Location: BG_SOC @ 38820a34c0a0 / parameter_finder / kinetic_parameters_SOC.py

Author:

Shelley Fong <sfon036@UoA.auckland.ac.nz>

Date:

2025-07-24 11:01:15+12:00

Desc:

Finding new param, adding V_mem argument, updating Ca conc

Permanent Source URI:

https://staging.physiomeproject.org/workspace/d41/rawfile/38820a34c0a013adb80420c96ba30c837b9e123b/parameter_finder/kinetic_parameters_SOC.py

## kinetic parameters for the LCC channel, adapted from Pan et al
## in the format of the other channels in the BG library

## hardcode the parameters from Pan's optimisation for ionic permeability and gate variables directly
import numpy as np 

def kinetic_parameters(M, include_type2_reactions, dims, V):

    # Set the kinetic rate constants

    num_cols = dims['num_cols']
    num_rows = dims['num_rows']

    # constants are stored in V
    F = V['F']
    N_A = V['N_A']

    G_GHK = 5.0759e-09 # from matlab fitting

    # convert    to    permeability
    P_SOC = G_GHK / F * 1e12 #Unit    pL / s
    channel_k = P_SOC #/ x_Cab_channel

    kf =[channel_k]
    kr =[channel_k]
    k_kinetic = kf + kr

    # CONSTRAINTS
    N_cT = []
    K_C = []

    # volume vector
    # [ outside / inside / ER ]
    W = [1] * num_cols + [V['V_o'], V['V_myo'], V['V_ER']]

    return (k_kinetic, N_cT, K_C, W)