value     description
# Convention:
#   - first line are skipped
#   - comment start with #
#   - first 14 columns are for numbers
#     only a single digit before decimal point
#     a dot is required
#   - old value, line start with ##
#   - optional value, line start with #
#   - heading title, line start and end with ###

0.00000d+00   rand flag (0=use clock,1=use seed)
2.07621d+05   rand seed
#6.00d2        num_records_per_chunk (HDF5 only) !use with 20,000 CRU
2.00d3

### release site configuration ###
1.0d4         N  (number of release site)
#5.0d2  
4.9d1         nR (number of RyR/release site)
7.0d0         nL (number of DHPR/release site)

### simulation settings ###
-8.5d1        V_rest, mV
+1.00d1       V_stim (triggered voltage) mV
-6.51890d0    I_stim (triggered current) uA/cm^2
#0.0d0
0.0d0         t_start (time start) [sec]
#2.50d1        t_end   (time end) [sec]
3.0d1
0.0d0         first_beat I/O (0=No / 1=Yes)
#5.0d0         last_beats I/O (duration)
3.0d1
1.0d0         write_restart_file (0=No / 1=Yes)

1.0d-8        dt_LB [sec]
1.0d-6        dt_UB [sec]
1.0d-1        t_V_stim_start [sec]
1.0d-1        t_V_stim_duration [sec]
0.d0          t_I_stim_start [sec]
5.d-3         t_I_stim_duration [sec]
1.d0          Hz (num. of stimulus per second)
1.0d-3        output_interval (how often data I/O) sec

### initial condition ###
1.02d4        Na_i [uM]
1.43720d5     K_i  [uM]
#9.00000d-02   Ca_myo  [uM]
1.00000d-01 
#9.0000d-02
1.00000d+03   Ca_nsr  [uM]

### constant ###
9.6485d4      F (Faraday)  [C/mol]
8.314d3       R (universal gas) [mJ mol-1 K-1]
3.10d2        T (temperature) [K]
1.4d5         Na_o (ion concentration) [uM]
1.8d3         Ca_o uM
5.4d3         K_o  uM

### volume [pL] ### based on Vcell = 36(pL)
1.8d1         V_myo_T [pL]  (50%)
1.152d0       V_nsr_T [pL] (3.2%)
#1.08d0        
1.08d-1       V_jsr_T [pL] (0.3%)
#9.0d-2 
#1.70d-1
2.7d-2        V_ds_T [pL]
### buffering parameters ###xo
0.1d0         beta_ds   (buffering fraction)
1.0d0         beta_nsr
1.23000d+02   B_myoT (total buffer concentration) [uM]
1.40000d+04   B_jsrT [uM]
9.60000d-01   Km_myo   [uM]
6.38000d+02   Km_jsr   [uM]
1.40000d+02   B_htrpnT   #Total troponin conc. (uM)
2.37000d+00   kon_htrpn  #troponin Ca on rate (1/(uM*s))
3.20000d-02   koff_htrpn #troponin Ca off rate (1/s)

### Calcium diffusion (velocity) ###
#5.0d0         v_refill_T
2.5d0        
#3.0d2         v_efflux_T
2.5d2
0.0d0         v_leak
5.64279d1     v_ryr_T (based on 7x7 cluster) [1/sec] (0.2pA)
#5.078890d1      (0.18pA)
#4.908890d1      (0.17?pA)
#4.79673d1      (0.17pA)
#4.51457d1      (0.16pA)
#4.23209134d1   (0.15pA)
#2.3589d-4     P_dhpr_T (permeability), 10^-6 L/sec
1.87213d-4      (idhpr=0.25nA)
#1.1233d-4        (idhpr=0.15nA)
5.0d-2        prcent_ryr-nj 
1.0d-1        prcent_dhpr-nj

### SERCA parameters ###
1.50d2        Ap  [uM]
0.91d3        Kp_myo [uM]
#2.24d3        Kp_nsr [uM]
1.90d3
#2.02d3


### Membrane conductance parameters ###
#7.36351d-04   g_bCa   mS/uF (use with cmyo=0.09)
8.6918d-4     g_bCa  (use with cmyo=0.1)
1.3d1         g_Na
0.2d0         g_K1
2.10500d-02   g_Kss (0.5xgKss)
#4.21d-2      g_Kss
0.0798d0      g_Ktof
3.14500d-02   g_Ktos (0.5xgKtos)
#6.29d-2      g_Ktos
1.0666d-4     g_bNa
0.0d0         g_bK
1.534d-4      Am (cell surface), cm^2
1.0d0         Csc (specific membrane capacitance) uF/cm^2

### PMCA and NCX rates ###
0.75d0        I_pmca_bar, uA/uF
1.0d3         I_ncx_bar
0.88d0        I_NaK_bar

2.2d0         eta RyR (hill coefficient)
#2.3d0           (more stabilizing ryr at rest)
2.00000d+00   eta LCC
0.0714d0      Ej (a*) (7x7 RyR cluster)
#-9.20000d-01  Ecc
-1.02200d-00  Ecc
#-8.50000d-01  Eoo
-1.45000d-00  Eoo
2.30000d-04   k_jsr0   uM^-1
2.00000d-02   k_jsr1   unitless
2.00000d+00   V_theta1
6.50000d+00   V_sigma1
0.00000d+00   V_theta2
0.00000d+00   V_sigma2

############### SPATIAL DATA ###############
# cell size (um)
1.00d2        x_length
2.00d1        y_length
1.80d1        z_length
#0.1d0         dX (um)
#0.1d0         dY 
#0.1d0         dZ 
0.2d0         dX (um)
0.2d0         dY 
0.2d0         dZ 

# diffusion coefficient
2.50d2        Dmyo_x (um^2/sec)
2.50d2        Dmyo_y
2.50d2        Dmyo_z
6.00d1        Dnsr_x
6.00d1        Dnsr_y
6.00d1        Dnsr_z

2.000d1       Ddye (x,y,z) (um^2/s)
5.000d1       F_T (uM)
8.000d1       kon_F (uM^-1.s^-1)
7.200d1       koff_F (s^-1)



# END

