questions regarding myelinated axon

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shwetakgp
Posts: 36
Joined: Sun Jun 16, 2013 1:21 am

questions regarding myelinated axon

Post 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
ted
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Location: Yale University School of Medicine
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Re: questions regarding myelinated axon

Post 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.
shwetakgp
Posts: 36
Joined: Sun Jun 16, 2013 1:21 am

Re: questions regarding myelinated axon

Post 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) 



    
shwetakgp
Posts: 36
Joined: Sun Jun 16, 2013 1:21 am

Re: questions regarding myelinated axon

Post by shwetakgp »

dear ted,
please reply to my query
ted
Site Admin
Posts: 5786
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: questions regarding myelinated axon

Post 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.
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