Clean up K_T and K_P.

mechanisms/allen/CaDynamics.mod

@@ -9,28 +9,26 @@ NEURON {
 }
 
 UNITS {
-    (mV)	= (millivolt)
-    (mA)	= (milliamp)
-    (molar)	= (1/liter)
-    (mM)	= (millimolar)
-    (um)	= (micron)
+    (mV)    = (millivolt)
+    (mA)    = (milliamp)
+    (molar) = (1/liter)
+    (mM)    = (millimolar)
+    (um)    = (micron)
 }
 
 PARAMETER {
-    F		= 96485.3321233100184	(coulomb/mole)	: Faraday's constant
-    gamma	= 0.05			()		: percent of free calcium (not buffered)
-    decay	= 80			(ms)		: rate of removal of calcium
-    depth	= 0.1			(um)		: depth of shell
-    minCai	= 1e-4			(mM)
+    F        = 96485.3321233100184  (coulomb/mole) : Faraday's constant
+    gamma    = 0.05                 ()             : percent of free calcium (not buffered)
+    decay    = 80                   (ms)           : rate of removal of calcium
+    depth    = 0.1                  (um)           : depth of shell
+    minCai   = 1e-4                 (mM)
 }
 
 INITIAL {
     cai = minCai
 }
 
-STATE {
-    cai (mM)
-}
+STATE { cai (mM) }
 
 BREAKPOINT {
     SOLVE states METHOD cnexp

mechanisms/allen/Ca_HVA.mod

@@ -1,4 +1,5 @@
-: Reference:        Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993
+: Reference: Reuveni, Friedman, Amitai, and Gutnick,
+:            J. Neurosci. 1993
 
 NEURON {
     SUFFIX Ca_HVA
@@ -16,43 +17,41 @@ PARAMETER {
     gbar = 0.00001 (S/cm2)
 }
 
-STATE {
-    m
-    h
-}
+STATE { m h }
 
 BREAKPOINT {
     SOLVE states METHOD cnexp
-    ica = gbar*m*m*h*(v-eca)
+    LOCAL g
+    g = gbar*m*m*h
+    ica = g*(v-eca)
 }
 
 DERIVATIVE states {
-    LOCAL mAlpha, mBeta, hAlpha, hBeta, mRat, hRat
-
-    mAlpha = 0.055*vtrap(-27 - v, 3.8)
-    mBeta  = 0.94*exp((-75-v)/17)
-    mRat   = mAlpha + mBeta					 
-
-    hAlpha = 0.000457*exp((-13-v)/50)
-    hBeta  = 0.0065/(exp((-v-15)/28)+1)
-    hRat = hAlpha + hBeta					      
-
-    m' = mAlpha - m*mRat
-    h' = hAlpha - h*hRat
+    LOCAL mAlpha, mBeta, hAlpha, hBeta
+
+    mAlpha = m_alpha(v)
+    mBeta  = m_beta(v)
+    hAlpha = h_alpha(v)
+    hBeta  = h_beta(v)
+
+    m' = mAlpha - m*(mAlpha + mBeta)
+    h' = hAlpha - h*(hAlpha + hBeta)
 }
 
 INITIAL {
     LOCAL mAlpha, mBeta, hAlpha, hBeta
-
-    mAlpha = 0.055*vtrap(-27 - v, 3.8)
-    mBeta  = 0.94*exp((-75 - v)/17)
-    m      = mAlpha/(mAlpha + mBeta)
 
-    hAlpha =  0.000457*exp((-13-v)/50)
-    hBeta  =  0.0065/(exp((-v-15)/28) + 1)
+    mAlpha = m_alpha(v)
+    mBeta  = m_beta(v)
+    hAlpha = h_alpha(v)
+    hBeta  = h_beta(v)
+
+    m = mAlpha/(mAlpha + mBeta)
     h = hAlpha/(hAlpha + hBeta)
 }
 
-FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations
-    vtrap = y*exprelr(x/y)			       
-}
+FUNCTION vtrap(x, y) { vtrap = y*exprelr(x/y) }
+FUNCTION m_alpha(v) { m_alpha = 0.055*vtrap(-27 - v, 3.8) }
+FUNCTION h_alpha(v) { h_alpha = 0.000457*exp(-(v + 13)/50) }
+FUNCTION m_beta(v)  { m_beta  = 0.94*exp((-75 - v)/17) }
+FUNCTION h_beta(v)  { h_beta  = 0.0065/(exp(-(v + 15)/28) + 1) }

mechanisms/allen/Ca_LVA.mod

@@ -1,12 +1,14 @@
-: Comment: LVA ca channel. Note: mtau is an approximation from the plots
-: Reference:        Avery and Johnston 1996, tau from Randall 1997
-: Comment: shifted by -10 mv to correct for junction potential
-: Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21
+: Comment: LVA ca channel.
+:          Note:
+:          - mtau is an approximation from the plots
+:          - shifted by -10 mv to correct for junction potential
+:          - corrected rates using q10 = 2.3, target temperature 34, orginal 21
+: Reference: Avery and Johnston 1996, tau from Randall 1997
 
 NEURON {
     SUFFIX Ca_LVA
     USEION ca READ eca WRITE ica
-    RANGE gbar
+    RANGE gbar, qt
 }
 
 UNITS {
@@ -20,35 +22,32 @@ PARAMETER {
     celsius
 }
 
-ASSIGNED {
-    qt
-}
+ASSIGNED { qt }
 
-STATE {
-    m
-    h
-}
+STATE { m h }
 
 BREAKPOINT {
     SOLVE states METHOD cnexp
-    ica = gbar*m*m*h*(v - eca)
+    LOCAL g
+    g = gbar*m*m*h
+    ica = g*(v - eca)
 }
 
 DERIVATIVE states {
-    LOCAL mInf, mRat, hInf, hRat
-
-    mInf = 1/(1 + exp((v + 40)/-6))
-    hInf = 1/(1 + exp((v + 90)/6.4))
-    mRat = qt/(5  + 20/(1 + exp((v + 35)/5)))				
+    LOCAL mRat, hRat
+
+    mRat = qt/(5  + 20/(1 + exp((v + 35)/5)))
     hRat = qt/(20 + 50/(1 + exp((v + 50)/7)))
 
-    m' = (mInf - m)*mRat
-    h' = (hInf - h)*hRat
+    m' = (m_inf(v) - m)*mRat
+    h' = (h_inf(v) - h)*hRat
 }
 
 INITIAL {
     qt = 2.3^((celsius-21)/10)
-
-    m = 1/(1 + exp((v + 40)/-6))
-    h = 1/(1 + exp((v + 90)/6.4))
+    m = m_inf(v)
+    h = h_inf(v)
 }
+
+FUNCTION h_inf(v) { h_inf = 1/(1 + exp( (v + 90)/6.4)) }
+FUNCTION m_inf(v) { m_inf = 1/(1 + exp(-(v + 40)/6)) }

mechanisms/allen/Ih.mod

@@ -1,4 +1,5 @@
-: Reference:        Kole,Hallermann,and Stuart, J. Neurosci. 2006
+: Reference: Kole, Hallermann, and Stuart
+:            J. Neurosci. 2006
 
 NEURON {
     SUFFIX Ih
@@ -7,44 +8,40 @@ NEURON {
 }
 
 UNITS {
-    (S) = (siemens)
+    (S)  = (siemens)
     (mV) = (millivolt)
     (mA) = (milliamp)
 }
 
 PARAMETER {
-    gbar = 0.00001 (S/cm2)
-    ehcn =  -45.0 (mV)
+    gbar =   0.00001 (S/cm2)
+    ehcn = -45.0     (mV)
 }
 
-STATE {
-    m
-}
+STATE { m }
 
 BREAKPOINT {
     SOLVE states METHOD cnexp
-    ihcn = gbar*m*(v - ehcn)
+    LOCAL g
+    g = gbar*m
+    ihcn = g*(v - ehcn)
 }
 
 DERIVATIVE states {
-   LOCAL mAlpha, mBeta, mRat
-
-    mAlpha = 0.001*6.43*vtrap(v + 154.9, 11.9)
-    mBeta  = 0.001*193*exp(v/33.1)
-    mRat   = mAlpha + mBeta
-
-    m' = mAlpha - m*mRat
+    LOCAL ma, mb
+    ma = m_alpha(v)
+    mb = m_beta(v)
+    m' = ma - m*(ma + mb)
 }
 
 INITIAL {
-    LOCAL mAlpha, mBeta
-
-    mAlpha = 0.001 * 6.43 * vtrap(v + 154.9, 11.9)
-    mBeta  =  0.001*193*exp(v/33.1)
-
-    m = mAlpha/(mAlpha + mBeta)
+    LOCAL ma, mb
+    ma = m_alpha(v)
+    mb = m_beta(v)
+    m  = ma/(ma + mb)
 }
 
-FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations
-    vtrap = y*exprelr(x/y)			       
-}
+: Traps for 0 in denominator of rate equations
+FUNCTION vtrap(x, y) { vtrap   = y*exprelr(x/y) }
+FUNCTION m_alpha(v)  { m_alpha = 0.001 * 6.43 * vtrap(v + 154.9, 11.9) }
+FUNCTION m_beta(v)   { m_beta  = 0.001*193*exp(v/33.1) }

mechanisms/allen/Im.mod

@@ -1,22 +1,23 @@
-: Reference:        Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones
-: Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21
+: Reference: M-currents and other potassium currents in bullfrog sympathetic neurones
+:            Adams et al. 1982
+: Comment:   corrected rates using q10 = 2.3, target temperature 34, orginal 21
 
 NEURON {
     SUFFIX Im
     USEION k READ ek WRITE ik
-    RANGE gbar
+    RANGE gbar, qt
 }
 
 UNITS {
-    (S) = (siemens)
+    (S)  = (siemens)
     (mV) = (millivolt)
     (mA) = (milliamp)
 }
 
 PARAMETER {
     gbar = 0.00001 (S/cm2) 
-    v   (mV)
-    celsius (degC)
+    v              (mV)
+    celsius        (degC)
 }
 
 ASSIGNED { qt }
@@ -27,7 +28,7 @@ BREAKPOINT {
     SOLVE states METHOD cnexp
     LOCAL g
     g = gbar*m
-    ik = g*(v-ek)
+    ik = g*(v - ek)
 }
 
 DERIVATIVE states {
@@ -39,9 +40,9 @@ DERIVATIVE states {
 
 INITIAL {
     LOCAL a, b
+    qt = 2.3^(0.1*(celsius - 21))
     a = alpha(v)
     b = beta(v)
-    qt = 2.3^((celsius-21)/10)
     m = a/(a + b)
 }
 

mechanisms/allen/Im_v2.mod

@@ -3,7 +3,7 @@
 NEURON   {
    SUFFIX Im_v2
    USEION k READ ek WRITE ik
-   RANGE gbar
+   RANGE gbar, qt
 }
 
 UNITS {
@@ -17,37 +17,32 @@ PARAMETER {
    gbar = 0.00001   (S/cm2)
 }
 
-STATE {
-   m
-}
+ASSIGNED { qt }
+STATE { m }
 
 BREAKPOINT {
    SOLVE states METHOD cnexp
    ik = gbar*m*(v - ek)
 }
 
 DERIVATIVE states {
-    LOCAL qt, mAlpha, mBeta, mInf, mRat, iab
-
-    qt = 2.3^((celsius - 30)/10)
-
-    mAlpha = 0.007 * exp(( 6 *       0.4 * (v + 48))/26.12)
-    mBeta  = 0.007 * exp((-6 * (1 - 0.4) * (v + 48))/26.12)
+    LOCAL mAlpha, mBeta, mAlphaBeta
 
-    iab    = 1/(mAlpha + mBeta)
+    mAlpha     = m_alpha(v)
+    mBeta      = m_beta(v)
+    mAlphaBeta = mAlpha + mBeta
 
-    mInf = mAlpha*iab
-    mRat = qt/(15 + iab)
-
-    m' = (mInf - m)*mRat
+    m' = qt*(mAlpha - m*mAlphaBeta)/(1 + 15*mAlphaBeta)
 }
 
 INITIAL {
     LOCAL mAlpha, mBeta
 
-    mAlpha = 0.007*exp(( 6 *      0.4  * (v + 48))/26.12)
-    mBeta  = 0.007*exp((-6 * (1 - 0.4) * (v + 48))/26.12)
-
+    mAlpha = m_alpha(v)
+    mBeta  = m_beta(v)
     m = mAlpha/(mAlpha + mBeta)
+    qt = 2.3^((celsius - 30)/10)
 }
 
+FUNCTION m_alpha(v) { m_alpha = 0.007*exp(( 6 *      0.4  * (v + 48))/26.12) }
+FUNCTION m_beta(v)  { m_beta  = 0.007*exp((-6 * (1 - 0.4) * (v + 48))/26.12) }