- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-06-10 14:57:36+12:00
- Desc:
- Removing tension component from CaTRPN reaction
- Permanent Source URI:
- https://models.cellml.org/workspace/7fb/rawfile/8b7889fe7e9032b182e293133b5b10fa44adcd01/parameter_finder/kinetic_parameters_crossbridge_TRPN.py
# crossbridge model from S.Land et al 2017
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))
rs = 0.25
rw = 0.5
k_TRPN = 100 # [=] 1/s
k_TRPN_on = k_TRPN/pow(2.5e-3,2) # [=] 1/mM^2.s #100e3 # [=] 1/mM.s
k_TRPN_off = k_TRPN #200 # [=] 1/s
kBUm = 1e3 # [=] 1/s
kBUp = kBUm/(1-rs-((1-rs)*rw)) # [=] 1/s
kUWp = 26 # [=] 1/s
kUWm = 170 # [=] 1/s
kWSp = 4 # [=] 1/s
kWSm = smallReverse # [=] 1/s
kSUp = 18 # [=] 1/s
# use detailed balance to find kSUm
if True:
kSUm = kUWp*kWSp*kSUp/(kUWm*kWSm)
else:
kSUm = smallReverse # [=] 1/s
k_kinetic = [k_TRPN_on,kBUp,kUWp,kWSp,kSUp,
k_TRPN_off,kBUm,kUWm,kWSm,kSUm]
# 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)
