/* ===========================================================

        Author: Daniel Keller
	Institution: Ecole Polytechnique Federale de Lausanne

	"An exclusion zone for Ca2+ channels around docked vesicles explains 
	release control by multiple channels at a CNS synapse"
	PLoS Computational Biology, 2015

============================================================= */

/* --- contains (almost) all variables --- */
 

chckpnt_state = 1
currents = 1
/*epsp_time = 20e-3   Time in seconds */

Cabase=70e-9

D_Ca= 2.2e-6
D_Glu=2e-6
D_CB=0
n_Glu=0 * 2000

Ca_HVA_density_neck=0 * 4
Ca_HVA_density_head=0 * 4
Ca_HVA_density_dend=0 * 4
Ca_LVA_density_neck=0
Ca_LVA_density_head=0
Ca_LVA_density_dend=0


psd_diameter = 350*1e-3  /* diamter of PSD in nanometers */
psd_size = 350*1e-3  /* length of square PSD in nanometers */

AMPA_number =0 * 80
NMDA_number =0 * 10

AMPA_density = AMPA_number / (0.25*psd_diameter*psd_diameter*3.1416)
NMDA_density = NMDA_number / (0.25*psd_diameter*psd_diameter*3.1416)

GluT_density=1000

/*evenly distributed pumps */


NCX_pump_density =0 * 200
NCX_spine_pump_bound_fraction = 0.3
NCX_dend_pump_bound_fraction = NCX_spine_pump_bound_fraction
NCX_pump_density_neck = NCX_pump_density
NCX_spine_pump_bound_fraction_neck = 0.3
NCX_dend_pump_bound_fraction_neck = NCX_spine_pump_bound_fraction_neck 
NCX_pump_density_dendrite = NCX_pump_density

ex_pump_density =  0*  800
ex_spine_pump_bound_fraction = 0.3
ex_dend_pump_bound_fraction = ex_spine_pump_bound_fraction

/*ex_pump_density_neck = ex_pump_density*/
ex_pump_density_neck = 0 * 800
ex_spine_pump_bound_fraction_neck = 0.3
ex_dend_pump_bound_fraction_neck =ex_spine_pump_bound_fraction_neck 

ex_pump_density_dendrite =0 * 800
ex_spine_pump_bound_fraction_dendrite = 0.0
ex_dend_pump_bound_fraction_dendrite =ex_spine_pump_bound_fraction_dendrite 

EGTA_bound_fraction=EGTA_on * (Cabase)/(EGTA_off+EGTA_on * (Cabase))
EGTA_unbound_fraction=1-EGTA_bound_fraction

BAPTA_bound_fraction=BAPTA_on * (Cabase)/(BAPTA_off+BAPTA_on * (Cabase))
BAPTA_unbound_fraction=1-BAPTA_bound_fraction

concentration_to_density = 7.528e6 /* based on sheets 12.5nm apart */
conversion_to_density= 6.02e8 /*number per mole per cubic micron*/


atp_concentration = 2000e-6
bound_atp_fraction=(Cabase * katpMgback * katpCafor)/(katpCaback * katpMgback + Cabase * katpMgback * katpCafor + katpCaback * katpMgfor * Mgbase)
mgbound_atp_fraction=(katpCaback * katpMgfor * Mgbase)/(katpCaback * katpMgback + Cabase * katpMgback * katpCafor + katpCaback * katpMgfor * Mgbase)
unbound_atp_fraction=(katpCaback * katpMgback)/(katpCaback * katpMgback + Cabase * katpMgback * katpCafor + katpCaback * katpMgfor * Mgbase)

parvalbumin_concentration = 100e-6
bound_parvalbumin_fraction=(Cabase * kparvMU * kparvUB)/(kparvBU * kparvMU + Cabase * kparvMU * kparvUB + kparvBU * kparvUM * Mgbase)
mgbound_parvalbumin_fraction=(kparvBU * kparvUM * Mgbase)/(kparvBU * kparvMU + Cabase * kparvMU * kparvUB + kparvBU * kparvUM * Mgbase)
unbound_parvalbumin_fraction=(kparvBU * kparvMU)/(kparvBU * kparvMU + Cabase * kparvMU * kparvUB + kparvBU * kparvUM * Mgbase)


fast_sp_concentration_psd=0 * conversion_to_density
fast_cbp_concentration = 0e-6 * conversion_to_density
medium_cbp_concentration = 0e-6 * conversion_to_density
slow_cbp_concentration = 400e-6 
v_slow_cbp_concentration = 00e-6 * conversion_to_density


bound_cbp_fraction = ((Cabase) )/((slow_off/slow_on + Cabase) )
unbound_cbp_fraction = 1 - bound_cbp_fraction

bound_cbp_fraction_spine = bound_cbp_fraction
unbound_cbp_fraction_spine = 1 - bound_cbp_fraction

bound_cbp_fraction_dend = bound_cbp_fraction
unbound_cbp_fraction_dend = 1 - bound_cbp_fraction

calbindin_concentration =0 * 45e-6 * conversion_to_density 

EGTA_concentration=0e-3
BAPTA_concentration=0e-3

sensor_concentration =  0e-6  * conversion_to_density 
bound_sensor_fraction_spine = 0.25
unbound_sensor_fraction_spine = 1 - bound_sensor_fraction_spine
bound_sensor_fraction_dend = bound_sensor_fraction_spine
unbound_sensor_fraction_dend = 1 - bound_sensor_fraction_dend

bound_calbindin_H0M0_fraction = 52685 /99741
bound_calbindin_H1M0_fraction = 15456/99741
bound_calbindin_H2M0_fraction = 10314/99741
bound_calbindin_H0M1_fraction = 11194 /99741
bound_calbindin_H1M1_fraction = 10075/99741
bound_calbindin_H2M1_fraction = 4/99741
bound_calbindin_H0M2_fraction = 8 /99741
bound_calbindin_H1M2_fraction = 0 /99741
bound_calbindin_H2M2_fraction = 0 /99741



/*calmodulin_concentration_psd = 260e-6 * 1.5056e7
calmodulin_concentration_head = 5e-6 * 1.5056e7*/
/*calmodulin_concentration_psd = 260e-6 * conversion_to_density
calmodulin_concentration_head = 0 * 5e-6 * conversion_to_density*/
calmodulin_concentration_psd =  0e-6 * conversion_to_density
calmodulin_concentration_head = 0e-6 * conversion_to_density

bound_calmodulin_1_fraction = 0.053 

leak_density = 1280

I_HVA = "hva_IV.dat"
I_LVA = "lva_IV.dat"
I_NMDA = "nmda_IV.dat"
I_leak = 0 * 20

dt=0.5e-8
it=100e4
/*it=60e4*/
/*it=1001*/
grid_density = 20000
freq=2000 *dt