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questions regarding myelinated axon
Posted: Thu Aug 22, 2013 11:56 am
by shwetakgp
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
Re: questions regarding myelinated axon
Posted: Thu Aug 22, 2013 1:26 pm
by ted
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
Posted: Mon Aug 26, 2013 10:30 am
by shwetakgp
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
Posted: Tue Aug 27, 2013 1:26 pm
by shwetakgp
dear ted,
please reply to my query
Re: questions regarding myelinated axon
Posted: Wed Aug 28, 2013 12:17 pm
by ted
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.