//genesis
/* FILE INFORMATION
** The 1991 Traub set of voltage and concentration dependent channels
** Implemented as tabchannels by : Dave Beeman
** R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson
** Journal of Neurophysiology, Vol. 66, p. 635 (1991)
**
** This file depends on functions and constants defined in defaults.g
** As it is also intended as an example of the use of the tabchannel
** object to implement concentration dependent channels, it has extensive
** comments. Note that the original units used in the paper have been
** converted to SI (MKS) units. Also, we define the ionic equilibrium
** potentials relative to the resting potential, EREST_ACT. In the
** paper, this was defined to be zero. Here, we use -0.060 volts, the
** measured value relative to the outside of the cell.
*/
/* November 1999 update for GENESIS 2.2: Previous versions of this file used
a combination of a table, tabgate, and vdep_channel to implement the
Ca-dependent K Channel - K(C). This new version uses the new tabchannel
"instant" field, introduced in GENESIS 2.2, to implement an
"instantaneous" gate for the multiplicative Ca-dependent factor in the
conductance. This allows these channels to be used with the fast
hsolve chanmodes > 1.
*/
// Now updated for Traub et al. J Neurophysiol 2003;89:909-921.
// CONSTANTS
float EREST_ACT = -0.060 /* hippocampal cell resting potl */
float ENAP23RSa = 0.115 + EREST_ACT // 0.055
float EKP23RSa = -0.015 + EREST_ACT // -0.075
float ECAP23RSa = 0.140 + EREST_ACT // 0.080
float EARP23RSa = 0.025 + EREST_ACT // -0.035
float SOMA_A = 3.320e-9 // soma area in square meters
/*
For these channels, the maximum channel conductance (Gbar) has been
calculated using the CA3 soma channel conductance densities and soma
area. Typically, the functions which create these channels will be used
to create a library of prototype channels. When the cell reader creates
copies of these channels in various compartments, it will set the actual
value of Gbar by calculating it from the cell parameter file.
*/
//========================================================================
// Tabchannel gNa-transient, gNa(F) 2005/03
//========================================================================
function make_NaF1
str chanpath = "NaF1"
if ({exists NaF1})
return
end
create tabchannel NaF1
setfield NaF1 \
Ek 0.05 \
Ik 0 \
Xpower 3 \
Ypower 1
setfield NaF1 \
Gbar 1875 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call NaF1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v < -26.5 )
tau = 0.025 + 0.14 * { exp { {v + 26.5} / 10} }
else
tau = 0.02 + 0.145 * { exp { -1 * {v + 26.5} / 10.0} }
end
v = v * 0.001 // reset v
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
v = v * 1000 // v to units of equation
inf = 1 / { 1 + {exp { -1*{v + 34.5} / 10}} }
v = v * 0.001 // reset v
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF1 X_A->table[{i}] {alpha}
setfield NaF1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF1 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call NaF1 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 0.15 + 1.15 / { 1 + { exp {{v + 37} / 15} } }
v = v * 0.001 // reset v
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
v = v * 1000 // v to units of equation
inf = 1 / { 1 + {exp { {v + 62.9} / 10.7}} }
v = v * 0.001 // reset v
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF1 Y_A->table[{i}] {alpha}
setfield NaF1 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF1 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP1
str chanpath = "NaP1"
if ({exists NaP1})
return
end
create tabchannel NaP1
setfield NaP1 \
Ek 0.05 \
Ik 0 \
Xpower 1
setfield NaP1 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call NaP1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v < -40 )
tau = 0.025 + 0.14 * {exp {{ v + 40 }/10}}
else
tau = 0.02 + 0.145 * {exp {-1 * {v + 40}/ 10}}
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -10, Vhalf = -48, in units: Physiological Units
// A = 1, B = -0.01, Vhalf = -0.048
inf = 1 / ( {exp {(v + 0.048) / -0.01}} + 1)
// alpha and beat
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaP1 X_A->table[{i}] {alpha}
setfield NaP1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaP1 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR1
if ({exists AR1})
return
end
create tabchannel AR1
setfield AR1 \
Ek -0.035 \
Ik 0 \
Xpower 1
setfield AR1 \
Gbar 2.5 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call AR1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 1 /{{exp {-14.6 - {0.086 * v} }} + {exp {-1.87 + {0.07 * v}}}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 5.5, Vhalf = -75, in units: Physiological Units
// A = 1, B = 0.0055, Vhalf = -0.075
inf = 1 / ( {exp {(v + 0.075) / 0.0055}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield AR1 X_A->table[{i}] {alpha}
setfield AR1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield AR1 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR1
if ({exists KDR1})
return
end
create tabchannel KDR1
setfield KDR1 \
Ek -0.095 \
Ik 0 \
Xpower 4
setfield KDR1 \
Gbar 1250 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call KDR1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v < -10 )
tau = 0.25 + 4.35 * {exp {{ v + 10 }/10}}
else
tau = 0.25 + 4.35 * {exp {{- v - 10}/ 10}}
end
v = v * 0.001 // reset v
tau = tau * 0.001 // correct units of tau
// inf
float inf
// A = 1, B = -10, Vhalf = -29.5, in units: Physiological Units
// A = 1, B = -0.01, Vhalf = -0.0295
inf = 1 / ( {exp {(v + 0.0295) / -0.01}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KDR1 X_A->table[{i}] {alpha}
setfield KDR1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KDR1 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA1
if ({exists KA1})
return
end
create tabchannel KA1
setfield KA1 \
Ek -0.095 \
Ik 0 \
Xpower 4 \
Ypower 1
setfield KA1 \
Gbar 300 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call KA1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 0.185 + 0.5 / {{exp {{ v + 35.8 }/19.7}} + {exp {{-v - 79.7}/12.7}}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
float A, B, Vhalf
// ChannelML form of equation: inf which is of form sigmoid, with params:
// A = 1, B = -8.5, Vhalf = -60, in units: Physiological Units
// A = 1, B = -0.0085, Vhalf = -0.06
inf = 1 / ( {exp {(v + 0.06) /-0.0085}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KA1 X_A->table[{i}] {alpha}
setfield KA1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA1 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call KA1 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v < -63.0 )
tau = 0.5 / {{exp {{ v + 46 }/5}} + {exp {{ -v - 238 }/37.5}}}
else
tau = 9.5
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 6, Vhalf = -78, in units: Physiological Units
// A = 1, B = 0.006, Vhalf = -0.078
inf = 1 / ( {exp {(v + 0.078) / 0.006}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KA1 Y_A->table[{i}] {alpha}
setfield KA1 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA1 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K21
if ({exists K21})
return
end
create tabchannel K21
setfield K21 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Ypower 1
setfield K21 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call K21 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equat.
tau = 4.95 + 0.5 / { {exp { {v - 81} / 25.6}} + {exp { {- v - 132} / 18 }}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -17, Vhalf = -10, in units: Physiological Units
// A = 1, B = -0.017, Vhalf = -0.01
inf = 1 / ( {exp {(v + 0.01) / -0.017}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K21 X_A->table[{i}] {alpha}
setfield K21 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K21 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call K21 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 60 + 0.5 / {{exp {{ v - 1.33 }/200}} + {exp {{- v - 130}/ 7.1}}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 10.6, Vhalf = -58, in units: Physiological Units
// A = 1, B = 0.0106, half = -0.058
inf = 1 / ( {exp {(v + 0.058) / 0.0106}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K21 Y_A->table[{i}] {alpha}
setfield K21 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K21 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM1
if ({exists KM1})
return
end
create tabchannel KM1
setfield KM1 \
Ek -0.095 \
Ik 0 \
Xpower 1
setfield KM1 \
Gbar 75 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call KM1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
// A = 0.02, B = -5, Vhalf = -20, in units: Physiological Units
// A = 20, B = -0.005, Vhalf = -0.02
alpha = 20 / ( {exp {(v + 0.02) / -0.005}} + 1)
// beta
float beta
// A = 0.01, B = -18, Vhalf = -43, in units: Physiological Units
// A = 10, B = -0.018, Vhalf = -0.043
beta = 10 * {exp {(v + 0.043) / -0.018}}
// alpha and beta
float tau = 1/(alpha + beta)
setfield KM1 X_A->table[{i}] {alpha}
setfield KM1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KM1 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// P23RS Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL1
if ({exists CaL1})
return
end
create tabchannel CaL1
setfield CaL1 \
Ek 0.125 \
Ik 0 \
Xpower 2 \
Ypower 1
setfield CaL1 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call CaL1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 0.204 + 0.333 / { {exp {{15.8 + v} / 18.2 }} + {exp {{- v - 131} / 16.7}} }
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
float A, B, Vhalf
// A = 1, B = -6.2, Vhalf = -56.0, in units: Physiological Units
// A = 1, B = -0.0062, Vhalf = -0.056
inf = 1 / ( {exp {(v + 0.056) / -0.0062}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL1 X_A->table[{i}] {alpha}
setfield CaL1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL1 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call CaL1 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v < -81.0 )
tau = 0.333 * {exp {{ v + 466 } / 66.6}}
else
tau = 9.32 + 0.333 * {exp {{ - v - 21 } / 10.5}}
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 4, Vhalf = -80, in units: Physiological Units
// A = 1, B = 0.004, Vhalf = -0.08
inf = 1 / ( {exp {(v + 0.08) / 0.004}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL1 Y_A->table[{i}] {alpha}
setfield CaL1 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL1 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//==========================================================================
// P23RS Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH1
if ({exists CaH1})
return
end
create tabchannel CaH1
setfield CaH1 \
Ek 0.125 \
Ik 0 \
Xpower 2
setfield CaH1 \
Gbar 5 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call CaH1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
// A = 1.6, B = -13.888889, Vhalf = 5, in units: Physiological Units
// A = 1600, B = -0.013888889000000001, Vhalf = 0.005
alpha = 1600 / ( {exp {(v - 0.005) / -0.013888889000000001}} + 1)
// beta
float beta
// A = 0.1, B = -5, Vhalf = -8.9, in units: Physiological Units
// A = 100, B = -0.005, Vhalf = -0.0089
if ( {abs {(v + 0.0089)/ -0.005}} < 1e-6)
beta = 100 * (1 + (v + 0.0089)/-0.005/2)
else
beta = 100 * ((v + 0.0089) / -0.005) /(1 - {exp {-1 * (v + 0.0089)/-0.005}})
end
// alpha and beta
float tau = 1/(alpha + beta)
setfield CaH1 X_A->table[{i}] {alpha}
setfield CaH1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaH1 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// P23RS Ca conc, Traub et al. J Neurophysiol 2003;89:909-921.
//========================================================================
/****************************************************************************
Next, we need an element to take the Calcium current calculated by the Ca
channel and convert it to the Ca concentration. The "Ca_concen" object
solves the equation dC/dt = B*I_Ca - C/tau, and sets Ca = Ca_base + C. As
it is easy to make mistakes in units when using this Calcium diffusion
equation, the units used here merit some discussion.
With Ca_base = 0, this corresponds to Traub's diffusion equation for
concentration, except that the sign of the current term here is positive, as
GENESIS uses the convention that I_Ca is the current flowing INTO the
compartment through the channel. In SI units, the concentration is usually
expressed in moles/m^3 (which equals millimoles/liter), and the units of B
are chosen so that B = 1/(ion_charge * Faraday * volume). Current is
expressed in amperes and one Faraday = 96487 coulombs. However, in this
case, Traub expresses the concentration in arbitrary units, current in
microamps and uses tau = 13.33 msec (50 msec soma, 20 msec dendrites in the
2003 J Neurophys paper). If we use the same concentration units,
but express current in amperes and tau in seconds, our B constant is then
10^12 times the constant (called "phi") used in the paper. The actual value
used will typically be determined by the cell reader from the cell
parameter file (will vary inversely with surface area of compartment).
However, for the prototype channel we will use Traub's
corrected value for the soma. (An error in the paper gives it as 17,402
rather than 17.402.) In our units, this will be 17.402e12.
****************************************************************************/
function make_Ca_s1
if ({exists Ca_s1})
return
end
create Ca_concen Ca_s1
// params for soma Ca pool
setfield Ca_s1 \
tau { 1.0 / 10 } \
Ca_base 0
addfield Ca_s1 addmsg1
setfield Ca_s1 \
addmsg1 "../CaH1 . I_Ca Ik"
// addfield Ca_s1 addmsg2
// setfield Ca_s1 \
// addmsg2 "../CaL1 . I_Ca Ik"
end
/*
This Ca_concen element should receive an "I_Ca" message from the calcium
channel, accompanied by the value of the calcium channel current. As we
will ordinarily use the cell reader to create copies of these prototype
elements in one or more compartments, we need some way to be sure that the
needed messages are established. Although the cell reader has enough
information to create the messages which link compartments to their channels
and to other adjacent compartments, it must be provided with the information
needed to establish additional messages. This is done by placing the
message string in a user-defined field of one of the elements which is
involved in the message. The cell reader recognizes the added field names
"addmsg1", "addmsg2", etc. as indicating that they are to be
evaluated and used to set up messages. The paths are relative to the
element which contains the message string in its added field. Thus,
"../Ca_hip_traub91" refers to the sibling element Ca_hip_traub91 and "."
refers to the Ca_hip_conc element itself.
*/
/****************************************************************************/
function make_Ca_d1
if ({exists Ca_d1})
return
end
create Ca_concen Ca_d1
// params for dend. Ca pool model
setfield Ca_d1 \
tau { 1.0 / 50 } \
Ca_base 0
addfield Ca_d1 addmsg1
setfield Ca_d1 \
addmsg1 "../CaH1 . I_Ca Ik"
// addfield Ca_d1 addmsg2
// setfield Ca_d1 \
// addmsg2 "../CaL1 . I_Ca Ik"
end
/*
This Ca_concen element should receive an "I_Ca" message from the calcium
channel, accompanied by the value of the calcium channel current. As we
will ordinarily use the cell reader to create copies of these prototype
elements in one or more compartments, we need some way to be sure that the
needed messages are established. Although the cell reader has enough
information to create the messages which link compartments to their channels
and to other adjacent compartments, it must be provided with the information
needed to establish additional messages. This is done by placing the
message string in a user-defined field of one of the elements which is
involved in the message. The cell reader recognizes the added field names
"addmsg1", "addmsg2", etc. as indicating that they are to be
evaluated and used to set up messages. The paths are relative to the
element which contains the message string in its added field. Thus,
"../Ca_hip_traub91" refers to the sibling element Ca_hip_traub91 and "."
refers to the Ca_hip_conc element itself.
*/
//===============================================================================
// P23RS Ca-dependent K Channel K(C)
//===============================================================================
/*
The expression for the conductance of the potassium C-current channel has a
typical voltage and time dependent activation gate, where the time dependence
arises from the solution of a differential equation containing the rate
parameters alpha and beta. It is multiplied by a function of calcium
concentration that is given explicitly rather than being obtained from a
differential equation. Therefore, we need a way to multiply the activation
by a concentration dependent value which is determined from a lookup table.
This is accomplished by using the Z gate with the new tabchannel "instant"
field, introduced in GENESIS 2.2, to implement an "instantaneous" gate for
the multiplicative Ca-dependent factor in the conductance.
*/
function make_KCs1
if ({exists KCs1})
return
end
create tabchannel KCs1
setfield KCs1 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCs1 \
Gbar 120 \
Gk 0
float tab_divs = 1041
float v_min = -0.12
float v_max = 0.14
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call KCs1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
v = v * 1000 // v to units of equation
if (v < -10 )
alpha = {2 / 37.95} * { exp { {{v + 50 } / 11} - {{ v + 53.5} / 27} } }
else
alpha = 2 * {exp { { {-1 * v} - 53.5 } / 27 }}
end
v = v * 0.001 // reset v
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // v to units of equation
alpha = alpha * 0.001 // alpha to units of equation
if (v < -10 )
beta = 2 * {exp { { {-1 * v} - 53.5 } / 27 }} - alpha
else
beta = 0.0
end
v = v * 0.001 // reset v
alpha = alpha * 1000 // resetting alpha
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KCs1 X_A->table[{i}] {alpha}
setfield KCs1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCs1 X_A->calc_mode 1 X_B->calc_mode 1
// Ca dependent term (voltage independent)
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCs1 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
ca_conc = ca_conc * 1000000 //reset ca_conc
setfield KCs1 Z_A->table[{i}] {0}
setfield KCs1 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCs1 Z
addfield KCs1 addmsg1
setfield KCs1 addmsg1 "../Ca_s1 . CONCEN Ca"
end
function make_KCd1
if ({exists KCd1})
return
end
create tabchannel KCd1
setfield KCd1 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCd1 \
Gbar 120 \
Gk 0
float tab_divs = 1041
float v_min = -0.12
float v_max = 0.14
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call KCd1 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
v = v * 1000 // v to units of equation
if (v < -10 )
alpha = {2 / 37.95} * { exp { {{v + 50 } / 11} - {{ v + 53.5} / 27} } }
else
alpha = 2 * {exp { { {-1 * v} - 53.5 } / 27 }}
end
v = v * 0.001 // reset v
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // v to units of equation
alpha = alpha * 0.001 // alpha to units of equation
if (v < -10 )
beta = 2 * {exp { { {-1 * v} - 53.5 } / 27 }} - alpha
else
beta = 0.0
end
v = v * 0.001 // reset v
alpha = alpha * 1000 // resetting alpha
// correct units of beta
beta = beta * 1000
//alpha and beta
float tau = 1/(alpha + beta)
setfield KCd1 X_A->table[{i}] {alpha}
setfield KCd1 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCd1 X_A->calc_mode 1 X_B->calc_mode 1
// Ca dependent term (voltage independent)
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCd1 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
ca_conc = ca_conc * 1000000 //reset ca_conc
setfield KCd1 Z_A->table[{i}] {0}
setfield KCd1 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCd1 Z
addfield KCd1 addmsg1
setfield KCd1 addmsg1 "../Ca_d1 . CONCEN Ca"
end
//========================================================================
// P23RS Ca-dependent K AHP Channel,gK(AHP)
//========================================================================
/* This is a tabchannel which gets the calcium concentration from Ca pool
in order to calculate the activation of its Z gate. It is set up much
like the Ca channel, except that the A and B tables have values which are
functions of concentration, instead of voltage.
*/
function make_KAHPs1
if ({exists KAHPs1})
return
end
create tabchannel KAHPs1
setfield KAHPs1 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPs1 \
Gbar 1 \
Gk 0
float tab_divs = 1041
// Ca dependent channel
float c
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KAHPs1 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// alpha
float alpha
float v
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.0001 )
alpha = ca_conc/0.01
else
alpha = 0.01
end
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
beta = 0.01
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KAHPs1 Z_A->table[{c}] {alpha}
setfield KAHPs1 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPs1 Z_conc 1
setfield KAHPs1 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPs1 addmsg1
setfield KAHPs1 \
addmsg1 "../Ca_s1 . CONCEN Ca"
end
function make_KAHPd1
if ({exists KAHPd1})
return
end
create tabchannel KAHPd1
setfield KAHPd1 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPd1 \
Gbar 1 \
Gk 0
float tab_divs = 1041
float c
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KAHPd1 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// alpha
float alpha
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.0001 )
alpha = ca_conc/0.01
else
alpha = 0.01
end
ca_conc = ca_conc * 1000000 // reset ca_conc
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
beta = 0.01
ca_conc = ca_conc * 1000000 // reset ca_conc
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KAHPd1 Z_A->table[{c}] {alpha}
setfield KAHPd1 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPd1 Z_conc 1
setfield KAHPd1 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPd1 addmsg1
setfield KAHPd1 \
addmsg1 "../Ca_d1 . CONCEN Ca"
end