dear ted,
i was studying about myelinated axon from mclntyre(2002) and couldnt understand some things-
Ra=rhoa*(1/(paraD1/fiberD)^2)/10000
cm=2*paraD1/fiberD
insert pas
g_pas=0.001*paraD1/fiberD
e_pas=v_init
insert extracellular xraxial=Rpn1 xg=mygm/(nl*2) xc=mycm/(nl*2)
how have these terms been calculated?
what are paranodes1 and 2 and what is meant by this term space_p1=0.00 and how nodes have been connected
questions regarding myelinated axon
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Re: questions regarding myelinated axon
The authors of that model will have explained this in their paper. Have you read it? The pdf is probably available from the journal at no charge.
Re: questions regarding myelinated axon
i have understood about those things from the paper. i want to make a cell with myelinated axon.i tried to include it by doing some changes but i cnt figure out much. how should i include this into a cell. i tried this. i have not made many changes i just added morphology of soma and connected MYSA[0](0) to soma(1)......help is deeply appreciated..
Code: Select all
topology()
create soma
soma_area=3774
soma_nseg=1
forall insert xtra
forall insert extracellular
proc model_globels() {
celsius=37
v_init=-80 //mV//
dt=0.005 //ms//
tstop=10
//Intracellular stimuluation parameters//
istim=2
delay=1
pw=0.1
//topological parameters//
axonnodes=21
paranodes1=40
paranodes2=40
axoninter=120
axontotal=221
//morphological parameters//
fiberD=10.0 //choose from 5.7, 7.3, 8.7, 10.0, 11.5, 12.8, 14.0, 15.0, 16.0
paralength1=3
nodelength=1.0
space_p1=0.002
space_p2=0.004
space_i=0.004
//electrical parameters//
rhoa=0.7e6 //Ohm-um//
mycm=0.1 //uF/cm2/lamella membrane//
mygm=0.001 //S/cm2/lamella membrane//
}
model_globels ()
proc dependent_var() {
if (fiberD==5.7) {g=0.605 axonD=3.4 nodeD=1.9 paraD1=1.9 paraD2=3.4 deltax=500 paralength2=35 nl=80}
if (fiberD==7.3) {g=0.630 axonD=4.6 nodeD=2.4 paraD1=2.4 paraD2=4.6 deltax=750 paralength2=38 nl=100}
if (fiberD==8.7) {g=0.661 axonD=5.8 nodeD=2.8 paraD1=2.8 paraD2=5.8 deltax=1000 paralength2=40 nl=110}
if (fiberD==10.0) {g=0.690 axonD=6.9 nodeD=3.3 paraD1=3.3 paraD2=6.9 deltax=1150 paralength2=46 nl=120}
if (fiberD==11.5) {g=0.700 axonD=8.1 nodeD=3.7 paraD1=3.7 paraD2=8.1 deltax=1250 paralength2=50 nl=130}
if (fiberD==12.8) {g=0.719 axonD=9.2 nodeD=4.2 paraD1=4.2 paraD2=9.2 deltax=1350 paralength2=54 nl=135}
if (fiberD==14.0) {g=0.739 axonD=10.4 nodeD=4.7 paraD1=4.7 paraD2=10.4 deltax=1400 paralength2=56 nl=140}
if (fiberD==15.0) {g=0.767 axonD=11.5 nodeD=5.0 paraD1=5.0 paraD2=11.5 deltax=1450 paralength2=58 nl=145}
if (fiberD==16.0) {g=0.791 axonD=12.7 nodeD=5.5 paraD1=5.5 paraD2=12.7 deltax=1500 paralength2=60 nl=150}
Rpn0=(rhoa*.01)/(PI*((((nodeD/2)+space_p1)^2)-((nodeD/2)^2)))
Rpn1=(rhoa*.01)/(PI*((((paraD1/2)+space_p1)^2)-((paraD1/2)^2)))
Rpn2=(rhoa*.01)/(PI*((((paraD2/2)+space_p2)^2)-((paraD2/2)^2)))
Rpx=(rhoa*.01)/(PI*((((axonD/2)+space_i)^2)-((axonD/2)^2)))
interlength=(deltax-nodelength-(2*paralength1)-(2*paralength2))/6
}
dependent_var()
objectvar stim
create node[axonnodes], MYSA[paranodes1], FLUT[paranodes2], STIN[axoninter]
access node[0] //APD
proc initialize(){
for i=0,axonnodes-1 {
node[i]{
nseg=1
diam=nodeD
L=nodelength
Ra=rhoa/10000
cm=2
insert extracellular xraxial=Rpn0 xg=1e10 xc=0
}
}
for i=0, paranodes1-1 {
MYSA[i]{
nseg=1
diam=fiberD
L=paralength1
Ra=rhoa*(1/(paraD1/fiberD)^2)/10000
cm=2*paraD1/fiberD
insert pas
g_pas=0.001*paraD1/fiberD
e_pas=v_init
insert extracellular xraxial=Rpn1 xg=mygm/(nl*2) xc=mycm/(nl*2)
}
}
for i=0, paranodes2-1 {
FLUT[i]{
nseg=1
diam=fiberD
L=paralength2
Ra=rhoa*(1/(paraD2/fiberD)^2)/10000
cm=2*paraD2/fiberD
insert pas
g_pas=0.0001*paraD2/fiberD
e_pas=v_init
insert extracellular xraxial=Rpn2 xg=mygm/(nl*2) xc=mycm/(nl*2)
}
}
for i=0, axoninter-1 {
STIN[i]{
nseg=1
diam=fiberD
L=interlength
Ra=rhoa*(1/(axonD/fiberD)^2)/10000
cm=2*axonD/fiberD
insert pas
g_pas=0.0001*axonD/fiberD
e_pas=v_init
insert extracellular xraxial=Rpx xg=mygm/(nl*2) xc=mycm/(nl*2)
}
}
for i=0, axonnodes-2 {
connect MYSA[0](0), soma(1)
connect MYSA[2*i](0), node[i](1)
connect FLUT[2*i](0), MYSA[2*i](1)
connect STIN[6*i](0), FLUT[2*i](1)
connect STIN[6*i+1](0), STIN[6*i](1)
connect STIN[6*i+2](0), STIN[6*i+1](1)
connect STIN[6*i+3](0), STIN[6*i+2](1)
connect STIN[6*i+4](0), STIN[6*i+3](1)
connect STIN[6*i+5](0), STIN[6*i+4](1)
connect FLUT[2*i+1](0), STIN[6*i+5](1)
connect MYSA[2*i+1](0), FLUT[2*i+1](1)
connect node[i+1](0), MYSA[2*i+1](1)
}
finitialize(v_init)
fcurrent()
}
initialize()
//intracellular stimulus//
proc stimul() {
node[10]{
stim=new IClamp()
stim.loc(.5)
stim.del=delay
stim.dur=pw
stim.amp=istim
}
}
stimul()
xpanel("Stimulus parameters")
xvalue("Stimulus Amplitude (nA)", "istim", 1, "stimul()", 1)
xvalue("Pulse Duration (ms)", "pw", 1)
xvalue("Onset Delay (ms)", "delay", 1)
xpanel(100,100)
Re: questions regarding myelinated axon
dear ted,
please reply to my query
please reply to my query
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Re: questions regarding myelinated axon
There are too many problems in the code you provided to be addressed here, and I am already engaged in enough other tasks that there isn't time to write an entire program for you to do whatever you want. In my opinion you need to start a close collaboration with someone who can take on the responsibility of doing most or all of the programming that your projects might require.