself once it hits a node( ion channel).
To answer this question I'll have to be able to reproduce this for myself. Can you zip up just the files that are required to reproduce the observation (read What to include in a zip file, and what to leave out and No rar, doc, or winmail.dat files, please! in the Hot tips area of the NEURON Forum) and send them to meAnother question was about running a myelinated model. I have a simple myelinated model that runs without error but when I go to graph it, the action potential will not show unless I change the initial voltage to -70 for the default of -65 in the GUI.
Figures it out for itself. If you save the graph to a session file (not sure how? see What is a ses (session) file? in NEURON's FAQ list (link is on the Documentation page at http://www.neuron.yale.edu/) and examine the contents of that file, you will see something that looks like this:dsengupta wrote:1. How does NEURON deternime how long the x axis has to be on the graph
objectvar save_window_, rvp_
. . . a bunch of code . . .
rvp_ = new RangeVarPlot("v")
. . . more code . . .
Use an IClamp. Can be created with hoc statements (see Programmer's reference documentation of the IClamp class) or via the GUI (seeHow do you inject a current/ impulse at a specific point along the axon.
First a comment: in NEURON the units of length are microns. The behavior of your nonmyelinated model suggests to me that its spatial discretization parameter nseg is 1, so the entire axon is treated as a single compartment. You might try executingwhen I am graphing the myelinated model in a space plot, I am getting waves, but when I am running the unmyelinated model I am getting I flat line moving up and down. I think this is because the default x axis of the unmyelinated space plot is much shorter (1000 units) than the myelinated model (35000 units).
run a simulation
UNTIL there is no significant change from the previous simulation results
The axon does nothing because no stimulus is applied to it.dsengupta wrote:I have a simple myelinated model that runs without error but when I go to graph it, the action potential will not show
This is "anode break excitation," also sometimes called "rebound excitation." The resting potential of the Hodgkin-Huxley squid axon model is -65 mV. Specifying an initial membrane potential of -70 mV is equivalent to injecting hyperpolarizing current throughout the entire model. When the simulation begins, this hyperpolarizing current stops and the membrane potential is free to change. Naturally it tries to return to -65 mV, and this causes both sodium channels and potassium channels to open. However, the sodium channels are faster than the potassium channels, so they generate an inward current that makes the cell's membrane potential depolarize even more, which opens more sodium channels etc., and you get a spike.unless I change the initial voltage to -70 for the default of -65 in the GUI.
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