- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-11-17 10:27:24+13:00
- Desc:
- Using sympy for rational nullspace
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6e3/rawfile/4eff70506ca8336d6d1ba7a7ee1f10fba9004650/parameter_finder/kinetic_parameters_RyR.py
# linalg for Ryanodine channel: gated by Ca, and allowing passage of Ca.
import numpy as np
def kinetic_parameters(M, include_type2_reactions, dims, Vol):
num_cols = dims['num_cols']
num_rows = dims['num_rows']
R = 8.3143
T = 310
F = 96485
z = 2
N_A = 6.022e23
x_ryr = 1e15*50e3/N_A # fmol Hinch: 50000 units
c_di = 1.7374E-04 # mM
c_sr = 5.5545E-01 # mM
# channel conductance (without gating)
k_ryr = 25 # 1/ms (Shannon/Stern value) WRONG UNITS FOR A CHANNEL
g_ryr = 103 # pS
E_Ca = (R*T/(z*F))*np.log(c_di/c_sr)
# finding permeability value by setting I_ohmic = I_ghk:
# P [=] pL/s (permeability)
V = -E_Ca
P_ryr = 1e3*(V - E_Ca)*g_ryr*R*T*(1-np.exp(-z*F*V/(R*T)))/(((z*F)^2)*(c_sr-(c_di*np.exp(-z*F*V/(R*T)))))
k_ryr = P_ryr / x_ryr # 1/mM.s both fwd and bwd
# gate transitions
ko = 35e3 # 1/(mM2.s)
ki = 500 # 1/(mM.s)
kim = 5 # 1/s
kom = 60 # 1/s
# rxnID: [RyR OC CCI CII IO]
# set up ensures detailed balance already
kf = [k_ryr, kom, ki, ko, kim]
kr = [k_ryr, ko, kim, kom, ki]
k = kf + kr
N_cT = []
K_C = []
# volume vector
W = [1]*num_cols + [Vol['V_SR']] + [Vol['V_di']] + [1]*4
return (k, [N_cT], K_C, W)
