- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-26 10:34:53+12:00
- Desc:
- using constants_BG.cellml import
- Permanent Source URI:
- https://models.cellml.org/workspace/6ba/rawfile/47694b8f711b353699c389455b6ef97fa61a71b8/MATLAB/kinetic_parameters.m
% B1AR module
function [k_kinetic, N_cT, K_C] = kinetic_parameters(M, include_type2_reactions, num_cols)
% Set the kinetic rate constants.
% original model had reactions that omitted enzymes as substrates e.g. BARK
% convert unit from 1/s to 1/uM.s by dividing by conc of enzyme
% all reactions were irreversible, made reversible by letting kr ~= 0
% CONVERT TO fM
% oncentration of BARK = 0.6uM (crude approx from litsearch, for GRK)
bigNum = 1e6;
fastKineticConstant = bigNum;
smallReverse = fastKineticConstant/(bigNum^2);
u_to_f = 1e9;
cBARK = 0.6*u_to_f; %fM
cPKACI = 0.0587898478276673*u_to_f; %fM
kB11p = 1.1e-3 / cBARK; % 1/fM.s
kB11m = 2.2e-3; % 1/s
kB12p = fastKineticConstant;%1/s
kB12m = smallReverse; % 1/fM.s
kB21p = kB11p; % 1/fM.s
kB21m = kB11m; % 1/s
kB22p = fastKineticConstant;%1/s
kB22m = smallReverse; % 1/fM.s
kP1p = 2.2e-3/ cPKACI; % 1/fM.s (kp_kam)
kP1m = smallReverse; % 1/s
kP2p = fastKineticConstant; % 1/s
kP2m = 3.6e-3/u_to_f; % 1/fM.s (kp_kap)
% detailed balance for kP2p
kP2p = kP2m*kP1m/kP1p;
k_kinetic = [
kB11p, kB12p, kB21p, kB22p, kP1p, kP2p,...
kB11m, kB12m, kB21m, kB22m, kP1m, kP2m
]';
% CONSTRAINTS
N_cT = zeros(1,size(M,2));
% substrate B1ARp is in eqlm with product B1ARtot
N_cT(1,num_cols + 7) = 1;
N_cT(1,num_cols + 8) = -1;
Kc = ones(1,size(N_cT,1));
return
