Location: BG_TRPN @ 97c70a3d4262 / parameter_finder / kinetic_parameters_TRPN.py

Author:

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

Date:

2025-03-28 12:56:58+13:00

Desc:

Adding ml

Permanent Source URI:

https://staging.physiomeproject.org/workspace/7a9/rawfile/97c70a3d4262d1818e2bc7d2e5e1f5bf81ebad8d/parameter_finder/kinetic_parameters_TRPN.py

# TRPN troponin module
# rates are based on Niederer et al 2006

# assuming that k_off is constant, disregarding dependency on Tension, for now i.e. let Tension = 0

import numpy as np 

def kinetic_parameters(M, include_all_reactions, dims, V):
    # Set the kinetic rate constants.
    # all reactions are reversible. no closed loops.

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

    # CONVERT TO fM 
    bigNum = 1e6
    fastKineticConstant = bigNum
    smallReverse = fastKineticConstant/(pow(bigNum,2))

    k_on = 100e3 # [=] 1/mM.s
    k_off = 200  # [=] 1/ms

    k_kinetic = [k_on, k_off]


    # CONSTRAINTS
    N_cT = []
    K_C = []
    
    # volume vector
    W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))

    return (k_kinetic, [N_cT], K_C, W)