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

Text File | 2000-03-03 | 1KB | 49 lines

@CLASSNAME: CatalyzedMassActionReactor

@BASECLASS: FluxReactor
@AUTHOR: Kouichi Takahashi
@EMAIL: [e-mail]
@DATE: 29/6/1999

%VERSION: ecs-v09, 0.1

@BRIEF_DESCRIPTION: Reaction rate directrly depends on the
concentrations of the catalyst and substances

@DESCRIPTION: A reactor class in which general mass action equation is
embeded.  A 'catalyst' is defined as a molecular species that does not
change itself but affects reaction rate following
general mass action low.

Velocity is calculated as a product of the catalyst
and substrates concentration, and a kinetic constant (see Equation).

@EQUATION:$$v=k \prod_{i=0}^n [S_i]^{c_i}$$

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

%PARAMETER: k, Float, ,  Velocity Constant

@REACT_FUNC:
  Float velocity = k*N_A;
  velocity *= _substrateList[0]->substance().supersystem()->volume();
  velocity *= catalyst(0)->quantity();

  int i = numSubstrate();
  do{
    --i;
    // calculate velocity
    int j = substrate(i)->coefficient();
    do{
      j--;
      velocity *= substrate(i)->concentration();
      } while(j != 0);
  } while(i != 0);


  // now we have change in number of molecules per second

  process(velocity);