A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015)

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Accession:206238
A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites. The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232.
References:
1 . Basu I, Kudela P, Korzeniewska A, Franaszczuk PJ, Anderson WS (2015) A study of the dynamics of seizure propagation across micro domains in the vicinity of the seizure onset zone. J Neural Eng 12:046016 [PubMed]
2 . Basu I, Kudela P, Anderson WS (2014) Determination of seizure propagation across microdomains using spectral measures of causality. Conf Proc IEEE Eng Med Biol Soc 2014:6349-52 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Thalamus reticular nucleus GABA cell; Neocortex spiking low threshold (LTS) neuron; Neocortex spiking regular (RS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron;
Channel(s): I Na,p; I Na,t; I K; I A; I M; I h; I K,Ca; I A, slow; I L high threshold; I T low threshold; I Calcium;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; GabaA; NMDA;
Gene(s):
Transmitter(s): Glutamate; Gaba; Amino Acids;
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Epilepsy;
Implementer(s): Anderson, WS ; Kudela, Pawel ;
Search NeuronDB for information about:  Thalamus reticular nucleus GABA cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow; Amino Acids; Gaba; Glutamate;
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BasuEtAl2015
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ModelDescription.pdf
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P6RSd_P6RSc.g
P6RSd_P6RSd.g
P6RSd_P6RSd_Gap.g
P6RSd_raninput.g
P6RSd_ST4RS.g
P6RSd_synapsedefs.g
P6RSd_TCR.g
P6RSdcell3Dpk.p
P6RSdchanpk.g
P6RSdprotodefs.g
P6RSsyncond.g
pgenesis_command
protodefs.g
protospikeB23FS.g
protospikeB5FS.g
protospikeC23FS.g
protospikeC5FS.g
protospikeI23LTS.g
protospikeI5LTS.g
protospikenRT.g
protospikeP23FRBa.g
protospikeP23RSa.g
protospikeP23RSb.g
protospikeP23RSc.g
protospikeP23RSd.g
protospikeP5IBa.g
protospikeP5IBb.g
protospikeP5IBc.g
protospikeP5IBd.g
protospikeP5RSa.g
protospikeP6RSa.g
protospikeP6RSb.g
protospikeP6RSc.g
protospikeP6RSd.g
protospikeST4RS.g
protospikeTCR.g
randominputdefs.g
spikedefs.g
ST4RS.g
ST4RS_B23FS.g
ST4RS_B5FS.g
ST4RS_C23FS.g
ST4RS_C5FS.g
ST4RS_I23LTS.g
ST4RS_I5LTS.g
ST4RS_P23FRBa.g
ST4RS_P23RSa.g
ST4RS_P23RSb.g
ST4RS_P23RSc.g
ST4RS_P23RSd.g
ST4RS_P5IBa.g
ST4RS_P5IBb.g
ST4RS_P5IBc.g
ST4RS_P5IBd.g
ST4RS_P5RSa.g
ST4RS_P6RSa.g
ST4RS_P6RSb.g
ST4RS_P6RSc.g
ST4RS_P6RSd.g
ST4RS_raninput.g
ST4RS_ST4RS.g
ST4RS_ST4RS_Gap.g
ST4RS_synapsedefs.g
ST4RScell3Dpk.p
ST4RSchanpk.g
ST4RSprotodefs.g
ST4RSsyncond.g
synapticdelays.g *
synapticprobsTraub.g
synchansB23FS.g *
synchansB5FS.g *
synchansC23FS.g *
synchansC5FS.g *
synchansI23LTS.g *
synchansI5LTS.g *
synchansnRT.g *
synchansP23FRBa.g *
synchansP23RSa.g *
synchansP23RSb.g *
synchansP23RSc.g *
synchansP23RSd.g *
synchansP5IBa.g *
synchansP5IBb.g *
synchansP5IBc.g *
synchansP5IBd.g *
synchansP5RSa.g *
synchansP6RSa.g *
synchansP6RSb.g *
synchansP6RSc.g *
synchansP6RSd.g *
synchansSPIKEs.g *
synchansSPIKEs_base.g
synchansST4RS.g
synchansTCR.g *
syncond.g
syncond2.g
TCR.g
TCR_B23FS.g
TCR_B5FS.g
TCR_C23FS.g
TCR_C5FS.g
TCR_nRT.g
TCR_P23FRBa.g
TCR_P23RSa.g
TCR_P23RSb.g
TCR_P23RSc.g
TCR_P23RSd.g
TCR_P5IBa.g
TCR_P5IBb.g
TCR_P5IBc.g
TCR_P5IBd.g
TCR_P5RSa.g
TCR_P6RSa.g
TCR_P6RSb.g
TCR_P6RSc.g
TCR_P6RSd.g
TCR_raninput.g
TCR_ST4RS.g
TCR_synapsedefs.g
TCRcellpk.p
TCRchanpk.g
TCRprotodefs.g
TCRsyncond.g
                            
//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 ENAP23RSa = 0.115 + EREST_ACT // 0.055
float EKP23RSa = -0.015 + EREST_ACT // -0.075
float ECAP23RSa = 0.140 + EREST_ACT // 0.080
float EARP23RSa = 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_NaF1
        str chanpath = "NaF1"
        if ({exists NaF1})
            return
        end
        create tabchannel NaF1
        setfield NaF1 \ 
            Ek              0.05 \
            Ik              0  \
            Xpower          3 \
            Ypower          1
        setfield NaF1 \
            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 NaF1 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  < -26.5 )
                tau =  0.025 + 0.14 * { exp { {v  + 26.5} / 10} } 
            else
                tau =  0.02 + 0.145 * { exp { -1 * {v + 26.5} / 10.0} }
            end
            v = v * 0.001 // reset v
            
            // Set 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 + 34.5} / 10}} } 
            v = v * 0.001 // reset v
            

            // alpha and beta
            float alpha
            float beta
            alpha = inf / tau   
            beta = (1- inf)/tau
            
            setfield NaF1 X_A->table[{i}] {alpha}
            setfield NaF1 X_B->table[{i}] {alpha + beta}
            v = v + dv

        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield NaF1 X_A->calc_mode 1 X_B->calc_mode 1
                    
        // Y table for gate h
        float dv = ({v_max} - {v_min})/{tab_divs}
        call NaF1 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 = 0.15 + 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 // 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 NaF1 Y_A->table[{i}] {alpha}
            setfield NaF1 Y_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield NaF1 Y_A->calc_mode 1 Y_B->calc_mode 1
end

//========================================================================
// P23RS   Tabchannel gNa-persistent (non-inactivating), gNa(P) 2005/03
//========================================================================
function make_NaP1
        str chanpath = "NaP1"
        if ({exists NaP1})
            return
        end
        create tabchannel NaP1
        setfield NaP1 \ 
            Ek              0.05 \
            Ik              0  \
            Xpower          1
        setfield NaP1 \
            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 NaP1 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 < -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
            // correct units of tau
            tau = tau * 0.001

            // inf
            float inf
            // A = 1, B = -10, Vhalf = -48, in units: Physiological Units
            // A = 1, B = -0.01, Vhalf = -0.048
            inf = 1 / ( {exp {(v + 0.048) / -0.01}} + 1)

            // alpha and beat
            float alpha
            float beta
            alpha = inf / tau   
            beta = (1- inf)/tau
            setfield NaP1 X_A->table[{i}] {alpha}
            setfield NaP1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield NaP1 X_A->calc_mode 1 X_B->calc_mode 1
end

//========================================================================
//   P23RS    Tabchannel Anomalous Rectifier, gAR 2005/03
//========================================================================
function make_AR1
        if ({exists AR1})
            return
        end
        create tabchannel AR1
        setfield AR1 \ 
            Ek              -0.035 \
            Ik              0  \
            Xpower          1
        
        setfield AR1 \
            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 AR1 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 /{{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 units: 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 AR1 X_A->table[{i}] {alpha}
            setfield AR1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield AR1 X_A->calc_mode 1 X_B->calc_mode 1
end

//========================================================================
//  P23RS    Tabchannel gK-delayed rectifier, gK(DR) 2005/03
//========================================================================
function make_KDR1
        if ({exists KDR1})
            return
        end
        create tabchannel KDR1
        setfield KDR1 \ 
            Ek              -0.095 \
            Ik              0  \
            Xpower          4
        
        setfield KDR1 \
            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 KDR1 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
            tau = tau * 0.001 // correct units of tau

            //  inf
            float inf
            // A = 1, B = -10, Vhalf = -29.5, in units: Physiological Units
            // A = 1, B = -0.01, Vhalf = -0.0295
            inf = 1 / ( {exp {(v + 0.0295) / -0.01}} + 1)

            
            // alpha and beta 
            float alpha
            float beta
            alpha = inf / tau   
            beta = (1- inf)/tau
            setfield KDR1 X_A->table[{i}] {alpha}
            setfield KDR1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield KDR1 X_A->calc_mode 1 X_B->calc_mode 1
end

//========================================================================
//   P23RS       Tabchannel gK-transient, gK(A) 2005/03
//========================================================================
function make_KA1
        if ({exists KA1})
            return
        end
        create tabchannel KA1
        setfield KA1 \ 
            Ek              -0.095 \
            Ik              0  \
            Xpower          4 \
            Ypower          1
        setfield KA1 \
            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 KA1 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
                
            float A, B, Vhalf
                             

            // ChannelML form of equation: inf which is of form sigmoid, with params:
            // A = 1, B = -8.5, Vhalf = -60, in units: 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 KA1 X_A->table[{i}] {alpha}
            setfield KA1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
        setfield KA1 X_A->calc_mode 1 X_B->calc_mode 1
                    
        // Y table for gate h
        float dv = ({v_max} - {v_min})/{tab_divs}
        call KA1 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 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 KA1 Y_A->table[{i}] {alpha}
            setfield KA1 Y_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield KA1 Y_A->calc_mode 1 Y_B->calc_mode 1
end

//========================================================================
// P23RS          Tabchannel gK2-slow, gK2 2005/03
//========================================================================
function make_K21
        if ({exists K21})
            return
        end
        create tabchannel K21
        setfield K21 \ 
            Ek              -0.095 \
            Ik              0  \
            Xpower          1 \
            Ypower          1
        
        setfield K21 \
            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 K21 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 equat.
            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 units: 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 K21 X_A->table[{i}] {alpha}
            setfield K21 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield K21 X_A->calc_mode 1 X_B->calc_mode 1
                    
        // Y table for gate h
        float dv = ({v_max} - {v_min})/{tab_divs}
        call K21 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 units: Physiological Units
            // A = 1, B = 0.0106, half = -0.058
            inf = 1 / ( {exp {(v + 0.058) / 0.0106}} + 1)

            // alpha and beta
            float alpha
            float beta
            alpha = inf / tau   
            beta = (1- inf)/tau
            setfield K21 Y_A->table[{i}] {alpha}
            setfield K21 Y_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield K21 Y_A->calc_mode 1 Y_B->calc_mode 1
end

//========================================================================
// P23RS    Tabchannel gK-muscarinic receptor supressed, gK(M) 2005/03
//========================================================================
function make_KM1
        if ({exists KM1})
            return
        end
        create tabchannel KM1
        setfield KM1 \ 
            Ek              -0.095 \
            Ik              0  \
            Xpower          1
        setfield KM1 \
            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 KM1 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
            // 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 units: 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 KM1 X_A->table[{i}] {alpha}
            setfield KM1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
        setfield KM1 X_A->calc_mode 1 X_B->calc_mode 1
end

//========================================================================
//  P23RS   Tabchannel gCa(L)-low threshold, transient, gCa(L) 2005/03
//========================================================================
function make_CaL1
        if ({exists CaL1})
            return
        end
        create tabchannel CaL1
        setfield CaL1 \ 
            Ek              0.125 \
            Ik              0  \
            Xpower          2 \
            Ypower          1
        
        setfield CaL1 \
            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 CaL1 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 = 0.204 + 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
                
            float A, B, Vhalf
            // A = 1, B = -6.2, Vhalf = -56.0, in units: Physiological Units
            // A = 1, B = -0.0062, Vhalf = -0.056
            inf = 1 / ( {exp {(v + 0.056) / -0.0062}} + 1)
        
            // alpha and beta
            float alpha
            float beta
            alpha = inf / tau   
            beta = (1- inf)/tau
            setfield CaL1 X_A->table[{i}] {alpha}
            setfield CaL1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield CaL1 X_A->calc_mode 1 X_B->calc_mode 1
                    
        // Y table for gate h
        float dv = ({v_max} - {v_min})/{tab_divs}
        call CaL1 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 < -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
            // A = 1, B = 0.004, Vhalf = -0.08
            inf = 1 / ( {exp {(v + 0.08) / 0.004}} + 1)
        

            // alpha and beta
            float alpha
            float beta
            alpha = inf / tau   
            beta = (1- inf)/tau
            setfield CaL1 Y_A->table[{i}] {alpha}
            setfield CaL1 Y_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield CaL1 Y_A->calc_mode 1 Y_B->calc_mode 1
end

//==========================================================================
// P23RS    Tabchannel gCaH-high threshold calcium, gCa(L) "long" 2003/05
//==========================================================================
function make_CaH1
        if ({exists CaH1})
            return
        end
        create tabchannel CaH1
        setfield CaH1 \ 
            Ek              0.125 \
            Ik              0  \
            Xpower          2
        
        setfield CaH1 \
            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 CaH1 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 units: 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 units: Physiological 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 and beta 
            float tau = 1/(alpha + beta)
            setfield CaH1 X_A->table[{i}] {alpha}
            setfield CaH1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield CaH1 X_A->calc_mode 1 X_B->calc_mode 1
end

//========================================================================
//   P23RS   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_s1
        if ({exists Ca_s1})
            return
        end
        create Ca_concen Ca_s1
        // params for soma Ca pool 
        setfield Ca_s1 \
            tau                   { 1.0 / 10 }    \
            Ca_base               0
        addfield Ca_s1 addmsg1
        setfield Ca_s1 \
                addmsg1        "../CaH1 . I_Ca Ik"
//        addfield Ca_s1 addmsg2
//        setfield Ca_s1 \
//                addmsg2        "../CaL1 . 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_d1
        if ({exists Ca_d1})
            return
        end
        create Ca_concen Ca_d1
        // params for dend. Ca pool model
        setfield Ca_d1 \
            tau                   { 1.0 / 50 }    \
            Ca_base               0

        addfield Ca_d1 addmsg1
        setfield Ca_d1 \
                addmsg1        "../CaH1 . I_Ca Ik"
//        addfield Ca_d1 addmsg2
//        setfield Ca_d1 \
//                addmsg2        "../CaL1 . 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.
*/

//===============================================================================
//  P23RS Ca-dependent K Channel K(C)
//===============================================================================
/*
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_KCs1
        if ({exists KCs1})
            return
        end
        create tabchannel KCs1
        setfield KCs1 \ 
            Ek              -0.095 \
            Ik              0  \
            Xpower          1 \
            Zpower          1
        setfield KCs1 \
            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 KCs1 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 / 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 // v to units of equation
            alpha = alpha * 0.001 // 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 KCs1 X_A->table[{i}] {alpha}
            setfield KCs1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield KCs1 X_A->calc_mode 1 X_B->calc_mode 1
                    
        // Ca 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 KCs1 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 KCs1 Z_A->table[{i}] {0}
            setfield KCs1 Z_B->table[{i}] {const_state}
            ca_conc= ca_conc + dc
        end
        tweaktau KCs1 Z
        
        addfield KCs1 addmsg1
        setfield KCs1 addmsg1  "../Ca_s1  . CONCEN Ca"
end


function make_KCd1
        if ({exists KCd1})
            return
        end
        create tabchannel KCd1
        setfield KCd1 \ 
            Ek              -0.095 \
            Ik              0  \
            Xpower          1 \
            Zpower          1
        setfield KCd1 \
            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 KCd1 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 / 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 // v to units of equation
            alpha = alpha * 0.001 // 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 KCd1 X_A->table[{i}] {alpha}
            setfield KCd1 X_B->table[{i}] {alpha + beta}
            v = v + dv
        end // end of for (i = 0; i <= ({tab_divs}); i = i + 1)
            
        setfield KCd1 X_A->calc_mode 1 X_B->calc_mode 1
                    
        // Ca 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 KCd1 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 KCd1 Z_A->table[{i}] {0}
            setfield KCd1 Z_B->table[{i}] {const_state}
            ca_conc= ca_conc + dc
        end
        tweaktau KCd1 Z
        
        addfield KCd1 addmsg1
        setfield KCd1 addmsg1  "../Ca_d1  . CONCEN Ca"
end


//========================================================================
//              P23RS  Ca-dependent K AHP Channel,gK(AHP) 
//========================================================================

/* This is a tabchannel which gets the calcium concentration from Ca pool
   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_KAHPs1
        if ({exists KAHPs1})
            return
        end
        create tabchannel KAHPs1
        setfield KAHPs1 \ 
            Ek              -0.095 \
            Ik              0  \
            Zpower          1
        
        setfield KAHPs1 \
            Gbar 1 \
            Gk              0 
        float tab_divs = 1041
        // Ca dependent channel 
        float c
        float conc_min = 0
        float conc_max = 1000
        float dc = ({conc_max} - {conc_min})/{tab_divs}
        float ca_conc = {conc_min}
        call KAHPs1 TABCREATE Z {tab_divs} {conc_min} {conc_max}
        for (c = 0; c <= ({tab_divs}); c = c + 1)
                    
            // alpha
            float alpha
            float v
            ca_conc = ca_conc * 0.000001 // ca_conc to units of equation
            if (ca_conc < 0.0001 )
                alpha =  ca_conc/0.01 
            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 = 0.01
            ca_conc = ca_conc * 1000000 // resetting ca_conc 
            // correct units of beta
            beta = beta * 1000

            // alpha and beta 

            float tau = 1/(alpha + beta)
            setfield KAHPs1 Z_A->table[{c}] {alpha}
            setfield KAHPs1 Z_B->table[{c}] {alpha + beta}
                    ca_conc = ca_conc + dc
        end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
                
        setfield KAHPs1 Z_conc 1
        setfield KAHPs1 Z_A->calc_mode 1 Z_B->calc_mode 1

        addfield KAHPs1 addmsg1
        setfield KAHPs1  \
                addmsg1        "../Ca_s1 . CONCEN Ca"
end


function make_KAHPd1
        if ({exists KAHPd1})
            return
        end
        create tabchannel KAHPd1
        setfield KAHPd1 \ 
            Ek              -0.095 \
            Ik              0  \
            Zpower          1
        setfield KAHPd1 \
            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 KAHPd1 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 < 0.0001 )
                alpha =  ca_conc/0.01 
            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 // ca_conc to units of equation
            beta = 0.01
            ca_conc = ca_conc * 1000000 // reset ca_conc 
            // correct units of beta
            beta = beta * 1000

            // alpha and beta
            float tau = 1/(alpha + beta)
            
            setfield KAHPd1 Z_A->table[{c}] {alpha}
            setfield KAHPd1 Z_B->table[{c}] {alpha + beta}
                    ca_conc = ca_conc + dc
        end // end of for (c = 0; c <= ({tab_divs}); c = c + 1)
                
        setfield KAHPd1 Z_conc 1
        setfield KAHPd1 Z_A->calc_mode 1 Z_B->calc_mode 1

        addfield KAHPd1 addmsg1
        setfield KAHPd1  \
                addmsg1        "../Ca_d1 . CONCEN Ca"
end


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