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myelinBiophysics.hoc
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myelinBiophysics.hoc
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/*
* Assigns biophysical parameters to myelinated axon
* should have created SectionLists: Myelin_secList, Node_secList, UnMyelin_secList, iseg_secList, and axonal
* AUTHOR: Aman Aberra, Duke University
* CONTACT: aman.aberra@duke.edu
*/
proc myelin_biophys() { localobj axon_bp //iseg_secList,Node_secList,Myelin_seclist,Unmyelin_secList
axon_bp = get_axon_biophys()
forsec cell.somatic {
cm=1 // uF/cm2
}
forsec cell.apical {
cm = 2 // uF/cm2
}
forsec cell.basal {
cm = 2 // uF/cm2
}
forsec axonal { // cell.axonal still not formed
insert pas
e_pas = axon_bp.x[12] // usually -75 mV
Ra = 100 // Ohm*cm
cm = 1 // µF/cm2
g_pas = axon_bp.x[13] // usually 3e-5 S/cm2
}
//forsec axonal {
forsec Node_secList {
//insert Ca_HVA
insert SKv3_1
//insert SK_E2
//insert CaDynamics_E2
insert Nap_Et2
insert K_Pst
insert K_Tst
//insert Ca_LVAst
insert NaTa_t
//insert NaTa2_t
for(x,0){
if (ismembrane("NaTa_t")) gNaTa_tbar_NaTa_t(x) = 2*axon_bp.x[0] //2.5
//if (ismembrane("NaTa2_t")) gNaTa2_tbar_NaTa2_t(x) = axon_bp.x[0] // New sodium channel for axon proper
if (ismembrane("K_Tst")) gK_Tstbar_K_Tst(x) = axon_bp.x[1] //2
if (ismembrane("CaDynamics_E2")) gamma_CaDynamics_E2(x) = axon_bp.x[2]
if (ismembrane("Nap_Et2")) gNap_Et2bar_Nap_Et2(x) = axon_bp.x[3]
if (ismembrane("SK_E2")) gSK_E2bar_SK_E2(x) = axon_bp.x[4]
if (ismembrane("Ca_HVA")) gCa_HVAbar_Ca_HVA(x) = axon_bp.x[5]
if (ismembrane("K_Pst")) gK_Pstbar_K_Pst(x) = axon_bp.x[6] //2
if (ismembrane("SKv3_1")) gSKv3_1bar_SKv3_1(x) = axon_bp.x[7] //2
if (ismembrane("CaDynamics_E2")) decay_CaDynamics_E2(x) = axon_bp.x[8]
if (ismembrane("Ca_LVAst")) gCa_LVAstbar_Ca_LVAst(x) = axon_bp.x[9]
if (ismembrane("Im")) gImbar_Im(x) = axon_bp.x[10]
if (ismembrane("Ca")) gCabar_Ca(x) = axon_bp.x[11]
}
// don't change e_pas or g_pas
//g_pas = 3e-5 // 0.02 - Mainen 1995
ena = 50
ek = -85
}
forsec Myelin_secList {
cm = 0.02 // Mainen 1996, 0.02 - Eyal 2014
g_pas = 1/1.125e6 // 1/1.125e6 - Eyal 2014
}
forsec Unmyelin_secList {
//insert Ca_HVA
insert SKv3_1
//insert SK_E2
//insert CaDynamics_E2
insert Nap_Et2
insert K_Pst
insert K_Tst
//insert Ca_LVAst
insert NaTa_t
for (x,0) {
if (ismembrane("NaTa_t")) gNaTa_tbar_NaTa_t(x) = axon_bp.x[0]
if (ismembrane("K_Tst")) gK_Tstbar_K_Tst(x) = axon_bp.x[1]
if (ismembrane("CaDynamics_E2")) gamma_CaDynamics_E2(x) = axon_bp.x[2]
if (ismembrane("Nap_Et2")) gNap_Et2bar_Nap_Et2(x) = axon_bp.x[3]
if (ismembrane("SK_E2")) gSK_E2bar_SK_E2(x) = axon_bp.x[4]
if (ismembrane("Ca_HVA")) gCa_HVAbar_Ca_HVA(x) = axon_bp.x[5]
if (ismembrane("K_Pst")) gK_Pstbar_K_Pst(x) = axon_bp.x[6]
if (ismembrane("SKv3_1")) gSKv3_1bar_SKv3_1(x) = axon_bp.x[7]
if (ismembrane("CaDynamics_E2")) decay_CaDynamics_E2(x) = axon_bp.x[8]
if (ismembrane("Ca_LVAst")) gCa_LVAstbar_Ca_LVAst(x) = axon_bp.x[9]
if (ismembrane("Im")) gImbar_Im(x) = axon_bp.x[10]
if (ismembrane("Ca")) gCabar_Ca(x) = axon_bp.x[11]
}
ena = 50
ek = -85
}
}
// get conductances from original cell.axon[0], save to vector
obfunc get_axon_biophys() { localobj axon_bp
axon_bp = new Vector(14)
access cell.axon[0]
if (ismembrane("NaTa_t")) axon_bp.x[0] = gNaTa_tbar_NaTa_t
if (ismembrane("K_Tst")) axon_bp.x[1] = gK_Tstbar_K_Tst
if (ismembrane("CaDynamics_E2")) axon_bp.x[2] = gamma_CaDynamics_E2
if (ismembrane("Nap_Et2")) axon_bp.x[3] = gNap_Et2bar_Nap_Et2
if (ismembrane("SK_E2")) axon_bp.x[4] = gSK_E2bar_SK_E2
if (ismembrane("Ca_HVA")) axon_bp.x[5] = gCa_HVAbar_Ca_HVA
if (ismembrane("K_Pst")) axon_bp.x[6] = gK_Pstbar_K_Pst
if (ismembrane("SKv3_1")) axon_bp.x[7] = gSKv3_1bar_SKv3_1
if (ismembrane("CaDynamics_E2")) axon_bp.x[8] = decay_CaDynamics_E2
if (ismembrane("Ca_LVAst")) axon_bp.x[9] = gCa_LVAstbar_Ca_LVAst
if (ismembrane("Im")) axon_bp.x[10] = gImbar_Im
if (ismembrane("Ca")) axon_bp.x[11] = gCabar_Ca
axon_bp.x[12] = e_pas
axon_bp.x[13] = g_pas
return axon_bp
}