//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 = -0.070 /* hippocampal cell resting potl */
float ENAP5IBc = 0.11 + EREST_ACT // 0.05
float EKP5IBc = -0.025 + EREST_ACT // -0.095
float ECAP5IBc = 0.195 + EREST_ACT // 0.125
float EARP5IBc = 0.035 + 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_NaF8
if ({exists NaF8})
return
end
create tabchannel NaF8
setfield NaF8 \
Ek 0.05 \
Ik 0 \
Xpower 3 \
Ypower 1
setfield NaF8 \
Gbar 1875 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call NaF8 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// Looking at rate: tau
float tau
v = v * 1000 // temporarily set v to units of equation...
if ({v - 3.5} < -30 )
tau = 0.025 + 0.14 * { exp { {{v - 3.5} + 30} / 10} }
else
tau = 0.02 + 0.145 * { exp { -1 * {{v - 3.5} + 30} / 10.0} }
end
v = v * 0.001 // reset v
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
v = v * 1000 // temporarily set v to units of equation...
inf = 1 / { 1 + {exp { { -1 * {v - 3.5} - 38} / 10}} }
v = v * 0.001 // reset v
// Working out the "real" alpha and beta expressions from the tau and inf
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF8 X_A->table[{i}] {alpha}
setfield NaF8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF8 X_A->calc_mode 1 X_B->calc_mode 1
// Creating table for gate h, using name Y for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call NaF8 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 // temporarily set 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
// Looking at rate: inf
float inf
v = v * 1000 // temporarily set v to units of equation...
inf = 1 / { 1 + {exp {{ v + 62.9 } / 10.7}} }
v = v * 0.001 // reset v
// Working out the "real" alpha and beta expressions from the tau and inf
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF8 Y_A->table[{i}] {alpha}
setfield NaF8 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF8 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP8
if ({exists NaP8})
return
end
create tabchannel NaP8
setfield NaP8 \
Ek 0.05 \
Ik 0 \
Xpower 1
setfield NaP8 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call NaP8 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 // temporarily set 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
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
float A, B, Vhalf
inf = 1 / ( {exp {(v +0.048) / -0.01}} + 1)
// alpha & beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaP8 X_A->table[{i}] {alpha}
setfield NaP8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaP8 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR8
if ({exists AR8})
return
end
create tabchannel AR8
setfield AR8 \
Ek -0.035 \
Ik 0 \
Xpower 1
setfield AR8 \
Gbar 2.5 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call AR8 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 // temporarily set 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
inf = 1 / ( {exp {(v + 0.075) / 0.0055}} + 1)
// alpha &beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield AR8 X_A->table[{i}] {alpha}
setfield AR8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield AR8 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR8
if ({exists KDR8})
return
end
create tabchannel KDR8
setfield KDR8 \
Ek -0.095 \
Ik 0 \
Xpower 4
setfield KDR8 \
Gbar 1250 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call KDR8 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// Looking at rate: tau
float tau
v = v * 1000 // temporarily set 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
// correct units of tau
tau = tau * 0.001
// inf
float inf
inf = 1 / ( {exp {(v + 0.0295) / -0.01}} + 1)
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KDR8 X_A->table[{i}] {alpha}
setfield KDR8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KDR8 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA8
if ({exists KA8})
return
end
create tabchannel KA8
setfield KA8 \
Ek -0.095 \
Ik 0 \
Xpower 4 \
Ypower 1
setfield KA8 \
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 KA8 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 // temporarily set 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
// A = 1, B = -8.5, Vhalf = -60, in p.u.
// A = 1 B = -0.0085 Vhalf = -0.06 in SI
inf = 1 / ( {exp {(v + 0.05) / -0.0085}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KA8 X_A->table[{i}] {alpha}
setfield KA8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA8 X_A->calc_mode 1 X_B->calc_mode 1
// Creating table for gate h, using name Y for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call KA8 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 // temporarily set v to units of equation...
if (v < -63.0 )
tau = 2.6 * 0.5 / {{exp {{ v + 46 }/5}} + {exp {{ -v - 238 }/37.5}}}
else
tau = 2.6 * 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 KA8 Y_A->table[{i}] {alpha}
setfield KA8 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA8 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K28
if ({exists K28})
return
end
create tabchannel K28
setfield K28 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Ypower 1
setfield K28 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call K28 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 // temporarily set v to units of equation...
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 p.u.
// A = 1 B = -0.017 Vhalf = -0.01 in SI
inf = 1 / ( {exp {(v + 0.01) / -0.017}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K28 X_A->table[{i}] {alpha}
setfield K28 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K28 X_A->calc_mode 1 X_B->calc_mode 1
// Creating table for gate h, using name Y for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call K28 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 // temporarily set 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 p.u.
// A = 1 B = 0.0106 Vhalf = -0.058 in SI
inf = 1 / ( {exp {(v + 0.058 ) / 0.0106}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K28 Y_A->table[{i}] {alpha}
setfield K28 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K28 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM8
if ({exists KM8})
return
end
create tabchannel KM8
setfield KM8 \
Ek -0.095 \
Ik 0 \
Xpower 1
setfield KM8 \
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 KM8 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 p.u.
// A = 20 B = -0.005 Vhalf = -0.02 in SI
alpha = 20 / ( {exp {(v + 0.02) / -0.005}} + 1)
// beta
float beta
// A = 0.01, B = -18, Vhalf = -43, in p.u.
// A = 10 B = -0.018 Vhalf = -0.043 in SI
beta = 10 * {exp {(v + 0.043) / -0.018}}
// tables
float tau = 1/(alpha + beta)
setfield KM8 X_A->table[{i}] {alpha}
setfield KM8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KM8 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL8
if ({exists CaL8})
return
end
create tabchannel CaL8
setfield CaL8 \
Ek 0.125 \
Ik 0 \
Xpower 2 \
Ypower 1
setfield CaL8 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call CaL8 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 // temporarily set 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
// A = 1, B = -6.2, Vhalf = -56.0, in physiological unit
inf = 1 / ( {exp {(v + 0.056) / -0.0062}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL8 X_A->table[{i}] {alpha}
setfield CaL8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL8 X_A->calc_mode 1 X_B->calc_mode 1
// Creating table for gate h, using name Y for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call CaL8 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 // temporarily set 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
inf = 1 / ( {exp {(v + 0.08) / 0.004}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL8 Y_A->table[{i}] {alpha}
setfield CaL8 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL8 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//==========================================================================
// Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH8
if ({exists CaH8})
return
end
create tabchannel CaH8
setfield CaH8 \
Ek 0.125 \
Ik 0 \
Xpower 2
setfield CaH8 \
Gbar 5 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.08
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call CaH8 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// Looking at rate: alpha
float alpha
// A = 1.6, B = -13.888889, Vhalf = 5, in physiological units
alpha = 1600 / ( {exp {(v - 0.005) / -0.013888889000000001}} + 1)
// beta
float beta
// A = 0.1, B = -5, Vhalf = -8.9, in units: Physiological Units
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 CaH8 X_A->table[{i}] {alpha}
setfield CaH8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaH8 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// 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_s8
if ({exists Ca_s8})
return
end
create Ca_concen Ca_s8
// params for a pool model in soma
setfield Ca_s8 \
tau { 1.0 / 10 } \
Ca_base 0
addfield Ca_s8 addmsg1
setfield Ca_s8 \
addmsg1 "../CaH8 . I_Ca Ik"
addfield Ca_s8 addmsg2
setfield Ca_s8 \
addmsg2 "../CaL8 . 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_d8
if ({exists Ca_d8})
return
end
create Ca_concen Ca_d8
// par. for a pool model
setfield Ca_d8 \
tau { 1.0 / 75 } \
Ca_base 0
addfield Ca_d8 addmsg1
setfield Ca_d8 \
addmsg1 "../CaH8 . I_Ca Ik"
addfield Ca_d8 addmsg2
setfield Ca_d8 \
addmsg2 "../CaL8 . I_Ca Ik"
end
function make_Ca_db8
if ({exists Ca_db8})
return
end
create Ca_concen Ca_db8
setfield Ca_db8 \
tau { 1.0 / 20 } \
Ca_base 0
addfield Ca_db8 addmsg1
setfield Ca_db8 \
addmsg1 "../CaH8 . I_Ca Ik"
addfield Ca_db8 addmsg2
setfield Ca_db8 \
addmsg2 "../CaL8 . I_Ca Ik"
end
//===============================================================================
// Ca-dependent K Channel - K(C) - (vdep_channel with table and tabgate)2005/03
//===============================================================================
/*
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_KCs8
if ({exists KCs8})
return
end
create tabchannel KCs8
setfield KCs8 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCs8 \
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 KCs8 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 // temporarily set 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 // temporarily set v to units of equation...
// Equation depends on alpha, so converting it...
alpha = alpha * 0.001
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 to populate the tables
float tau = 1/(alpha + beta)
setfield KCs8 X_A->table[{i}] {alpha}
setfield KCs8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCs8 X_A->calc_mode 1 X_B->calc_mode 1
// Adding voltage independent concentration term
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCs8 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
// Equation is in different set of units...
ca_conc = ca_conc * 0.000001
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
// Converting back...
ca_conc = ca_conc * 1000000
setfield KCs8 Z_A->table[{i}] {0}
setfield KCs8 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCs8 Z
addfield KCs8 addmsg1
setfield KCs8 addmsg1 "../Ca_s8 . CONCEN Ca"
end
function make_KCd8
if ({exists KCd8})
return
end
create tabchannel KCd8
setfield KCd8 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCd8 \
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 KCd8 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 // temporarily set 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 // temporarily set v to units of equation
alpha = alpha * 0.001 // and set 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 KCd8 X_A->table[{i}] {alpha}
setfield KCd8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCd8 X_A->calc_mode 1 X_B->calc_mode 1
// Adding voltage independent concentration term
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCd8 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
// Equation is in different set of units...
ca_conc = ca_conc * 0.000001
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
// Converting back...
ca_conc = ca_conc * 1000000
setfield KCd8 Z_A->table[{i}] {0}
setfield KCd8 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCd8 Z
addfield KCd8 addmsg1
setfield KCd8 addmsg1 "../Ca_d8 . CONCEN Ca"
end
function make_KCdb8
if ({exists KCdb8})
return
end
create tabchannel KCdb8
setfield KCdb8 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCdb8 \
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 KCdb8 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 // temporarily set 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 // temporarily set v to units of equation...
alpha = alpha * 0.001 //and set alpha too
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 KCdb8 X_A->table[{i}] {alpha}
setfield KCdb8 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCdb8 X_A->calc_mode 1 X_B->calc_mode 1
// now voltage independent concentration term
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCdb8 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
// Equation is in different set of units...
ca_conc = ca_conc * 0.000001
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
// Converting back...
ca_conc = ca_conc * 1000000
setfield KCdb8 Z_A->table[{i}] {0}
setfield KCdb8 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCdb8 Z
addfield KCdb8 addmsg1
setfield KCdb8 addmsg1 "../Ca_db8 . CONCEN Ca"
end
//========================================================================
// Tabulated Ca-dependent K AHP Channel,gK(AHP) 2003/05
//========================================================================
/* This is a tabchannel which gets the calcium concentration from Ca_hip_conc
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_KAHPs8
if ({exists KAHPs8})
return
end
create tabchannel KAHPs8
setfield KAHPs8 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPs8 \
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 KAHPs8 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
//alpha
float alpha
float v
v = v * 1000 // temporarily set v to units of equation...
ca_conc = ca_conc * 0.000001 // set Ca conc to units of equation
if (ca_conc < 0.0001 )
alpha = ca_conc/0.01
else
alpha = 0.01
end
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// Set correct units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // temporarily set v to units of equation...
ca_conc = ca_conc * 0.000001 // set Ca conc to units of equation
beta = 0.001
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KAHPs8 Z_A->table[{c}] {alpha}
setfield KAHPs8 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPs8 Z_conc 1
setfield KAHPs8 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPs8 addmsg1
setfield KAHPs8 \
addmsg1 "../Ca_s8 . CONCEN Ca"
end
function make_KAHPd8
if ({exists KAHPd8})
return
end
create tabchannel KAHPd8
setfield KAHPd8 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPd8 \
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 KAHPd8 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// alpha
float alpha
float v
v = v * 1000 // temporarily set v to units of equation...
ca_conc = ca_conc * 0.000001 // set ca_conc to units of equation...
if (ca_conc < 0.0001 )
alpha = ca_conc/0.01
else
alpha = 0.01
end
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// Set correct units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // temporarily set v to units of equation...
ca_conc = ca_conc * 0.000001 // set ca_conc to units of equation...
beta = 0.001
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of beta
beta = beta * 1000
//alpha & beata
float tau = 1/(alpha + beta)
setfield KAHPd8 Z_A->table[{c}] {alpha}
setfield KAHPd8 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPd8 Z_conc 1
setfield KAHPd8 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPd8 addmsg1
setfield KAHPd8 \
addmsg1 "../Ca_d8 . CONCEN Ca"
end
function make_KAHPdb8
if ({exists KAHPdb8})
return
end
create tabchannel KAHPdb8
setfield KAHPdb8 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPdb8 \
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 KAHPdb8 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// alpha
float alpha
float v
v = v * 1000 // temporarily set v to units of equation...
ca_conc = ca_conc * 0.000001 //set ca_conc to units of equation...
if (ca_conc < 0.0001 )
alpha = ca_conc/0.01
else
alpha = 0.01
end
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // temporarily set v to units of equation...
ca_conc = ca_conc * 0.000001 //set ca_cnonc to to units of equation...
beta = 0.001
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KAHPdb8 Z_A->table[{c}] {alpha}
setfield KAHPdb8 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPdb8 Z_conc 1
setfield KAHPdb8 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPdb8 addmsg1
setfield KAHPdb8 \
addmsg1 "../Ca_db8 . CONCEN Ca"
end