pyfibers 0.4.2__py3-none-any.whl

pyfibers/MOD/AXNODE_myel.mod

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+TITLE Motor Axon Node channels
+
+: 2/02
+: Cameron C. McIntyre
+:
+: Fast Na+, Persistant Na+, Slow K+, and Leakage currents
+: responsible for nodal action potential
+: Iterative equations H-H notation rest = -80 mV
+:
+: This model is described in detail in:
+:
+: McIntyre CC, Richardson AG, and Grill WM. Modeling the excitability of
+: mammalian nerve fibers: influence of afterpotentials on the recovery
+: cycle. Journal of Neurophysiology 87:995-1006, 2002.
+
+INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}
+
+NEURON {
+	SUFFIX axnode_myel
+	NONSPECIFIC_CURRENT ina
+	NONSPECIFIC_CURRENT inap
+	NONSPECIFIC_CURRENT ik
+	NONSPECIFIC_CURRENT il
+	RANGE gnapbar, gnabar, gkbar, gl, ena, ek, el
+	RANGE mp_inf, m_inf, h_inf, s_inf
+	RANGE tau_mp, tau_m, tau_h, tau_s
+}
+
+
+UNITS {
+	(mA) = (milliamp)
+	(mV) = (millivolt)
+}
+
+PARAMETER {
+
+	gnapbar = 0.01	(mho/cm2)
+	gnabar	= 3.0	(mho/cm2)
+	gkbar   = 0.08 	(mho/cm2)
+	gl	= 0.007 (mho/cm2)
+	ena     = 50.0  (mV)
+	ek      = -90.0 (mV)
+	el	= -90.0 (mV)
+	celsius		(degC)
+	dt              (ms)
+	v               (mV)
+	vtraub=-80
+	ampA = 0.01
+	ampB = 27
+	ampC = 10.2
+	bmpA = 0.00025
+	bmpB = 34
+	bmpC = 10
+	amA = 1.86
+	amB = 21.4
+	amC = 10.3
+	bmA = 0.086
+	bmB = 25.7
+	bmC = 9.16
+	ahA = 0.062
+	ahB = 114.0
+	ahC = 11.0
+	bhA = 2.3
+	bhB = 31.8
+	bhC = 13.4
+	asA = 0.3
+	asB = -27
+	asC = -5
+	bsA = 0.03
+	bsB = 10
+	bsC = -1
+}
+
+STATE {
+	mp m h s
+}
+
+ASSIGNED {
+	inap    (mA/cm2)
+	ina	(mA/cm2)
+	ik      (mA/cm2)
+	il      (mA/cm2)
+	mp_inf
+	m_inf
+	h_inf
+	s_inf
+	tau_mp
+	tau_m
+	tau_h
+	tau_s
+	q10_1
+	q10_2
+	q10_3
+}
+
+BREAKPOINT {
+	SOLVE states METHOD cnexp
+	inap = gnapbar * mp*mp*mp * (v - ena)
+	ina = gnabar * m*m*m*h * (v - ena)
+	ik   = gkbar * s * (v - ek)
+	il   = gl * (v - el)
+}
+
+DERIVATIVE states {   : exact Hodgkin-Huxley equations
+    evaluate_fct(v)
+	mp'= (mp_inf - mp) / tau_mp
+	m' = (m_inf - m) / tau_m
+	h' = (h_inf - h) / tau_h
+	s' = (s_inf - s) / tau_s
+}
+
+UNITSOFF
+
+INITIAL {
+:
+:	Q10 adjustment
+:
+
+	q10_1 = 2.2 ^ ((celsius-20)/ 10 )
+	q10_2 = 2.9 ^ ((celsius-20)/ 10 )
+	q10_3 = 3.0 ^ ((celsius-36)/ 10 )
+
+	evaluate_fct(v)
+	mp = mp_inf
+	m = m_inf
+	h = h_inf
+	s = s_inf
+}
+
+PROCEDURE evaluate_fct(v(mV)) { LOCAL a,b,v2
+
+	a = q10_1*vtrap1(v)
+	b = q10_1*vtrap2(v)
+	tau_mp = 1 / (a + b)
+	mp_inf = a / (a + b)
+
+	a = q10_1*vtrap6(v)
+	b = q10_1*vtrap7(v)
+	tau_m = 1 / (a + b)
+	m_inf = a / (a + b)
+
+	a = q10_2*vtrap8(v)
+	b = q10_2*vtrap9(v)
+	tau_h = 1 / (a + b)
+	h_inf = a / (a + b)
+
+	v2 = v - vtraub : convert to traub convention
+
+	a = q10_3*vtrap10(v)
+	b = q10_3*vtrap11(v)
+	tau_s = 1 / (a + b)
+	s_inf = a / (a + b)
+}
+
+:FUNCTION vtrap(x) {
+:	if (x < -50) {
+:		vtrap = 0
+:	}else{
+:		vtrap = bsA / (Exp((x+bsB)/bsC) + 1)
+:	}
+:}
+
+FUNCTION vtrap1(x) {
+	if (fabs((x+ampB)/ampC) < 1e-6) {
+		vtrap1 = ampA*ampC
+	}else if (x < -150){
+		vtrap1 = 0.00086725
+	}else{
+		vtrap1 = (ampA*(x+ampB)) / (1 - Exp(-(x+ampB)/ampC))
+	}
+}
+
+FUNCTION vtrap2(x) {
+	if (fabs((x+bmpB)/bmpC) < 1e-6) {
+		vtrap2 = bmpA*bmpC : Ted Carnevale minus sign bug fix
+	}else if (x > 150){
+		vtrap2 = 1.5855e-05
+	}else{
+		vtrap2 = (bmpA*(-(x+bmpB))) / (1 - Exp((x+bmpB)/bmpC))
+	}
+}
+
+FUNCTION vtrap6(x) {
+	if (fabs((x+amB)/amC) < 1e-6) {
+		vtrap6 = amA*amC
+	}else if (x < -150){
+		vtrap6 = 0.15733
+	}else{
+		vtrap6 = (amA*(x+amB)) / (1 - Exp(-(x+amB)/amC))
+	}
+}
+
+FUNCTION vtrap7(x) {
+	if (fabs((x+bmB)/bmC) < 1e-6) {
+		vtrap7 = bmA*bmC : Ted Carnevale minus sign bug fix
+	}else if (x > 150){
+		vtrap7 = 0.0057268
+	}else{
+		vtrap7 = (bmA*(-(x+bmB))) / (1 - Exp((x+bmB)/bmC))
+	}
+}
+
+FUNCTION vtrap8(x) {
+	if (fabs((x+ahB)/ahC) < 1e-6) {
+		vtrap8 = ahA*ahC : Ted Carnevale minus sign bug fix
+	}else if (x > 150){
+		vtrap8 = 0.0032594
+	}else{
+		vtrap8 = (ahA*(-(x+ahB))) / (1 - Exp((x+ahB)/ahC))
+	}
+}
+
+FUNCTION vtrap9(x) {
+	if (x < -150){
+		vtrap9 = 0.0014054
+	}else{
+		vtrap9 = bhA / (1 + Exp(-(x+bhB)/bhC))
+	}
+}
+
+FUNCTION vtrap10(x) {
+	if (x < -150){ :<-150 because asC is negative
+		vtrap10 = 3.3484e-05
+	}else{
+		vtrap10 = asA / (Exp((x-vtraub+asB)/asC) + 1)
+	}
+}
+
+FUNCTION vtrap11(x) {
+	:if (((x-vtraub+bsB)/bsC) > 600) { :(x > 150){
+	if (x < -150){ :<-150 because bsC is negative
+		vtrap11 = 3.3484e-06
+	}else{
+		vtrap11 = bsA / (Exp((x-vtraub+bsB)/bsC) + 1)
+	}
+}
+
+
+FUNCTION Exp(x) {
+	if (x < -100) {
+		Exp = 0
+	}else{
+		Exp = exp(x)
+	}
+}
+
+UNITSON

pyfibers/MOD/BK.mod

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+: This channel is implemented by Nathan Titus 2019.
+: Calcium-Activated potassium channel of BK and SK Channel Contributions
+: Kv7.2 (n) and Kv7.3 (m). Kv7.5 was considered "similar enough" to
+: Kv7.2 so as to be considered a part of that current (n).
+: Data From:
+
+NEURON {
+	SUFFIX bk
+	USEION k READ ek WRITE ik
+	USEION ca READ cai
+	RANGE gbar, ek, ik
+	RANGE tau_m,minf,tau_n,m,h,hinf,tau_h
+	RANGE minfshift, hinfshift, ik, gp, g
+}
+
+UNITS {
+	(S) = (siemens)
+	(mV) = (millivolts)
+	(mA) = (milliamp)
+}
+
+PARAMETER {
+	gbar 	(S/cm2)
+	q10 = 3
+
+    minfshift = 0 (mV)
+	hinfshift = 0 (mV)
+}
+
+ASSIGNED {
+	v	(mV) : NEURON provides this
+	ik	(mA/cm2)
+	g	(S/cm2)
+	tau_m	(ms)
+    tau_h  (ms)
+	cai		(mM)
+    minf
+	hinf
+	gp
+    ek	(mV)
+	celsius (degC)
+}
+
+STATE { m h }
+
+BREAKPOINT {
+	SOLVE states METHOD cnexp
+	gp = m*h
+	g = gbar*gp
+	ik = g * (v-ek)
+}
+
+INITIAL {
+	: assume that equilibrium has been reached
+    rates(v)
+	m=minf :BK
+    h=hinf :BK
+
+}
+
+DERIVATIVE states {
+	rates(v)
+	m' = (minf - m)/(tau_m)
+	h' = (hinf - h)/(tau_h)
+
+}
+
+? rates
+PROCEDURE rates(Vm (mV)) (/ms) {
+	LOCAL Q10,sf,v12,vh12,pca
+UNITSOFF
+		Q10 = q10^((celsius-22)/10)
+		pca = log10(cai)-3 :converts to log10(cai [molar])
+		v12 =  -50*pca-232
+		vh12 =  -8*pca+35
+        minf= 1/(1+exp(-1*(Vm - v12)/24))
+        hinf= 1/(1+exp((Vm - vh12)/47))
+		tau_m = 1/(exp((Vm+(58*pca)+303)/(3.2*pca))+exp(-1*(Vm+(107*pca)+453)/(6.8*pca)))+0.4
+		tau_h = 1/(exp((Vm+(3*pca)+100)/(3*pca))+exp(-1*(Vm+(191*pca)+600)/(17*pca)))
+
+
+        tau_m=tau_m/Q10
+        tau_h=tau_h/Q10
+UNITSON
+
+}

pyfibers/MOD/CaPump.mod

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+: Author: David Catherall
+: Created: November 2016
+:CaPump is the Calcium Pump in Schild 1994
+:  Adapted from Leo Medina's implementation from Lindblad et al Am J Physiol 1996 275:H1666
+
+: Neuron Block creates mechanism
+	NEURON {
+		SUFFIX CaPump						:Sets suffix of mechanism for insertion into models
+		USEION ca READ cai WRITE ica		:Lays out which NEURON variables will be used/modified by file
+		RANGE ICaPmax, KmCa, ica, icap		:Allows variables to be modified in hoc and collected in vectors
+	}
+
+: Defines Units different from NEURON base units
+	UNITS {
+		(mA) = (milliamp)
+		(mV) = (millivolt)
+		(molar) = (1/liter)
+		(mM) = (millimolar)
+
+	}
+
+: Defines variables which will have a constant value throughout any given simulation run
+	PARAMETER {
+		ICaPmax22 = 0.000859437(mA/cm2) <0,1e6>
+		KmCa = .0005 (mM)    <0,1e6>
+		Q10CaP = 2.30
+		Q10TempA = 22	(degC)		: Used to shift ICaPmax value based on temperature with equation : tau(T1)=tau(Q10TempA)*Q10^((Q10TempA-T1)/Q10TempB)
+		Q10TempB = 10	(degC)
+	}
+
+: Defines variables which will be used or calculated throughout the simulation which may not be constant. Also included NEURON provided variables, like v, celsius, and ina
+	ASSIGNED {
+
+		:NEURON provided Variables
+		celsius (degC)
+		v (mV)
+		cai (mM)
+		ica (mA/cm2)
+
+		:Model Specific Variables
+		icap (mA/cm2)
+		ICaPmax (mA/cm2)
+	}
+
+: This block iterates the variable calculations and uses those calculations to calculate currents
+	BREAKPOINT {
+
+		icap = ICaPmax*(cai/(cai+KmCa))
+
+		ica=icap
+	}
+
+:Initialize KNaCa, as it is temperature dependent
+	INITIAL {
+		ICaPmax = ICaPmax22*Q10CaP^((Q10TempA-celsius)/Q10TempB)
+	}
+:Note that there are no state variables, and as such, no differential equations

pyfibers/MOD/CaV12.mod

@@ -0,0 +1,89 @@
+: L-Type Voltage Dependent Calcium Channel
+
+: Coded and modified by Nathan Titus 2018
+: Development Notes:
+:
+:
+
+NEURON {
+	SUFFIX cav12
+	USEION ca READ eca WRITE ica
+	RANGE ica
+	RANGE gbar, minf, mtau, hinf, htau
+	RANGE q10, gp, g
+}
+
+UNITS {
+    (molar) = (1/liter)                     : moles do not appear in units
+    (mM)    = (millimolar)
+	(uA) = (microamp)
+	(mA) = (milliamp)
+	(mV) = (millivolt)
+	(um) = (micron)
+	(S) = (siemens)
+
+}
+
+PARAMETER {
+	gbar = 6.5e-9 (S/cm2) :from Schild et al 1994
+	q10 = 3
+}
+
+ASSIGNED {
+	v (mV)
+	celsius (degC)
+	g (S/cm2)
+	gp
+	minf
+	mtau
+	hinf
+	htau
+	ica (mA/cm2)
+	eca (mV)
+}
+
+
+INITIAL {
+	rates(v)
+	m = minf
+	h = hinf
+}
+
+STATE {
+	m h
+}
+
+BREAKPOINT {
+	SOLVE states METHOD cnexp
+	gp = m*m*m*h
+	g = gbar*gp
+	ica = g*(v-eca)
+
+}
+
+DERIVATIVE states {
+	rates(v)
+	m' = (minf - m)/(mtau)
+	h' = (hinf - h)/(htau)
+}
+
+? rates
+PROCEDURE rates(Vm (mV)) {
+	LOCAL Q10
+	TABLE minf,hinf,mtau,htau DEPEND celsius FROM -120 TO 100 WITH 440
+
+UNITSOFF
+	Q10 = q10^((celsius-22)/10)
+	:minf = 1/(1 + exp(-1*(Vm - 1.5)/6))
+	minf = (1/(1 + exp(-1*(Vm - 1.75)/10)))^(1/3)
+	:hinf = 1/(1 + exp((Vm + 61.5)/12))
+	hinf = 1/(1 + exp((Vm - 10)/8))
+	:mtau = 0.57 + 5.5/(exp((Vm + 4.6)/7.95) + exp(-1*(Vm - 8.9)/33.8))
+	mtau = 0.25 + 0.5/(exp((Vm - 15)/5) + exp(-1*(Vm + 27)/12))
+	:htau = 4.3 + 167/(exp((Vm + 15)/9.2) + exp(-1*(Vm + 38)/31)) + 80/(1+exp((Vm + 72)/5))
+	htau = 1.4/(exp((Vm - 145)/30) + exp(-1*(Vm + 150)/16.4))
+	mtau = mtau/Q10
+	htau = htau/Q10
+
+}
+UNITSON

pyfibers/MOD/CaV22.mod

@@ -0,0 +1,97 @@
+: N-Type Voltage Dependent Calcium Channel NOT FOR VAGAL AFFERENTS
+
+: Coded and modified by Nathan Titus 2018
+: Development Notes: Almost definitely a second inactivation gate or
+: concentration dependency. Insufficient data exists so inactivation tau
+: should be updated when more is understood about these channels.
+
+NEURON {
+	SUFFIX cav22
+	USEION ca READ eca WRITE ica
+	RANGE ica
+	RANGE gbar, minf, mtau, hinf, htau, sinf, stau
+	RANGE q10, gp, g
+}
+
+UNITS {
+    (molar) = (1/liter)                     : moles do not appear in units
+    (mM)    = (millimolar)
+	(uA) = (microamp)
+	(mA) = (milliamp)
+	(mV) = (millivolt)
+	(um) = (micron)
+	(S) = (siemens)
+
+}
+
+PARAMETER {
+	gbar = 6.5e-9 (S/cm2) :from Schild et al 1994
+	q10 = 3
+}
+
+ASSIGNED {
+	v (mV)
+	celsius (degC)
+	g (S/cm2)
+	gp
+	minf
+	mtau
+	hinf
+	htau
+	sinf
+	stau
+	ica (mA/cm2)
+	eca (mV)
+}
+
+
+INITIAL {
+	rates(v)
+	m = minf
+	h = hinf
+	s = sinf
+}
+
+STATE {
+	m h s
+}
+
+BREAKPOINT {
+	SOLVE states METHOD cnexp
+	gp = m*m*m*h*s
+	g = gbar*gp
+	ica = g*(v-eca)
+
+}
+
+DERIVATIVE states {
+	rates(v)
+	m' = (minf - m)/(mtau)
+	h' = (hinf - h)/(htau)
+	s' = (sinf - s)/(stau)
+}
+
+? rates
+PROCEDURE rates(Vm (mV)) {
+	LOCAL Q10
+	TABLE minf,hinf,sinf,mtau,htau,stau DEPEND celsius FROM -120 TO 100 WITH 440
+
+UNITSOFF
+	Q10 = q10^((celsius-22)/10)
+	:minf = 1/(1 + exp(-1*(Vm - 1.5)/6))
+	minf = (1/(1 + exp(-1*(Vm + 4)/7.5)))^(1/3)
+	:hinf = 1/(1 + exp((Vm + 61.5)/12))
+	hinf = 1/(1 + exp((Vm + 48)/7))
+	sinf = 1/(1 + exp((Vm + 81)/8.6))
+	mtau = .1 + 0.5/(exp((Vm-3)/6.7)+exp(-1*(Vm+37)/13.5))
+	htau = 36/(exp((Vm-35)/15.4)+exp(-1*(Vm+134)/26.6)) + 19 + 50/(1+exp((Vm+50)/10))
+	htau = 10/(exp((Vm-54)/23)+exp(-1*(Vm+150)/35))
+	stau = 50 + 30/(exp((Vm-50)/26)+exp(-1*(Vm+150)/26))
+
+	mtau = mtau/Q10
+	htau = htau/Q10
+	stau = stau/Q10
+
+}
+
+UNITSON

pyfibers/MOD/DNav18.mod

@@ -0,0 +1,107 @@
+: The m and h are form sheets  2007
+:s and u are form Delmas
+: run NaV18_delmas.m to plot the model
+
+NEURON {
+	SUFFIX nav1p8
+	USEION na READ ena WRITE ina
+ 	RANGE gbar, ena, ina, celsiusT
+}
+
+UNITS {
+	(S) = (siemens)
+	(mV) = (millivolts)
+	(mA) = (milliamp)
+}
+
+PARAMETER {
+	gbar = 0 (S/cm2) : =220e-9/(100e-12*1e8) (S/cm2) : 220(nS)/100(um)^2
+	kvot_qt
+        celsiusT
+	shift_act = 0 (mV)
+	shift_inact =0 (mV)
+}
+
+ASSIGNED {
+	v	(mV) : NEURON provides this
+	ina	(mA/cm2)
+	g	(S/cm2)
+	tau_h	(ms)
+   	tau_m	(ms)
+	tau_s	(ms)
+	tau_u	(ms)
+	minf
+	hinf
+	sinf
+	uinf
+        ena    	(mV)
+        am
+        bm
+}
+
+STATE { m h s u }
+
+BREAKPOINT {
+	SOLVE states METHOD cnexp
+	g = gbar * m^3* h * s * u
+	ina = g * (v-ena)
+}
+
+INITIAL {
+	: assume that equilibrium has been reached
+        rates(v)
+        m=minf
+        h=hinf
+        s=sinf
+        u=uinf
+
+
+}
+
+DERIVATIVE states {
+	rates(v)
+	m' = (minf - m)/tau_m
+	h' = (hinf - h)/tau_h
+	s' = (sinf - s)/tau_s
+	u' = (uinf - u)/tau_u
+}
+
+FUNCTION rates(Vm (mV)) {
+
+        am= 2.85-(2.839)/(1+exp((Vm-1.159)/13.95))
+        bm= (7.6205)/(1+exp((Vm+46.463)/8.8289))
+	tau_m = 1/(am+bm)
+	minf = am/(am+bm)
+
+        hinf= 1/(1+exp((Vm+32.2)/4))
+        tau_h=(1.218+42.043*exp(-((Vm+38.1)^2)/(2*15.19^2)))
+
+	tau_s = 1/(alphas(Vm) + betas(Vm))
+        sinf = 1/(1 + exp((Vm + 45)/8(mV)))
+ 	tau_u = 1/(alphau(Vm) + betau(Vm))
+	uinf = 1/(1 + exp((Vm + 51)/8(mV)))
+
+
+	kvot_qt=1/((2.5^((celsiusT-22)/10)))
+        tau_m=tau_m*kvot_qt
+        tau_h=tau_h*kvot_qt
+        tau_s=tau_s*kvot_qt
+        tau_u=tau_u*kvot_qt
+}
+
+
+FUNCTION alphas(Vm (mV)) (/ms) {
+	alphas=	0.001(/ms)*5.4203/(1 + exp((Vm + 79.816)/16.269(mV)))
+}
+
+FUNCTION alphau(Vm (mV)) (/ms) {
+	alphau=	0.0002(/ms)*2.0434/(1 + exp((Vm + 67.499)/19.51(mV)))
+}
+
+FUNCTION betas(Vm (mV)) (/ms) {
+	betas= 0.001(/ms)*5.0757/(1 + exp(-(Vm + 15.968)/11.542(mV)))
+}
+
+FUNCTION betau(Vm (mV)) (/ms) {
+	betau= 0.0002(/ms)*1.9952/(1 + exp(-(Vm + 30.963)/14.792(mV)))
+}