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parameters.mdl
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/* parameters for the nmj simulation */
INTERACTION_RADIUS = 0.003
iterations = 6300000 /*number of iterations */
default_onrate=0.22E8 /*default onrate for vesicles ca_binding_sites*/
default_offrate=910.0 /*default offrate for vesicles ca_binding_sites*/
divider = 1 /* factor used to modify vesicle ca_binding_rates */
sensor_onrate=default_onrate*divider /*final onrate for ca_binding sites*/
sensor_offrate=default_offrate*divider /*final offrate for ca binding sites*/
ca_diff_const=6E-6 /*calcium diffusion constant*/
sensor_Y_onrate = 10E6
sensor_Y_offrate = 15
fixed_buffer_onrate = 1E8 /* onrate for fixed ca buffer sites */
fixed_buffer_offrate = 10E3 /* offrate for fixed ca buffer sites */
fixed_buffer_concentration = 0.0020 /* concentration of fixed buffer in Molar */
fixed_buffer_diff_const=0
mobile_buffer_onrate = 1E8 /* onrate for mobile ca buffer molecules */
mobile_buffer_offrate = 10E3 /* offrate for mobile ca buffer molecules */
mobile_buffer_concentration = 0.00 /* concentration of mobile buffer in Molar */
mobile_buffer_diff_const = 0 /* mobile buffer diffusion constant */
/*mobile_buffer_diff_const = 0*/
time_step = 1e-8 /* simulation time step */
maximum_time_step = time_step*1 /* maximum simulation time step - set equal to time step for max accuracy */
reaction_output_time_step = 5e-7 /* interval between reaction data output data points */
effector_grid_density = 10000 /* density of the effector site grid */
/* ca binding site assignments. Set variable to 1 to turn on ca binding site */
/* core */
sensor_18_present = 0
sensor_19_present = 0
sensor_20_present = 0
sensor_21_present = 0
sensor_22_present = 0
sensor_23_present = 0
/* inner ring */
sensor_00_present = 1
sensor_01_present = 1
sensor_02_present = 1
sensor_03_present = 1
sensor_04_present = 1
sensor_05_present = 1
sensor_06_present = 1
sensor_07_present = 1
sensor_08_present = 1
sensor_09_present = 1
sensor_10_present = 1
sensor_11_present = 1
sensor_12_present = 1
sensor_13_present = 1
sensor_14_present = 1
sensor_15_present = 1
sensor_16_present = 1
sensor_17_present = 1
/* outer ring */
sensor_24_present = 1
sensor_25_present = 0
sensor_26_present = 1
sensor_27_present = 0
sensor_28_present = 0
sensor_29_present = 1
sensor_30_present = 0
sensor_31_present = 1
sensor_32_present = 0
sensor_33_present = 0
sensor_34_present = 1
sensor_35_present = 0
sensor_36_present = 1
sensor_37_present = 0
sensor_38_present = 1
sensor_39_present = 0
sensor_40_present = 1
sensor_41_present = 0
sensor_42_present = 0
sensor_43_present = 1
sensor_44_present = 0
sensor_45_present = 1
sensor_46_present = 0
sensor_47_present = 0
sensor_48_present = 1
sensor_49_present = 0
sensor_50_present = 1
sensor_51_present = 0
/* Y sensors*/
sensor_Y_0_present = 0
sensor_Y_1_present = 0
sensor_Y_2_present = 0
sensor_Y_3_present = 0
sensor_Y_4_present = 0
sensor_Y_5_present = 0
sensor_Y_6_present = 1
sensor_Y_7_present = 1
sensor_Y_8_present = 1
sensor_Y_9_present = 1
sensor_Y_10_present = 0
sensor_Y_11_present = 0
sensor_Y_12_present = 0
sensor_Y_13_present = 0
sensor_Y_14_present = 0
sensor_Y_15_present = 0
sensor_Y_16_present = 1
sensor_Y_17_present = 1
sensor_Y_18_present = 1
sensor_Y_19_present = 1
sensor_Y_20_present = 1
sensor_Y_21_present = 1
sensor_Y_22_present = 1
sensor_Y_23_present = 1
sensor_Y_24_present = 1
sensor_Y_25_present = 1
sensor_Y_26_present = 1
sensor_Y_27_present = 1
sensor_Y_28_present = 0
sensor_Y_29_present = 0
sensor_Y_30_present = 1
sensor_Y_31_present = 1
sensor_Y_32_present = 0
sensor_Y_33_present = 0
sensor_Y_34_present = 0
sensor_Y_35_present = 0