//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 ENAP5IBb = 0.11 + EREST_ACT // 0.05
float EKP5IBb = -0.025 + EREST_ACT // -0.095
float ECAP5IBb = 0.195 + EREST_ACT // 0.125
float EARP5IBb = 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_NaF7
if ({exists NaF7})
return
end
create tabchannel NaF7
setfield NaF7 \
Ek 0.05 \
Ik 0 \
Xpower 3 \
Ypower 1
setfield NaF7 \
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 NaF7 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 NaF7 X_A->table[{i}] {alpha}
setfield NaF7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF7 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 NaF7 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 NaF7 Y_A->table[{i}] {alpha}
setfield NaF7 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF7 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP7
if ({exists NaP7})
return
end
create tabchannel NaP7
setfield NaP7 \
Ek 0.05 \
Ik 0 \
Xpower 1
setfield NaP7 \
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 NaP7 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 NaP7 X_A->table[{i}] {alpha}
setfield NaP7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaP7 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR7
if ({exists AR7})
return
end
create tabchannel AR7
setfield AR7 \
Ek -0.035 \
Ik 0 \
Xpower 1
setfield AR7 \
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 AR7 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 AR7 X_A->table[{i}] {alpha}
setfield AR7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield AR7 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR7
if ({exists KDR7})
return
end
create tabchannel KDR7
setfield KDR7 \
Ek -0.095 \
Ik 0 \
Xpower 4
setfield KDR7 \
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 KDR7 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 KDR7 X_A->table[{i}] {alpha}
setfield KDR7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KDR7 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA7
if ({exists KA7})
return
end
create tabchannel KA7
setfield KA7 \
Ek -0.095 \
Ik 0 \
Xpower 4 \
Ypower 1
setfield KA7 \
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 KA7 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 KA7 X_A->table[{i}] {alpha}
setfield KA7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA7 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 KA7 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 KA7 Y_A->table[{i}] {alpha}
setfield KA7 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA7 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K27
if ({exists K27})
return
end
create tabchannel K27
setfield K27 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Ypower 1
setfield K27 \
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 K27 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 K27 X_A->table[{i}] {alpha}
setfield K27 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K27 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 K27 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 K27 Y_A->table[{i}] {alpha}
setfield K27 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K27 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM7
if ({exists KM7})
return
end
create tabchannel KM7
setfield KM7 \
Ek -0.095 \
Ik 0 \
Xpower 1
setfield KM7 \
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 KM7 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 KM7 X_A->table[{i}] {alpha}
setfield KM7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KM7 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL7
if ({exists CaL7})
return
end
create tabchannel CaL7
setfield CaL7 \
Ek 0.125 \
Ik 0 \
Xpower 2 \
Ypower 1
setfield CaL7 \
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 CaL7 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 CaL7 X_A->table[{i}] {alpha}
setfield CaL7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL7 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 CaL7 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 CaL7 Y_A->table[{i}] {alpha}
setfield CaL7 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL7 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//==========================================================================
// Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH7
if ({exists CaH7})
return
end
create tabchannel CaH7
setfield CaH7 \
Ek 0.125 \
Ik 0 \
Xpower 2
setfield CaH7 \
Gbar 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 CaH7 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 CaH7 X_A->table[{i}] {alpha}
setfield CaH7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaH7 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_s7
if ({exists Ca_s7})
return
end
create Ca_concen Ca_s7
// params for a pool model in soma
setfield Ca_s7 \
tau { 1.0 / 10 } \
Ca_base 0
addfield Ca_s7 addmsg1
setfield Ca_s7 \
addmsg1 "../CaH7 . I_Ca Ik"
addfield Ca_s7 addmsg2
setfield Ca_s7 \
addmsg2 "../CaL7 . 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_d7
if ({exists Ca_d7})
return
end
create Ca_concen Ca_d7
// par. for a pool model
setfield Ca_d7 \
tau { 1.0 / 75 } \
Ca_base 0
addfield Ca_d7 addmsg1
setfield Ca_d7 \
addmsg1 "../CaH7 . I_Ca Ik"
addfield Ca_d7 addmsg2
setfield Ca_d7 \
addmsg2 "../CaL7 . I_Ca Ik"
end
function make_Ca_db7
if ({exists Ca_db7})
return
end
create Ca_concen Ca_db7
setfield Ca_db7 \
tau { 1.0 / 20 } \
Ca_base 0
addfield Ca_db7 addmsg1
setfield Ca_db7 \
addmsg1 "../CaH7 . I_Ca Ik"
addfield Ca_db7 addmsg2
setfield Ca_db7 \
addmsg2 "../CaL7 . 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_KCs7
if ({exists KCs7})
return
end
create tabchannel KCs7
setfield KCs7 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCs7 \
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 KCs7 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 KCs7 X_A->table[{i}] {alpha}
setfield KCs7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCs7 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 KCs7 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 KCs7 Z_A->table[{i}] {0}
setfield KCs7 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCs7 Z
addfield KCs7 addmsg1
setfield KCs7 addmsg1 "../Ca_s7 . CONCEN Ca"
end
function make_KCd7
if ({exists KCd7})
return
end
create tabchannel KCd7
setfield KCd7 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCd7 \
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 KCd7 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 KCd7 X_A->table[{i}] {alpha}
setfield KCd7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCd7 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 KCd7 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 KCd7 Z_A->table[{i}] {0}
setfield KCd7 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCd7 Z
addfield KCd7 addmsg1
setfield KCd7 addmsg1 "../Ca_d7 . CONCEN Ca"
end
function make_KCdb7
if ({exists KCdb7})
return
end
create tabchannel KCdb7
setfield KCdb7 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCdb7 \
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 KCdb7 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 KCdb7 X_A->table[{i}] {alpha}
setfield KCdb7 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCdb7 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 KCdb7 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 KCdb7 Z_A->table[{i}] {0}
setfield KCdb7 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCdb7 Z
addfield KCdb7 addmsg1
setfield KCdb7 addmsg1 "../Ca_db7 . 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_KAHPs7
if ({exists KAHPs7})
return
end
create tabchannel KAHPs7
setfield KAHPs7 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPs7 \
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 KAHPs7 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 KAHPs7 Z_A->table[{c}] {alpha}
setfield KAHPs7 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPs7 Z_conc 1
setfield KAHPs7 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPs7 addmsg1
setfield KAHPs7 \
addmsg1 "../Ca_s7 . CONCEN Ca"
end
function make_KAHPd7
if ({exists KAHPd7})
return
end
create tabchannel KAHPd7
setfield KAHPd7 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPd7 \
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 KAHPd7 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 KAHPd7 Z_A->table[{c}] {alpha}
setfield KAHPd7 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPd7 Z_conc 1
setfield KAHPd7 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPd7 addmsg1
setfield KAHPd7 \
addmsg1 "../Ca_d7 . CONCEN Ca"
end
function make_KAHPdb7
if ({exists KAHPdb7})
return
end
create tabchannel KAHPdb7
setfield KAHPdb7 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPdb7 \
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 KAHPdb7 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 KAHPdb7 Z_A->table[{c}] {alpha}
setfield KAHPdb7 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPdb7 Z_conc 1
setfield KAHPdb7 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPdb7 addmsg1
setfield KAHPdb7 \
addmsg1 "../Ca_db7 . CONCEN Ca"
end
