bioinformatics.org/bioinformatics.org_software.tar/www.bioinformatics.org/download/ecell2/ecell220setup.exe/{app}/standard/STDR/RandomBiUniReactor.rd

Text File | 2000-03-03 | 3KB | 54 lines

@CLASSNAME:RandomBiUniReactor
@BASECLASS:FluxReactor
@BRIEF_DESCRIPTION: Random Bi Uni reaction system

%VERSION: ecs-v09, 0.1
@DATE: 30/6/1999

@AUTHOR: Masayuki Okayama
@EMAIL: [e-mail]

@DESCRIPTION: A reactor class for a random bireactant system in the Bi Uni direction.

Velocity is derived algebraically from steady-state assumptions and
the equation\\
is derived using the schematic method of King and Altman.

@EQUATION:$$v=\frac{M(P)\:[E]}{Den}$$\\
Where\\
$M(P)=k_{-1}k_{-2}k_{-5}(-k_{-3}-k_{-4})[P]+k_{+5}(k_{+1}k_{-2}k_{+3}+k_{-1}k_{+2}k_{+4})[S_{1}][S_{2}]-k_{-1}k_{-3}k_{+4}k_{-5}[S_{1}][P]-k_{-2}k_{+3}k_{-4}k_{-5}[S_{2}][P]+k_{+1}k_{+3}k_{+4}k_{+5}[S_{1}]^{2}[S_{2}]+k_{+2}k_{+3}k_{+4}k_{+5}[S_{1}][S_{2}]^{2}$\\
Where\\
$Den=k_{-1}k_{-2}(k_{-3}+k_{-4}+k_{+5})+(k_{+1}k_{-2}k_{-3}+k_{+1}k_{-2}k_{-4}+k_{+1}k_{-2}k_{+5}+k_{-1}k_{-3}k_{+4}+k_{-1}k_{+4}k_{+5})[S_{1}]+(k_{-1}k_{+2}k_{-3}+k_{-1}k_{+2}k_{-4}+k_{-1}k_{+2}k_{+5}+k_{-2}k_{+3}k_{-4}+k_{-2}k_{+3}k_{+5})[S_{2}]+k_{-5}(k_{-1}k_{-2}+k_{-1}k_{-4}+k_{-2}k_{-3})[P]+(k_{+1}k_{-2}k_{+3}+k_{+1}k_{+3}k_{-4}+k_{-1}k_{+2}k_{+4}+k_{+2}k_{-3}k_{+4}+k_{+3}k_{+4}k_{+5})[S_{1}][S_{2}]+k_{+1}k_{+4}(k_{-3}+k_{+5})[S_{1}]^{2}+k_{+2}k_{+3}(k_{-4}+k_{+5})[S_{2}]^{2}+k_{+4}k_{-5}(k_{-1}+k_{-3})[S_{1}][P]+k_{+3}k_{-5}(k_{-2}+k_{-4})[S_{2}][P]+k_{+1}k_{+3}k_{+4}[S_{1}]^{2}[S_{2}]+k_{+2}k_{+3}k_{+4}[S_{1}][S_{2}]^{2}+k_{+3}k_{+4}k_{-5}[S_{1}][S_{2}][P]$\\

%SUBSTANCE: Substrate, 2, 2,
%SUBSTANCE: Product, 1, 1,
%SUBSTANCE: Catalyst, 1, 1,

%PARAMETER:k1, Float,
%PARAMETER:k_1, Float,
%PARAMETER:k2, Float,
%PARAMETER:k_2, Float,
%PARAMETER:k3, Float,
%PARAMETER:k_3, Float,
%PARAMETER:k4, Float,
%PARAMETER:k_4, Float,
%PARAMETER:k5, Float,
%PARAMETER:k_5, Float,

@REACT_FUNC:

Float velocity = catalyst(0)->quantity();
Float S1= substrate(0)->concentration();
Float S2= substrate(1)->concentration();
Float P= product(0)->concentration();

Float MP = k_1*k_2*k_5*(k_3-k_4)*P+k5*(k1*k_2*k3+k_1*k2*k4)*S1*S2-k_1*k_3*k4*k_5*S1*P-k_2*k3*k_4*k_5*S2*P+k1*k3*k4*k5*pow(S1,2)*S2+k2*k3*k4*k5*S1*pow(S2,2);
Float Den= k_1*k_2*(k_3+k_4+k5)+(k1*k_2*k_3+k1*k_2*k_4+k1*k_2*k5+k_1*k_3*k4+k_1*k4*k5)*S1+(k_1*k2*k_3+k_1*k2*k_4+k_1*k2*k5+k_2*k3*k_4+k_2*k3*k5)*S2+k_5*(k_1*k_2+k_1*k_4+k_2*k_3)*P+(k1*k_2*k3+k1*k3*k_4+k_1*k2*k4+k2*k_3*k4+k3*k4*k5)*S1*S2+k1*k4*(k_3+k5)*pow(S1,2)+k2*k3*(k_4+k5)*pow(S2,2)+k4*k_5*(k_1+k_3)*S1*P+k3*k_5*(k_2+k_4)*S2*P+k1*k3*k4*pow(S1,2)*S2+k2*k3*k4*S1*pow(S2,2)+k3*k4*k_5*S1*S2*P;

velocity *= MP;
velocity /= Den;

process(velocity);