StochSecondOrderSingleSubstrate Class Reference

#include <RateTerm.h>

Inheritance diagram for StochSecondOrderSingleSubstrate:

Collaboration diagram for StochSecondOrderSingleSubstrate:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
unsigned int	getReactants (vector< unsigned int > &molIndex) const
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array. More...
void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)
	StochSecondOrderSingleSubstrate (double k, unsigned int y)
Public Member Functions inherited from ZeroOrder
double	getR1 () const
	Used by Zombie to return rate terms. More...
double	getR2 () const
	Used by Zombie to return rate terms. More...
void	setK (double k)
void	setR1 (double k1)
	Used by Zombie to assign rate terms. More...
void	setR2 (double k2)
	Used by Zombie to assign rate terms. More...
void	setRates (double k1, double k2)
	ZeroOrder (double k)
Public Member Functions inherited from RateTerm
	RateTerm ()
virtual	~RateTerm ()

Private Attributes
const unsigned int	y_

Additional Inherited Members
Static Public Attributes inherited from RateTerm
static const double	EPSILON = 1.0e-6
Protected Attributes inherited from ZeroOrder
double	k_

Detailed Description

The reason for this class is that if we have a single substrate acting in 2nd order, we must account for the removal of one molecule halfway through the reaction. This has a major effect when there is only one molecule to start with: the eventual # would become negative if we didn't do this correction!

Definition at line 434 of file RateTerm.h.

Constructor & Destructor Documentation

StochSecondOrderSingleSubstrate::StochSecondOrderSingleSubstrate ( double  k, unsigned int  y  )

inline

Definition at line 437 of file RateTerm.h.

Referenced by copyWithVolScaling().

            : ZeroOrder( k ), y_( y )
        {;}

Here is the caller graph for this function:

Member Function Documentation

RateTerm* StochSecondOrderSingleSubstrate::copyWithVolScaling ( double  vol, double  sub, double  prd  ) const

inlinevirtual

Duplicates rate term and then applies volume scaling. Arguments are volume of reference voxel, product of vol/refVol for all substrates: applied to R1 product of vol/refVol for all products: applied to R2

Note that unless the reaction is cross-compartment, the vol/refVol will be one.

Reimplemented from ZeroOrder.

Definition at line 461 of file RateTerm.h.

References ZeroOrder::k_, NA, StochSecondOrderSingleSubstrate(), and y_.

        {
            double ratio = sub * vol * NA;
            return new StochSecondOrderSingleSubstrate( k_ / ratio, y_ );
        }

Here is the call graph for this function:

unsigned int StochSecondOrderSingleSubstrate::getReactants ( vector< unsigned int > &  molIndex ) const

inlinevirtual

This function finds the reactant indices in the vector S. It returns the number of substrates found, which are the first entries in molIndex. The products are the remaining ones. Note that it does NOT find products for unidirectional reactions, which is a bit of a problem.

Reimplemented from ZeroOrder.

Definition at line 447 of file RateTerm.h.

References y_.

                                                                           {
            molIndex.resize( 2 );
            molIndex[0] = y_;
            molIndex[1] = y_;
            return 2;
        }

double StochSecondOrderSingleSubstrate::operator() ( const double *  S ) const

inlinevirtual

Computes the rate. The argument is the molecule array.

Reimplemented from ZeroOrder.

Definition at line 441 of file RateTerm.h.

References ZeroOrder::k_, and y_.

                                                    {
            double y = S[ y_ ];
            assert( !std::isnan( y ) );
            return k_ * ( y - 1 ) * y;
        }

void StochSecondOrderSingleSubstrate::rescaleVolume ( short  comptIndex, const vector< short > &  compartmentLookup, double  ratio  )

inlinevirtual

This is used to rescale the RateTerm kinetics when the compartment volume changes. This is needed because the kinetics are in extensive units, that is, mol numbers, rather than in intensive units like concentration. So when the volume changes the rate terms change. Each Rate term checks if any of its reactant molecules are affected, and if so, rescales. Ratio is newVol / oldVol

Reimplemented from ZeroOrder.

Definition at line 454 of file RateTerm.h.

References ZeroOrder::k_, and y_.

        {
            if ( comptIndex == compartmentLookup[ y_ ] )
                k_ /= ratio;
        }

Member Data Documentation

const unsigned int StochSecondOrderSingleSubstrate::y_

private

Definition at line 469 of file RateTerm.h.

Referenced by copyWithVolScaling(), getReactants(), operator()(), and rescaleVolume().

---

The documentation for this class was generated from the following file:

• moose-core/ksolve/RateTerm.h