//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.
// And for LTS and FS interneurons - Cunningham et al. PNAS 2004;101:7152-7157.
// CONSTANTS
float EREST_ACT = -0.070 /* cell resting potential */
float ENAI23LTS = 0.110 + EREST_ACT // 0.050
float EKI23LTS = -0.040 + EREST_ACT // -0.100
float ECAI23LTS = 0.185 + EREST_ACT // 0.125
float EARI23LTS = 0.020 + EREST_ACT // -0.040
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_NaF18
if ({exists NaF18})
return
end
create tabchannel NaF18
setfield NaF18 \
Ek 0.05 \
Ik 0 \
Xpower 3 \
Ypower 1
setfield NaF18 \
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 NaF18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if ({ v -2.5 } < -30 )
tau = 0.0125 + 0.1525 * { exp { {{v - 2.5} + 30} / 10} }
else
tau = 0.02 + 0.145 * { exp { -1 * {{v - 2.5} + 30} / 10} }
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
v = v * 1000 // v to units of equation
inf = 1 / { 1 + {exp { { -1 * {v - 2.5} - 38} / 10}} }
v = v * 0.001 // reset v
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF18 X_A->table[{i}] {alpha}
setfield NaF18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF18 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call NaF18 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 0.225 + 1.125 / { 1 + { exp {{v + 37} / 15} } }
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
v = v * 1000 // v to units of equation
inf = 1 / { 1 + {exp {{v + 58.3} / 6.7}} }
v = v * 0.001 // reset v
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaF18 Y_A->table[{i}] {alpha}
setfield NaF18 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaF18 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP18
if ({exists NaP18})
return
end
create tabchannel NaP18
setfield NaP18 \
Ek 0.05 \
Ik 0 \
Xpower 3
setfield NaP18 \
Gbar 32 \
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 NaP18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if ({v - 2.5} < -30 )
tau = 0.025 + 0.14 * { exp { {{v - 2.5} + 30} / 10} }
else
tau = 0.02 + 0.145 * { exp { -1 * {{v -2.5} + 30} / 10 } }
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
v = v * 1000 // v to units of equation
inf = 1 / { 1 + {exp { { -1 * {v - 2.5} - 38} / 10}} }
v = v * 0.001 // reset v
// alpha and beata
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield NaP18 X_A->table[{i}] {alpha}
setfield NaP18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield NaP18 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR18
if ({exists AR18})
return
end
create tabchannel AR18
setfield AR18 \
Ek -0.04 \
Ik 0 \
Xpower 1
setfield AR18 \
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 AR18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
float tau
v = v * 1000 // v to units of equation
tau = 1 /{{exp {-14.6 - {0.086 * v} }} + {exp {-1.87 + {0.07 * v}}}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 5.5, Vhalf = -75 in physiological units
// A = 1, B = 0.0055, Vhalf = -0.075
inf = 1 / ( {exp {(v + 0.075) / 0.0055}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield AR18 X_A->table[{i}] {alpha}
setfield AR18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield AR18 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR18
if ({exists KDR18})
return
end
create tabchannel KDR18
setfield KDR18 \
Ek -0.1 \
Ik 0 \
Xpower 4
setfield KDR18 \
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 KDR18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v <= -10 )
tau = 0.25 + 4.35 * {exp {{ v + 10 }/10}}
else
tau = 0.25 + 4.35 * {exp {{- v - 10}/ 10}}
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -11.5, Vhalf = -27, in physiological units
// A = 1, B = -0.0115, Vhalf = -0.027
inf = 1 / ( {exp {(v + 0.027) / -0.0115}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KDR18 X_A->table[{i}] {alpha}
setfield KDR18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KDR18 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA18
if ({exists KA18})
return
end
create tabchannel KA18
setfield KA18 \
Ek -0.1 \
Ik 0 \
Xpower 4 \
Ypower 1
setfield KA18 \
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 KA18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 0.185 + 0.5 / {{exp {{ v + 35.8 }/19.7}} + {exp {{-v - 79.7}/12.7}}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -8.5, Vhalf = -60 in physiological units
// A = 1, B = -0.0085, Vhalf = -0.06
inf = 1 / ( {exp {(v + 0.06) / -0.0085}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield KA18 X_A->table[{i}] {alpha}
setfield KA18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA18 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call KA18 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
if (v < -63.0 )
tau = 0.5 / {{exp {{ v + 46 }/5}} + {exp {{ -v - 238 }/37.5}}}
else
tau = 9.5
end
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 6, Vhalf = -78 in 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 KA18 Y_A->table[{i}] {alpha}
setfield KA18 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KA18 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K218
if ({exists K218})
return
end
create tabchannel K218
setfield K218 \
Ek -0.1 \
Ik 0 \
Xpower 1 \
Ypower 1
setfield K218 \
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 K218 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 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 physiological units
// A = 1, B = -0.017, Vhalf = -0.01
inf = 1 / ( {exp {(v + 0.01) / -0.017}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K218 X_A->table[{i}] {alpha}
setfield K218 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K218 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call K218 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 60 + 0.5 / {{exp {{ v - 1.33 }/200}} + {exp {{- v - 130}/ 7.1}}}
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 10.6, Vhalf = -58 in physiological units
// A = 1, B = 0.0106, Vhalf = -0.058
inf = 1 / ( {exp {(v + 0.058) / 0.0106}} + 1)
// alpha & beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield K218 Y_A->table[{i}] {alpha}
setfield K218 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield K218 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//========================================================================
// Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM18
if ({exists KM18})
return
end
create tabchannel KM18
setfield KM18 \
Ek -0.1 \
Ik 0 \
Xpower 1
setfield KM18 \
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 KM18 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 physiological units
// A = 20, B = -0.005, Vhalf = -0.02
alpha = 20 / ( {exp {(v + 0.02) / -0.005}} + 1)
// beta
float beta
// A = 0.01, B = -18, Vhalf = -43, in physiological units
// A = 10, B = -0.018, Vhalf = -0.043
beta = 10 * {exp {(v + 0.043) / -0.018}}
// alpha and beta
float tau = 1/(alpha + beta)
setfield KM18 X_A->table[{i}] {alpha}
setfield KM18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KM18 X_A->calc_mode 1 X_B->calc_mode 1
end
//========================================================================
// Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL18
if ({exists CaL18})
return
end
create tabchannel CaL18
setfield CaL18 \
Ek 0.125 \
Ik 0 \
Xpower 2 \
Ypower 1
setfield CaL18 \
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 CaL18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 1 + 0.33 / { {exp {{v + 27} / 10 }} + {exp {{- v - 102} / 15}} }
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = -7.4, Vhalf = -52 in physiological units
// A = 1, B = -0.0074, Vhalf = -0.052
inf = 1 / ( {exp {(v + 0.052) / -0.0074}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL18 X_A->table[{i}] {alpha}
setfield CaL18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL18 X_A->calc_mode 1 X_B->calc_mode 1
// Y table for gate h
float dv = ({v_max} - {v_min})/{tab_divs}
call CaL18 TABCREATE Y {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// tau
float tau
v = v * 1000 // v to units of equation
tau = 28.3 + 0.33 / {{exp {{ v + 48}/ 4}} + {exp { { -v - 407} / 50 }} }
v = v * 0.001 // reset v
// correct units of tau
tau = tau * 0.001
// inf
float inf
// A = 1, B = 5, Vhalf = -80 in physiological units
// A = 1, B = 0.005, Vhalf = -0.08
inf = 1 / ( {exp {(v + 0.08) / 0.005}} + 1)
// alpha and beta
float alpha
float beta
alpha = inf / tau
beta = (1- inf)/tau
setfield CaL18 Y_A->table[{i}] {alpha}
setfield CaL18 Y_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaL18 Y_A->calc_mode 1 Y_B->calc_mode 1
end
//==========================================================================
// Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH18
if ({exists CaH18})
return
end
create tabchannel CaH18
setfield CaH18 \
Ek 0.125 \
Ik 0 \
Xpower 2
setfield CaH18 \
Gbar 5 \
Gk 0
float tab_divs = 741
float v_min = -0.12
float v_max = 0.06
float v, dv, i
// X table for gate m
float dv = ({v_max} - {v_min})/{tab_divs}
call CaH18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
float alpha
// A = 1.6, B = -13.888889, Vhalf = 5 in physiological units
// A = 1600, B = -0.013888889000000001, Vhalf = 0.005
alpha = 1600 / ( {exp {(v - 0.005) / -0.013888889000000001}} + 1)
// beta
float beta
// A = 0.1, B = -5, Vhalf = -8.9 in physiol. units
// A = 100, B = -0.005, Vhalf = -0.0089
if ( {abs {(v + 0.0089)/ -0.005}} < 1e-6)
beta = 100 * (1 + (v + 0.0089)/-0.005/2)
else
beta = 100 * ((v + 0.0089) / -0.005) /(1 - {exp {-1 * (v + 0.0089)/-0.005}})
end
// alpha & beta
float tau = 1/(alpha + beta)
setfield CaH18 X_A->table[{i}] {alpha}
setfield CaH18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield CaH18 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 wlll 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_s18
if ({exists Ca_s18})
return
end
create Ca_concen Ca_s18
// params for Ca pool model
setfield Ca_s18 \
tau { 1.0 / 20 } \
Ca_base 0
addfield Ca_s18 addmsg1
setfield Ca_s18 \
addmsg1 "../CaH18 . 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_d18
if ({exists Ca_d18})
return
end
create Ca_concen Ca_d18
// params for Ca pool in dendrite
setfield Ca_d18 \
tau { 1.0 / 50 } \
Ca_base 0
addfield Ca_d18 addmsg1
setfield Ca_d18 \
addmsg1 "../CaH18 . 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_KCs18
if ({exists KCs18})
return
end
create tabchannel KCs18
setfield KCs18 \
Ek -0.1 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCs18 \
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 KCs18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
v = v * 1000 // v to units of equation
if (v < -10 )
alpha = 2 * {2 / 37.95} * { exp { {{v + 50 } / 11} - {{ v + 53.5} / 27} } }
else
alpha = 2 * 2 * {exp { { {-1 * v} - 53.5 } / 27 }}
end
v = v * 0.001 // reset v
// units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // v to units of equation
alpha = alpha * 0.001 // alpha to units of equation
if (v < -10 )
beta = 4 * {exp { { {-1 * v} - 53.5 } / 27 }} - alpha
else
beta = 0.0
end
v = v * 0.001 // reset v
alpha = alpha * 1000 // reset alpha
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KCs18 X_A->table[{i}] {alpha}
setfield KCs18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCs18 X_A->calc_mode 1 X_B->calc_mode 1
// concentration dependent term (voltage independent)
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCs18 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
ca_conc = ca_conc * 0.000001 // ica_conc to units of equation
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
ca_conc = ca_conc * 1000000 //reset ca_conc
setfield KCs18 Z_A->table[{i}] {0}
setfield KCs18 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCs18 Z
addfield KCs18 addmsg1
setfield KCs18 addmsg1 "../Ca_s18 . CONCEN Ca"
end
function make_KCd18
if ({exists KCd18})
return
end
create tabchannel KCd18
setfield KCd18 \
Ek -0.1 \
Ik 0 \
Xpower 1 \
Zpower 1
setfield KCd18 \
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 KCd18 TABCREATE X {tab_divs} {v_min} {v_max}
v = {v_min}
for (i = 0; i <= ({tab_divs}); i = i + 1)
// alpha
float alpha
v = v * 1000 // v to units of equation
if (v < -10 )
alpha = {4 / 37.95} * { exp { {{v + 50 } / 11} - {{ v + 53.5} / 27} } }
else
alpha = 4 * {exp { { {-1 * v} - 53.5 } / 27 }}
end
v = v * 0.001 // reset v
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
v = v * 1000 // v to units of equation
alpha = alpha * 0.001 // alpha to units of equation
if (v < -10 )
beta = 4 * {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 KCd18 X_A->table[{i}] {alpha}
setfield KCd18 X_B->table[{i}] {alpha + beta}
v = v + dv
end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
setfield KCd18 X_A->calc_mode 1 X_B->calc_mode 1
// concentration dependent term (voltage independent)
float conc_min = 0
float conc_max = 1000
float dc = ({conc_max} - {conc_min})/{tab_divs}
float ca_conc = {conc_min}
call KCd18 TABCREATE Z {tab_divs} {conc_min} {conc_max}
float const_state
for (i = 0; i <= ({tab_divs}); i = i + 1)
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.00025 )
const_state = {ca_conc / 0.00025}
else
const_state = 1
end
ca_conc = ca_conc * 1000000 //reset ca_conc
setfield KCd18 Z_A->table[{i}] {0}
setfield KCd18 Z_B->table[{i}] {const_state}
ca_conc= ca_conc + dc
end
tweaktau KCd18 Z
addfield KCd18 addmsg1
setfield KCd18 addmsg1 "../Ca_d18 . 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_KAHPs18
if ({exists KAHPs18})
return
end
create tabchannel KAHPs18
setfield KAHPs18 \
Ek -0.1 \
Ik 0 \
Zpower 1
setfield KAHPs18 \
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 KAHPs18 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// alpha
float alpha, v
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.0005 )
alpha = ca_conc/0.05
else
alpha = 0.01
end
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
beta = 0.001
ca_conc = ca_conc * 1000000 // resetting ca_conc
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KAHPs18 Z_A->table[{c}] {alpha}
setfield KAHPs18 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPs18 Z_conc 1
setfield KAHPs18 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPs18 addmsg1
setfield KAHPs18 \
addmsg1 "../Ca_s18 . CONCEN Ca"
end
function make_KAHPd18
if ({exists KAHPd18})
return
end
create tabchannel KAHPd18
setfield KAHPd18 \
Ek -0.1 \
Ik 0 \
Zpower 1
setfield KAHPd18 \
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 KAHPd18 TABCREATE Z {tab_divs} {conc_min} {conc_max}
for (c = 0; c <= ({tab_divs}); c = c + 1)
// alpha
float alpha
ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
if (ca_conc < 0.0005 )
alpha = ca_conc/0.05
else
alpha = 0.01
end
ca_conc = ca_conc * 1000000 // reset ca_conc
// correct units of alpha
alpha = alpha * 1000
// beta
float beta
ca_conc = ca_conc * 0.000001 //set ca_conc to units of equation
beta = 0.001
ca_conc = ca_conc * 1000000 // reset ca_conc
// correct units of beta
beta = beta * 1000
// alpha and beta
float tau = 1/(alpha + beta)
setfield KAHPd18 Z_A->table[{c}] {alpha}
setfield KAHPd18 Z_B->table[{c}] {alpha + beta}
ca_conc = ca_conc + dc
end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
setfield KAHPd18 Z_conc 1
setfield KAHPd18 Z_A->calc_mode 1 Z_B->calc_mode 1
addfield KAHPd18 addmsg1
setfield KAHPd18 \
addmsg1 "../Ca_d18 . CONCEN Ca"
end