MultiCompartmentModel/makeTransporters.hoc at master · hamadaio/MultiCompartmentModel · GitHub

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///////////////////////////////////////////////////////////////////////////////
// makeTransporters.hoc: inserts active ion transporters into each section
///////////////////////////////////////////////////////////////////////////////

//////////////////// procedure definitions ////////////////////////////////////

//-----------------------------------------------------------------------------
// transportersSoma()
//-----------------------------------------------------------------------------
// inserts transporters in the soma

proc transportersSoma() {
  forsec somatic {
    // KCC2 Co-transporters
    if (KCC2_soma) {
    	insert KCC2 																					// from KCC2.mod
			A_M_KCC2  = alpha_soma					// (/s) rate of transfer from cytosolic to membrane-bound KCC2
			B_M_KCC2  = beta_soma   					// (/s) rate of transfer from membrane-bound to cytosolic KCC2
			R_M_KCC2  = R_m_soma   				// (/s) KCC2 dephosphorylation coefficient
			R_MP_KCC2 = R_mp_soma   				// (/s) KCC2 phosphorylation coefficient
			R_K_KCC2  = R_k_soma   					// (mM) concent. of Ca2+ at which kinase activation rate is half max
			R_P_KCC2  = R_p_soma   					// (mM) concent. of Ca2+ at which phosphatase activation rate is half max
			V_K_KCC2  = maxK_soma   					// (/s) maximum rate of kinase activation
			V_P_KCC2  = maxP_soma   					// (/s) maximum rate of phosphatase activation
			H_K_KCC2  = HillK_soma   					// (1) Hill coefficient for kinase activation equation
			H_P_KCC2  = HillP_soma   					// (1) Hill coefficient for phosphatase activation equation
			B_K_KCC2  = inactK_soma  					// (/s) rate of kinase inactivation
			B_P_KCC2  = inactP_soma   					// (/s) rate of phosphatase inactivation
      	insert KCC2_Transport 																			// from KCC2_Trans.mod
			axD_KCC2_Transport 		= axD_soma     		// um^2/ms
			R_T_KCC2_Transport		= Michaelis_soma    // (mM)     < 0, 1e9 > : Michaelis constant for KCC2 ion transport
			r_T_KCC2_Transport    	= transp_soma    	// (/s)     < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
		}
  	}
}

//-----------------------------------------------------------------------------
// transportersProximal()
//-----------------------------------------------------------------------------
// inserts transporters in the proximal dendrites

proc transportersProximal() {

  forsec proximal {

    // KCC2 Co-transporters
    if (KCC2_prox) {
    	insert KCC2 																					// from KCC2.mod
			A_M_KCC2  = alpha_prox					// (/s) rate of transfer from cytosolic to membrane-bound KCC2
			B_M_KCC2  = beta_prox   					// (/s) rate of transfer from membrane-bound to cytosolic KCC2
			R_M_KCC2  = R_m_prox   				// (/s) KCC2 dephosphorylation coefficient
			R_MP_KCC2 = R_mp_prox   				// (/s) KCC2 phosphorylation coefficient
			R_K_KCC2  = R_k_prox   					// (mM) concent. of Ca2+ at which kinase activation rate is half max
			R_P_KCC2  = R_p_prox   					// (mM) concent. of Ca2+ at which phosphatase activation rate is half max
			V_K_KCC2  = maxK_prox   					// (/s) maximum rate of kinase activation
			V_P_KCC2  = maxP_prox   					// (/s) maximum rate of phosphatase activation
			H_K_KCC2  = HillK_prox   					// (1) Hill coefficient for kinase activation equation
			H_P_KCC2  = HillP_prox   					// (1) Hill coefficient for phosphatase activation equation
			B_K_KCC2  = inactK_prox  					// (/s) rate of kinase inactivation
			B_P_KCC2  = inactP_prox   					// (/s) rate of phosphatase inactivation
      	insert KCC2_Transport 																			// from KCC2_Trans.mod
			axD_KCC2_Transport 		= axD_prox     		// um^2/ms
			R_T_KCC2_Transport		= Michaelis_prox    // (mM)     < 0, 1e9 > : Michaelis constant for KCC2 ion transport
			r_T_KCC2_Transport    	= transp_prox    	// (/s)     < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
		}
  	}
}

//-----------------------------------------------------------------------------
// transportersMiddle()
//-----------------------------------------------------------------------------
// inserts transporters in the middle dendrites

proc transportersMiddle() {

  forsec middle {

// KCC2 Co-transporters
    if (KCC2_mid) {
    	insert KCC2 																					// from KCC2.mod
			A_M_KCC2  = alpha_mid					// (/s) rate of transfer from cytosolic to membrane-bound KCC2
			B_M_KCC2  = beta_mid   					// (/s) rate of transfer from membrane-bound to cytosolic KCC2
			R_M_KCC2  = R_m_mid   				// (/s) KCC2 dephosphorylation coefficient
			R_MP_KCC2 = R_mp_mid   				// (/s) KCC2 phosphorylation coefficient
			R_K_KCC2  = R_k_mid   					// (mM) concent. of Ca2+ at which kinase activation rate is half max
			R_P_KCC2  = R_p_mid   					// (mM) concent. of Ca2+ at which phosphatase activation rate is half max
			V_K_KCC2  = maxK_mid   					// (/s) maximum rate of kinase activation
			V_P_KCC2  = maxP_mid   					// (/s) maximum rate of phosphatase activation
			H_K_KCC2  = HillK_mid   					// (1) Hill coefficient for kinase activation equation
			H_P_KCC2  = HillP_mid   					// (1) Hill coefficient for phosphatase activation equation
			B_K_KCC2  = inactK_mid  					// (/s) rate of kinase inactivation
			B_P_KCC2  = inactP_mid   					// (/s) rate of phosphatase inactivation
      	insert KCC2_Transport 																			// from KCC2_Trans.mod
			axD_KCC2_Transport 		= axD_mid     		// um^2/ms
			R_T_KCC2_Transport		= Michaelis_mid    // (mM)     < 0, 1e9 > : Michaelis constant for KCC2 ion transport
			r_T_KCC2_Transport    	= transp_mid    	// (/s)     < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
		}
  	}
}
//-----------------------------------------------------------------------------
// transportersDistal()
//-----------------------------------------------------------------------------
// inserts transporters in the distal dendrites

proc transportersDistal() {

  forsec distal {

// KCC2 Co-transporters
    if (KCC2_dist) {
    	insert KCC2 																					// from KCC2.mod
			A_M_KCC2  = alpha_dist					// (/s) rate of transfer from cytosolic to membrane-bound KCC2
			B_M_KCC2  = beta_dist   					// (/s) rate of transfer from membrane-bound to cytosolic KCC2
			R_M_KCC2  = R_m_dist   				// (/s) KCC2 dephosphorylation coefficient
			R_MP_KCC2 = R_mp_dist   				// (/s) KCC2 phosphorylation coefficient
			R_K_KCC2  = R_k_dist   					// (mM) concent. of Ca2+ at which kinase activation rate is half max
			R_P_KCC2  = R_p_dist   					// (mM) concent. of Ca2+ at which phosphatase activation rate is half max
			V_K_KCC2  = maxK_dist   					// (/s) maximum rate of kinase activation
			V_P_KCC2  = maxP_dist   					// (/s) maximum rate of phosphatase activation
			H_K_KCC2  = HillK_dist   					// (1) Hill coefficient for kinase activation equation
			H_P_KCC2  = HillP_dist   					// (1) Hill coefficient for phosphatase activation equation
			B_K_KCC2  = inactK_dist  					// (/s) rate of kinase inactivation
			B_P_KCC2  = inactP_dist   					// (/s) rate of phosphatase inactivation
      	insert KCC2_Transport 																			// from KCC2_Trans.mod
			axD_KCC2_Transport 		= axD_dist     		// um^2/ms
			R_T_KCC2_Transport		= Michaelis_dist    // (mM)     < 0, 1e9 > : Michaelis constant for KCC2 ion transport
			r_T_KCC2_Transport    	= transp_dist    	// (/s)     < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
		}
  	}
}

//////////////////// procedure calls /////////////////////////////////////

// create the ion-transporters throughout the cell
transportersSoma()
transportersProximal()
transportersMiddle()
transportersDistal()