//genesis
/* FILE INFORMATION
** The 1991 Traub set of voltage and concentration dependent channels
** Implemented as tabchannels by : Dave Beeman
** R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson
** Journal of Neurophysiology, Vol. 66, p. 635 (1991)
**
** This file depends on functions and constants defined in defaults.g
** As it is also intended as an example of the use of the tabchannel
** object to implement concentration dependent channels, it has extensive
** comments. Note that the original units used in the paper have been
** converted to SI (MKS) units. Also, we define the ionic equilibrium
** potentials relative to the resting potential, EREST_ACT. In the
** paper, this was defined to be zero. Here, we use -0.060 volts, the
** measured value relative to the outside of the cell.
*/
/* November 1999 update for GENESIS 2.2: Previous versions of this file used
a combination of a table, tabgate, and vdep_channel to implement the
Ca-dependent K Channel - K(C). This new version uses the new tabchannel
"instant" field, introduced in GENESIS 2.2, to implement an
"instantaneous" gate for the multiplicative Ca-dependent factor in the
conductance. This allows these channels to be used with the fast
hsolve chanmodes > 1.
*/
// Now updated for Traub et al. J Neurophysiol 2003;89:909-921.
// CONSTANTS
float EREST_ACT = -0.060 /* hippocampal cell resting potl */
float ENAP6RSb = 0.115 + EREST_ACT // 0.055
float EKP6RSb = -0.015 + EREST_ACT // -0.075
float ECAP6RSb = 0.140 + EREST_ACT // 0.080
float EARP6RSb = 0.025 + EREST_ACT // -0.035
float SOMA_A = 3.320e-9 // soma area in square meters
/*
For these channels, the maximum channel conductance (Gbar) has been
calculated using the CA3 soma channel conductance densities and soma
area. Typically, the functions which create these channels will be used
to create a library of prototype channels. When the cell reader creates
copies of these channels in various compartments, it will set the actual
value of Gbar by calculating it from the cell parameter file.
*/
//========================================================================
// Tabchannel gNa-transient, gNa(F) 2005/03
//========================================================================
function make_NaF12
str chanpath = "NaF12"
if ({exists NaF12})
return
end
create tabchannel NaF12
setfield NaF12 \
Ek 0.05 \
Ik 0 \
Xpower 3 \
Ypower 1
setfield NaF12 \
Gbar 1875 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call NaF12 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 - 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 } }
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
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF12 X_A->table[{i}] {alpha}
setfield NaF12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF12 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 NaF12 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
// 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
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF12 Y_A->table[{i}] {alpha}
setfield NaF12 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF12 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP12
str chanpath = "NaP12"
if ({exists NaP12})
return
end
create tabchannel NaP12
setfield NaP12 \
Ek 0.05 \
Ik 0 \
Xpower 1
setfield NaP12 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call NaP12 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
// A = 1, B = -10, Vhalf = -48 in physiological units
inf = 1 / ( {exp {(v + 0.048) / -0.01}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaP12 X_A->table[{i}] {alpha}
setfield NaP12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaP12 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR12
str chanpath = "AR12"
if ({exists {chanpath}})
return
end
create tabchannel {chanpath}
setfield {chanpath} \
Ek -0.035 \
Ik 0 \
Xpower 1
setfield {chanpath} \
Gbar 2.5 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call {chanpath} 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
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 5.5, Vhalf = -75 in physiol units
inf = 1 / ( {exp {(v + 0.075 ) / 0.0055}} + 1)
// alpha & beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield {chanpath} X_A->table[{i}] {alpha}
setfield {chanpath} X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield {chanpath} X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR12
str chanpath = "KDR12"
if ({exists KDR12})
return
end
create tabchannel KDR12
setfield KDR12 \
Ek -0.095 \
Ik 0 \
Xpower 4
setfield KDR12 \
Gbar 1250 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call KDR12 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 < -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
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -10, Vhalf = -29.5, in physiological units
inf = 1 / ( {exp {(v + 0.0295) / -0.01}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KDR12 X_A->table[{i}] {alpha}
setfield KDR12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KDR12 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA12
str chanpath = "KA12"
if ({exists KA12})
return
end
create tabchannel KA12
setfield KA12 \
Ek -0.095 \
Ik 0 \
Xpower 4 \
Ypower 1
setfield KA12 \
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 KA12 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
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -8.5, Vhalf = -60, in units: Physiological Units
inf = 1 / ( {exp {(v + 0.06) / -0.0085}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KA12 X_A->table[{i}] {alpha}
setfield KA12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA12 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call KA12 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 = 0.5 / {{exp {{ v + 46 }/5}} + {exp {{ -v - 238 }/37.5}}}
else
tau = 9.5
end
v = v * 0.001 // reset v
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 6, Vhalf = -78, in physiological units
inf = 1 / ( {exp {(v + 0.078) / 0.006}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KA12 Y_A->table[{i}] {alpha}
setfield KA12 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA12 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K212
str chanpath = "K212"
if ({exists K212})
return
end
create tabchannel K212
setfield K212 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Ypower 1
setfield K212 \
Gbar 1 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call K212 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
// Set correct units of tau
tau = tau * 0.001
// Looking at rate: inf
float inf
// A = 1, B = -17, Vhalf = -10, in physiological units
inf = 1 / ( {exp {(v + 0.01) / -0.017}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K212 X_A->table[{i}] {alpha}
setfield K212 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K212 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call K212 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
// Set correct units of tau
tau = tau * 0.001
//inf
float inf
// A = 1, B = 10.6, Vhalf = -58, in units: Physiological Units
inf = 1 / ( {exp {(v + 0.058) / 0.0106}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K212 Y_A->table[{i}] {alpha}
setfield K212 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K212 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM12
str chanpath = "KM12"
if ({exists KM12})
return
end
create tabchannel KM12
setfield KM12 \
Ek -0.095 \
Ik 0 \
Xpower 1
setfield KM12 \
Gbar 75 \
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 KM12 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
//alpha
float alpha
// A = 0.02, B = -5, Vhalf = -20, in units: Physiological Units
alpha = 20 / ( {exp {(v +0.02)/-0.005}} + 1)
//beta
float beta
// A = 0.01, B = -18, Vhalf = -43, in physiological Units
beta = 10 * {exp {(v +0.043) / -0.018}}
// Using the alpha and beta expressions to populate the tables
float tau = 1/(alpha + beta)
setfield KM12 X_A->table[{i}] {alpha}
setfield KM12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KM12 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL12
str chanpath = "CaL12"
if ({exists CaL12})
return
end
create tabchannel CaL12
setfield CaL12 \
Ek 0.125 \
Ik 0 \
Xpower 2 \
Ypower 1
setfield CaL12 \
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 CaL12 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...
tau = 0.204 + 0.333 / { {exp {{15.8 + v} / 18.2 }} + {exp {{- v - 131} / 16.7}} }
v = v * 0.001 // reset v
// Set correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -6.2, Vhalf = -56.0, in physiological Units
inf = 1 / ( {exp {(v + 0.056) / -0.0062}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL12 X_A->table[{i}] {alpha}
setfield CaL12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL12 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 CaL12 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
// Set 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 CaL12 Y_A->table[{i}] {alpha}
setfield CaL12 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL12 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//==========================================================================
// Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH12
str chanpath = "CaH12"
if ({exists CaH12})
return
end
create tabchannel CaH12
setfield CaH12 \
Ek 0.125 \
Ik 0 \
Xpower 2
setfield CaH12 \
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 CaH12 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
// A = 1.6, B = -13.888889, Vhalf = 5, in physiological Units
alpha = 1600 / ( {exp {(v - 0.005) /-0.013888889000000001}} + 1)
// beta
float beta
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
// Using the alpha and beta expressions to populate the tables
float tau = 1/(alpha + beta)
setfield CaH12 X_A->table[{i}] {alpha}
setfield CaH12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaH12 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_s12
str chanpath = "Ca_s12"
if ({exists Ca_s12})
return
end
create Ca_concen Ca_s12
// Setting params for a decaying_pool_model
setfield Ca_s12 \
tau { 1.0 / 10 } \
Ca_base 0
addfield Ca_s12 addmsg1
setfield Ca_s12 \
addmsg1 "../CaH12 . I_Ca Ik"
addfield Ca_s12 addmsg2
setfield Ca_s12 \
addmsg2 "../CaL12 . 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_d12
str chanpath = "Ca_d12"
if ({exists Ca_d12})
return
end
create Ca_concen Ca_d12
// Setting params for a decaying_pool_model
setfield Ca_d12 \
tau { 1.0 / 50 } \
Ca_base 0
addfield Ca_d12 addmsg1
setfield Ca_d12 \
addmsg1 "../CaH12 . I_Ca Ik"
addfield Ca_d12 addmsg2
setfield Ca_d12 \
addmsg2 "../CaL12 . 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.
*/
//===============================================================================
// 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_KCs12
if ({exists KCs12})
return
end
create tabchannel KCs12
setfield KCs12 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCs12 \
Gbar 120 \
Gk 0
float tab_divs = 1041
float v_min = -0.12
float v_max = 0.14
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call KCs12 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
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
// Set 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
// Set correct units of beta
beta = beta * 1000
// Using the alpha and beta expressions to populate the tables
float tau = 1/(alpha + beta)
setfield KCs12 X_A->table[{i}] {alpha}
setfield KCs12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCs12 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 KCs12 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 KCs12 Z_A->table[{i}] {0}
setfield KCs12 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCs12 Z
addfield KCs12 addmsg1
setfield KCs12 addmsg1 "../Ca_s12 . CONCEN Ca"
end
function make_KCd12
if ({exists KCd12})
return
end
create tabchannel KCd12
setfield KCd12 \
Ek -0.095 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCd12 \
Gbar 120 \
Gk 0
float tab_divs = 1041
float v_min = -0.12
float v_max = 0.14
float v, dv, i
// Creating table for gate m, using name X for it here
float dv = ({v_max} - {v_min})/{tab_divs}
call KCd12 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
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
// Set correct units of alpha
alpha = alpha * 1000
// Looking at rate: 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
// Set correct units of beta
beta = beta * 1000
// Using the alpha and beta expressions to populate the tables
float tau = 1/(alpha + beta)
setfield KCd12 X_A->table[{i}] {alpha}
setfield KCd12 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCd12 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 KCd12 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 KCd12 Z_A->table[{i}] {0}
setfield KCd12 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCd12 Z
addfield KCd12 addmsg1
setfield KCd12 addmsg1 "../Ca_d12 . 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_KAHPs12
if ({exists KAHPs12})
return
end
create tabchannel KAHPs12
setfield KAHPs12 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPs12 \
Gbar 1 \
Gk 0
float tab_divs = 1041
// Channel is dependent on concentration of: Calcium, rate equations will involve variable: ca_conc
float c
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KAHPs12 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// Looking at rate: alpha
float alpha
float v
v = v * 1000 // temporarily set v to units of equation...
// Equation depends on concentration, so converting that too...
ca_conc = ca_conc * 0.000001
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
// Looking at rate: beta
float beta
v = v * 1000 // temporarily set v to units of equation...
// Equation depends on concentration, so converting that too...
ca_conc = ca_conc * 0.000001
beta = 0.001
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// Set correct units of beta
beta = beta * 1000
// Using the alpha and beta expressions to populate the tables
float tau = 1/(alpha + beta)
setfield KAHPs12 Z_A->table[{c}] {alpha}
setfield KAHPs12 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPs12 Z_conc 1
setfield KAHPs12 Z_A->calc_mode 1 Z_B->calc_mode 1
// Use an added field to tell the cell reader to set up the
// CONCEN message from the Ca_concen element
addfield KAHPs12 addmsg1
setfield KAHPs12 \
addmsg1 "../Ca_s12 . CONCEN Ca"
end
function make_KAHPd12
if ({exists KAHPd12})
return
end
create tabchannel KAHPd12
setfield KAHPd12 \
Ek -0.095 \
Ik 0 \
Zpower 1
setfield KAHPd12 \
Gbar 1 \
Gk 0
float tab_divs = 1041
// Channel is dependent on concentration of: Calcium, rate equations will involve variable: ca_conc
float c
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KAHPd12 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// Looking at rate: alpha
float alpha
float v
v = v * 1000 // temporarily set v to units of equation...
// Equation depends on concentration, so converting that too...
ca_conc = ca_conc * 0.000001
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
// Looking at rate: beta
float beta
v = v * 1000 // temporarily set v to units of equation...
// Equation depends on concentration, so converting that too...
ca_conc = ca_conc * 0.000001
beta = 0.001
v = v * 0.001 // reset v
ca_conc = ca_conc * 1000000 // resetting ca_conc
// Set correct units of beta
beta = beta * 1000
// Using the alpha and beta expressions to populate the tables
float tau = 1/(alpha + beta)
setfield KAHPd12 Z_A->table[{c}] {alpha}
setfield KAHPd12 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPd12 Z_conc 1
setfield KAHPd12 Z_A->calc_mode 1 Z_B->calc_mode 1
// Use an added field to tell the cell reader to set up the
// CONCEN message from the Ca_concen element
addfield KAHPd12 addmsg1
setfield KAHPd12 \
addmsg1 "../Ca_d12 . CONCEN Ca"
end
