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specific_ion_channels.h

#ifndef __SPECIFIC_ION_CHANNELS_H_
#define __SPECIFIC_ION_CHANNELS_H_

#include "viongate.h"
#include "conciongate.h"
#include "activechannel.h"
#include "activecachannel.h"
#include "csimerror.h"

// parameters for voltage range transformations
#define V_REST_BIOL_MV   (-70)    // [mV] (general in publications used unit)
#define V_THRESH_BIOL_MV (-40)    // [mV]
#define V_REST_SIM    (0.0)   // [V]  (all simulation parameters are in SI units)
#define V_THRESH_SIM  (15e-3) // [V]

#define A_MEMBRANE (0.01e-2) // [cm2]

/* Transform biological Erev value to model voltage range */
/* Note that in the ActiveChannel constructor actual Neuron voltages are unknown */ 
#define TRANSFORM_EREV Erev = ((Erev - V_REST_BIOL_MV)*(V_THRESH_SIM - V_REST_SIM)/(V_THRESH_BIOL_MV-V_REST_BIOL_MV) + V_REST_SIM);


#define TRANSFORM_V    /* Transform model voltage value to biological voltage range */ \
                       V = (V - *Vresting)*(V_THRESH_BIOL_MV - V_REST_BIOL_MV)/(*VmScale) + V_REST_BIOL_MV

#define TSCALE 1000
#define VSCALE 1000

//============================================================

#define CASCALE 1.1180e+07

#define IONGATE_CA_MIN 0.0

#define IONGATE_CA_MAX 1000e-9

#define IONGATE_CA_INC 5.0e-10

#define IONGATE_CA_TABLE_SIZE      ((int)((IONGATE_CA_MAX - IONGATE_CA_MIN) / IONGATE_CA_INC + 1))

// Could only be connected to CaChannel_Yamada98 class, where the ca mechanism is included
class CaGate_Yamada98 : public VIonGate {

  DO_REGISTERING

public:
  CaGate_Yamada98(void) { k=2; Ca=0; Ts=1; C1=0; C2=0; }

  virtual ~CaGate_Yamada98(void) { if (getC1()) { free(getC1()); setC1(0); }
                                   if (getC2()) { free(getC2()); setC2(0); }}

  virtual double tau(double C) { return Ts/( pow(CASCALE*C,2) + 2.5); }

  virtual double infty(double C)  { return pow(CASCALE*C,2)/( pow(CASCALE*C,2) + 2.5); }

  virtual double pInfty(MembranePatchSimple *) { return 0;}

  virtual void reset(void);

  virtual void setCa(double *C) { Ca = C; }

  virtual int updateInternal(void);

  virtual int advance(void);

  virtual int addIncoming(Advancable *Incoming);

  double Ts;

protected:

  double *Ca;

  virtual double *getC1(void) { return C1; }
  virtual double *getC2(void) { return C2; }
  virtual void setC1(double *p) { C1=p; }
  virtual void setC2(double *p) { C2=p; }

  double *C1;

  double *C2;
};

//== Channels used by James Maciokas / Reno ==========================================================

// Ca mechanism is included in the channel class not the neuron class.
class CaChannel_Yamada98 : public ActiveChannel {

  DO_REGISTERING

public:

  CaChannel_Yamada98(void) {
    Erev = -5e-6 * VSCALE; // assumed resting potential Vresting = 0
    u = 200e-9;   // Mol
    Ts = 70e-3;   // Sec
    Ca = 0;       // Mol
    Gbar = 54e-9; // S
  }

  virtual void membraneSpikeNotify(double ) { Ca = Ca + u; };

  virtual void reset(void);

  virtual int updateInternal(void);

  virtual int advance(void);

  float u;

  float Ts;

  double Ca;

protected:

  float C1;
};


class MmGate_Wang98 : public VIonGate {
public:
  MmGate_Wang98(void) { k=1; }
  double tau(double V) { return TSCALE * exp(+( VSCALE * (V - *Vresting) - 12.3)/9.15) / 3800; }
  double infty(double V)  { return 1/(1 + exp(-( VSCALE * (V - *Vresting) - 13)/4.4)); }

  IONGATE_TABLES(MmGate_Wang98);
};



class MChannel_Wang98 : public ActiveChannel {

  DO_REGISTERING

public:

  MChannel_Wang98(void) {
    addGate(new MmGate_Wang98);

    Erev = -80; // [mV] biological value
    // Transform to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~MChannel_Wang98(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }
};

class AmGate_Hoffman97 : public VIonGate {
public:
  AmGate_Hoffman97(void) { k=1; }

  double tau(double ) { return TSCALE*0.2e-6; }
  double infty(double V)  { return 1/(1 + exp(-( VSCALE * (V - *Vresting) - 40.5)/9)); }

  IONGATE_TABLES(AmGate_Hoffman97);
};


class AhGate_Hoffman97 : public VIonGate {
public:
  AhGate_Hoffman97(void) { k=1; }

  double tau(double ) { return TSCALE*5e-6; }
  double infty(double V)  { return 1/(1 + exp(( VSCALE * (V - *Vresting) - 7)/4)); }

  IONGATE_TABLES(AhGate_Hoffman97);
};



class AChannel_Hoffman97 : public ActiveChannel {

  DO_REGISTERING

public:

  AChannel_Hoffman97(void) {
    addGate(new AmGate_Hoffman97);
    addGate(new AhGate_Hoffman97);

    Erev = -80; // [mV] biological value
    // Transform to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~AChannel_Hoffman97(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }
};

class SICmGate_Maciokas02 : public VIonGate {
public:
  SICmGate_Maciokas02(void) { k=1; }

  double tau(double ) { return TSCALE*0.2e-6; }
  double infty(double V)  { return 1/(1 + exp(-( VSCALE * (V - *Vresting) - 20)/2.5)); }

  IONGATE_TABLES(SICmGate_Maciokas02);
};

class SIChGate_Maciokas02 : public VIonGate {
public:
  SIChGate_Maciokas02(void) { k=1; }

  double tau(double ) { return TSCALE*5e-6; }
  double infty(double V)  { return 1/(1 + exp(( VSCALE * (V - *Vresting) - 15)/2.5)); }

  IONGATE_TABLES(SIChGate_Maciokas02);
};

class SICChannel_Maciokas02 : public ActiveChannel {

  DO_REGISTERING

public:

  SICChannel_Maciokas02(void) {
    addGate(new SICmGate_Maciokas02);
    addGate(new SIChGate_Maciokas02);

    Erev = -80; // [mV] biological value
    // Transform to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~SICChannel_Maciokas02(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }
};



//== Channels of neocortical pyramidal neurons from the SenseLab ModelDB archiv ========



class AnGate_Korngreen02 : public VIonGate {
public:
  AnGate_Korngreen02(void) { k=2;}

  double tau(double V) { TRANSFORM_V;
                         return (V < -50) ? 1e-3 * (1.25+175.03*exp(V*0.026)) : 1e-3 * (1.25+13*exp(-V*0.026)); }
  double infty(double V) { TRANSFORM_V;
                           return 1/(1+exp(-(V+14)/14.6)); }

  IONGATE_TABLES(AnGate_Korngreen02);
};

class AlGate_Korngreen02 : public VIonGate {
public:
  AlGate_Korngreen02(void) { k=1; }

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * (360+(1010+24*(V+55))*exp(-pow((V+75)/48,2))); }
  double infty(double V)  { TRANSFORM_V;
                            return 1/(1+exp((V+54)/11)); }

  IONGATE_TABLES(AlGate_Korngreen02);
};


class AChannel_Korngreen02 : public ActiveChannel {

  DO_REGISTERING

public:

  AChannel_Korngreen02(void) {
    addGate(new AnGate_Korngreen02);
    addGate(new AlGate_Korngreen02);
    Ts = 1;
    Gbar = 8e-3*A_MEMBRANE; // [S/cm2]*[cm2]
    Erev = -80;  // (original -90) [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~AChannel_Korngreen02(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};


class KnGate_Korngreen02 : public VIonGate {
public:
  KnGate_Korngreen02(void) { k=4;}

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * (0.34 + 0.92*exp(-pow((V+71)/59,2))); }
  double infty(double V) { TRANSFORM_V;
                           return 1/(1+exp(-(V+47)/29)); }

  IONGATE_TABLES(KnGate_Korngreen02);
};

class KlGate_Korngreen02 : public VIonGate {
public:
  KlGate_Korngreen02(void) { k=1; }

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * (8 + 49*exp(-pow((V+73)/23,2))); }
  double infty(double V)  { TRANSFORM_V;
                            return 1/(1+exp((V+66)/10)); }

  IONGATE_TABLES(KlGate_Korngreen02);
};


class KChannel_Korngreen02 : public ActiveChannel {

  DO_REGISTERING

public:

  KChannel_Korngreen02(void) {
    addGate(new KnGate_Korngreen02);
    addGate(new KlGate_Korngreen02);
    Ts = 1;
    Gbar = 8e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = -80;  // (original -90) [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~KChannel_Korngreen02(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};


class NPmGate_McCormick92 : public VIonGate {
public:
  NPmGate_McCormick92(void) { k=1; }

  double alpha(double V) { TRANSFORM_V;
                         return 1e3 * (0.091*(V+48)/(1.0-exp(-(V+48.0)/5.0))); }
  double beta(double V) { TRANSFORM_V;
                         return 1e3 * (-0.062*(V+48.0)/(1.0-exp((V+48.0)/5.0))); }
  double infty(double V)  { TRANSFORM_V;
                            return 1.0/(1.0+exp(-(49.0+V)/5)); }

  IONGATE_TABLES(NPmGate_McCormick92);
};


class NPChannel_McCormick02 : public ActiveChannel {

  DO_REGISTERING

public:

  NPChannel_McCormick02(void) {
    addGate(new NPmGate_McCormick92);
    Ts = 1;
    Gbar = 2.2e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = 55.0;  // [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~NPChannel_McCormick02(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};


class MnGate_Mainen96 : public VIonGate {
public:
  MnGate_Mainen96(void) { k=1; }

  double alpha(double V) { TRANSFORM_V;
                         return 1e3 * (0.001*(V+30)/(1-exp(-(V+30)/9))); }
  double beta(double V) { TRANSFORM_V;
                         return 1e3 * (-0.001*(V+30)/(1-exp((V+30)/9))); }

  IONGATE_TABLES(MnGate_Mainen96);
};


class MChannel_Mainen96 : public ActiveChannel {

  DO_REGISTERING

public:

  MChannel_Mainen96(void) {
    addGate(new MnGate_Mainen96);
    Ts = 1;
    Gbar = 1e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = -80.0;  // (original -90) [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~MChannel_Mainen96(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};

#define CELSIUS 30

class HnGate_Stuart98 : public VIonGate {
public:
  HnGate_Stuart98(void) { k=1; }

  double alpha(double V) { return  exp(1e-3*3*(V+88)*9.648e4/(8.315*(273.16+CELSIUS))); }
  double beta(double V) { return  exp(1e-3*3*0.4*(V+88)*9.648e4/(8.315*(273.16+CELSIUS))); }
  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * (beta(V)/(0.00057+0.00057*alpha(V))); }
  double infty(double V) { TRANSFORM_V;
                         return  1/(1+alpha(V)); }

  IONGATE_TABLES(HnGate_Stuart98);
};


class HChannel_Stuart98 : public ActiveChannel {

  DO_REGISTERING

public:

  HChannel_Stuart98(void) {
    addGate(new HnGate_Stuart98);
    Ts = 1;
    Gbar = 3e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = -35.0;  // [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~HChannel_Stuart98(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};

#define SECH(_V_)  2/(exp(2*_V_)+exp(-2*_V_))

class HVACAuGate_Brown93 : public VIonGate {
public:
  HVACAuGate_Brown93(void) { k=2;}

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * (1.25*SECH(-0.031*(V+37.1))); }
  double infty(double V) { TRANSFORM_V;
                           return 1/(1+exp(-(V+24.6)/11.3)); }

  IONGATE_TABLES(HVACAuGate_Brown93);
};

class HVACAvGate_Brown93 : public VIonGate {
public:
  HVACAvGate_Brown93(void) { k=1; }

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * 420; }
  double infty(double V)  { TRANSFORM_V;
                            return 1/(1+exp((V+12.6)/18.9)); }

  IONGATE_TABLES(HVACAvGate_Brown93);
};


class HVACAChannel_Brown93 : public ActiveCaChannel {

  DO_REGISTERING

public:

  HVACAChannel_Brown93(void) {
    addGate(new HVACAuGate_Brown93);
    addGate(new HVACAvGate_Brown93);
    Ts = 1;
    Gbar = 0.3e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = 140;  // [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~HVACAChannel_Brown93(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};


class CALmGate_Destexhe98 : public VIonGate {
public:
  CALmGate_Destexhe98(void) { k=2;}

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * 0.1; } /* Originally 0 */
  double infty(double V) { TRANSFORM_V;
                           return 1.0/(1+exp(-(V+57)/6.2)); }

  IONGATE_TABLES(CALmGate_Destexhe98);
};

class CALhGate_Destexhe98 : public VIonGate {
public:
  CALhGate_Destexhe98(void) { k=1; }

  double tau(double V) { TRANSFORM_V;
                         return 1e-3 * (30.8 + (211.4 + exp((V+113.2)/5))/(1+exp((V+84)/3.2))); }
  double infty(double V)  { TRANSFORM_V;
                            return 1.0/(1+exp((V+81)/4.0)); }

  IONGATE_TABLES(CALhGate_Destexhe98);
};


class CALChannel_Destexhe98 : public ActiveChannel {

  DO_REGISTERING

public:

  CALChannel_Destexhe98(void) {
    addGate(new CALmGate_Destexhe98);
    addGate(new CALhGate_Destexhe98);
    Ts = 1;
    Gbar = 2e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = 140;  // [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~CALChannel_Destexhe98(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};


class KCAnGate_Mainen96 : public ConcIonGate {
public:
  KCAnGate_Mainen96(void) { k=1; ConcType=CA;}


  double alpha(double C) { return 0.01*C*1e3; }
  double beta(double ) { return 0.02; }

  double tau(double C) { return 1e-3/(alpha(C) + beta(C)); }
  double infty(double C) { return alpha(C)/(alpha(C) + beta(C)); }

  IONGATE_TABLES(KCAnGate_Mainen96);
};


class KCAChannel_Mainen96 : public ActiveChannel {

   DO_REGISTERING

public:

  KCAChannel_Mainen96(void) {
    addGate(new KCAnGate_Mainen96);
    Ts = 1;
    Gbar = 1e-3*A_MEMBRANE; // [S/cm2]*[cm2]

    Erev = -80;  // (original -90) [mV] biological value
    // Transform biological Erev value to model voltage range
    TRANSFORM_EREV;
  }

  virtual ~KCAChannel_Mainen96(void) {
    for(int i=0;i<nGates;i++)
      delete gates[i];
  }

  virtual int updateInternal(void);

  double Ts;
};




#endif

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