//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 ENAP5IBa = 0.11 + EREST_ACT // 0.05
float EKP5IBa = -0.025 + EREST_ACT // -0.095
float ECAP5IBa = 0.195 + EREST_ACT // 0.125
float EARP5IBa = 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_NaF6
if ({exists NaF6})
return
end
create tabchannel NaF6
setfield NaF6 \
Ek 0.05 \
Ik 0 \
Xpower 3 \
Ypower 1
setfield NaF6 \
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 NaF6 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 NaF6 X_A->table[{i}] {alpha}
setfield NaF6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF6 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 NaF6 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 NaF6 Y_A->table[{i}] {alpha}
setfield NaF6 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF6 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP6
if ({exists NaP6})
return
end
create tabchannel NaP6
setfield NaP6 \
Ek 0.05 \
Ik 0 \
Xpower 1
setfield NaP6 \
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 NaP6 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 NaP6 X_A->table[{i}] {alpha}
setfield NaP6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaP6 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR6
if ({exists AR6})
return
end
create tabchannel AR6
setfield AR6 \
Ek -0.035 \
Ik 0 \
Xpower 1
setfield AR6 \
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 AR6 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 AR6 X_A->table[{i}] {alpha}
setfield AR6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield AR6 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR6
if ({exists KDR6})
return
end
create tabchannel KDR6
setfield KDR6 \
Ek -0.095 \
Ik 0 \
Xpower 4
setfield KDR6 \
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 KDR6 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 KDR6 X_A->table[{i}] {alpha}
setfield KDR6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KDR6 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA6
if ({exists KA6})
return
end
create tabchannel KA6
setfield KA6 \
Ek -0.095 \
Ik 0 \
Xpower 4 \
Ypower 1
setfield KA6 \
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 KA6 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 KA6 X_A->table[{i}] {alpha}
setfield KA6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA6 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 KA6 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 KA6 Y_A->table[{i}] {alpha}
setfield KA6 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA6 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K26
if ({exists K26})
return
end
create tabchannel K26
setfield K26 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Ypower 1
setfield K26 \
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 K26 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 K26 X_A->table[{i}] {alpha}
setfield K26 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K26 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 K26 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 K26 Y_A->table[{i}] {alpha}
setfield K26 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K26 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM6
if ({exists KM6})
return
end
create tabchannel KM6
setfield KM6 \
Ek -0.095 \
Ik 0 \
Xpower 1
setfield KM6 \
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 KM6 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 KM6 X_A->table[{i}] {alpha}
setfield KM6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KM6 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL6
if ({exists CaL6})
return
end
create tabchannel CaL6
setfield CaL6 \
Ek 0.125 \
Ik 0 \
Xpower 2 \
Ypower 1
setfield CaL6 \
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 CaL6 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 CaL6 X_A->table[{i}] {alpha}
setfield CaL6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL6 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 CaL6 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 CaL6 Y_A->table[{i}] {alpha}
setfield CaL6 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL6 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//==========================================================================
// Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH6
if ({exists CaH6})
return
end
create tabchannel CaH6
setfield CaH6 \
Ek 0.125 \
Ik 0 \
Xpower 2
setfield CaH6 \
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 CaH6 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 CaH6 X_A->table[{i}] {alpha}
setfield CaH6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaH6 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_s6
if ({exists Ca_s6})
return
end
create Ca_concen Ca_s6
// params for a pool model in soma
setfield Ca_s6 \
tau { 1.0 / 10 } \
Ca_base 0
addfield Ca_s6 addmsg1
setfield Ca_s6 \
addmsg1 "../CaH6 . I_Ca Ik"
addfield Ca_s6 addmsg2
setfield Ca_s6 \
addmsg2 "../CaL6 . 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_d6
if ({exists Ca_d6})
return
end
create Ca_concen Ca_d6
// par. for a pool model
setfield Ca_d6 \
tau { 1.0 / 75 } \
Ca_base 0
addfield Ca_d6 addmsg1
setfield Ca_d6 \
addmsg1 "../CaH6 . I_Ca Ik"
addfield Ca_d6 addmsg2
setfield Ca_d6 \
addmsg2 "../CaL6 . I_Ca Ik"
end
function make_Ca_db6
if ({exists Ca_db6})
return
end
create Ca_concen Ca_db6
setfield Ca_db6 \
tau { 1.0 / 20 } \
Ca_base 0
addfield Ca_db6 addmsg1
setfield Ca_db6 \
addmsg1 "../CaH6 . I_Ca Ik"
addfield Ca_db6 addmsg2
setfield Ca_db6 \
addmsg2 "../CaL6 . 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_KCs6
if ({exists KCs6})
return
end
create tabchannel KCs6
setfield KCs6 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCs6 \
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 KCs6 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 KCs6 X_A->table[{i}] {alpha}
setfield KCs6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCs6 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 KCs6 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 KCs6 Z_A->table[{i}] {0}
setfield KCs6 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCs6 Z
addfield KCs6 addmsg1
setfield KCs6 addmsg1 "../Ca_s6 . CONCEN Ca"
end
function make_KCd6
if ({exists KCd6})
return
end
create tabchannel KCd6
setfield KCd6 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCd6 \
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 KCd6 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 KCd6 X_A->table[{i}] {alpha}
setfield KCd6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCd6 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 KCd6 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 KCd6 Z_A->table[{i}] {0}
setfield KCd6 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCd6 Z
addfield KCd6 addmsg1
setfield KCd6 addmsg1 "../Ca_d6 . CONCEN Ca"
end
function make_KCdb6
if ({exists KCdb6})
return
end
create tabchannel KCdb6
setfield KCdb6 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCdb6 \
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 KCdb6 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 KCdb6 X_A->table[{i}] {alpha}
setfield KCdb6 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCdb6 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 KCdb6 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 KCdb6 Z_A->table[{i}] {0}
setfield KCdb6 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCdb6 Z
addfield KCdb6 addmsg1
setfield KCdb6 addmsg1 "../Ca_db6 . 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_KAHPs6
if ({exists KAHPs6})
return
end
create tabchannel KAHPs6
setfield KAHPs6 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPs6 \
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 KAHPs6 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 KAHPs6 Z_A->table[{c}] {alpha}
setfield KAHPs6 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPs6 Z_conc 1
setfield KAHPs6 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPs6 addmsg1
setfield KAHPs6 \
addmsg1 "../Ca_s6 . CONCEN Ca"
end
function make_KAHPd6
if ({exists KAHPd6})
return
end
create tabchannel KAHPd6
setfield KAHPd6 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPd6 \
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 KAHPd6 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 KAHPd6 Z_A->table[{c}] {alpha}
setfield KAHPd6 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPd6 Z_conc 1
setfield KAHPd6 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPd6 addmsg1
setfield KAHPd6 \
addmsg1 "../Ca_d6 . CONCEN Ca"
end
function make_KAHPdb6
if ({exists KAHPdb6})
return
end
create tabchannel KAHPdb6
setfield KAHPdb6 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPdb6 \
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 KAHPdb6 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 KAHPdb6 Z_A->table[{c}] {alpha}
setfield KAHPdb6 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPdb6 Z_conc 1
setfield KAHPdb6 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPdb6 addmsg1
setfield KAHPdb6 \
addmsg1 "../Ca_db6 . CONCEN Ca"
end