virtual void fire()
{
Real hkrd =
( 1 + ( S1.getMolarConc() / KiMgATP ) +
( (S0.getMolarConc() * 7 / 3) / KiGlc ) +
( ( S1.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KiGlc * KmMgATP ) ) +
( P1.getMolarConc() / KiMgADP ) +
( P0.getMolarConc() / KiGlc6P ) +
( ( P1.getMolarConc() * P0.getMolarConc() ) / ( KiGlc6P * KmMgADP ) ) +
( ( E1.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiB23PG * KiGlc ) ) +
( ( E2.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiGlc16P2 * KiGlc ) ) +
( ( P0.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiGlc6P * KiGlc ) ) +
( ( E3.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiGSH * KiGlc ) ) );
// fix me: * voli?
Real GG = E3.getMolarConc()/E4.getMolarConc();
Real velocity =
(GG/(K_GSSG + GG)) * ( HK / hkrd *
( ( theKcatf * (S0.getMolarConc() * 7 / 3) * S1.getMolarConc() ) /
( KiGlc * KmMgATP ) -
( theKcatr * P0.getMolarConc() * P1.getMolarConc() ) /
( KiGlc6P * KmMgADP ) ) );
//velocity = velocity * getSuperSystem()->getSize() * N_A * ( 20.0 / 7.0 );
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux( velocity );
}
virtual void fire(){
Real GG = E3.getMolarConc()/E4.getMolarConc();
Real velocity = GG/(K_GSSG + GG);
Real ActCo = E0.getVariable()->getValue();
if( ActCo == 0 ){
velocity = ConstAct;
}
else{
Real NADP = 1000000 * S0.getVariable()->getMolarConc();
Real G6P = 1000000 * S1.getVariable()->getMolarConc();
Real NADPH = 1000000 * P1.getVariable()->getMolarConc();
Real ATP = 1000000 * E1.getVariable()->getMolarConc();
Real DPG = 1000000 * E2.getVariable()->getMolarConc();
Real L = 1 + G6P / K_G6P;
Real M = 1 + NADP * L / K_NADP + NADPH / K_NADPH + ATP
/ K_ATP + DPG / K_DPG;
velocity *= Vm * ( NADP * G6P / ( K_NADP * K_G6P ) ) / M;
velocity *= ActCo / 1000 / 1000000;
velocity *= N_A * S0.getVariable()->getSuperSystem()->getSize();
}
setFlux( velocity );
}
virtual void fire(){
Real PO2 = S0.getVariable()->getValue();
Real dammy = P0.getVariable()->getValue();
Real TAG = E0.getVariable()->getValue();
Real pk0;
Real pk1;
if ( TAG == 0 )
{
pk1=0;
pk0=k0;
}
else
{
pk0=0;
pk1=k1;
}
Real velocity = ((pk0 - pk1)*(PO2-base));
setFlux(velocity);
}
virtual void fire(){
Real PO2 = S0.getVariable()->getValue();
Real dammy = P0.getVariable()->getValue();
Real TAG = E0.getVariable()->getValue();
Real pk0;
Real pk1;
if ( TAG == 0 )
{
pk1=0;
pk0=k0;
}
else
{
pk0=0;
pk1=k1;
}
// std::cout << "k0=" << k0 << std::endl;
// std::cout << "k1=" << k1 << std::endl;
// std::cout << "PO2=" << PO2 << std::endl;
// std::cout << "dammy=" << dammy << std::endl;
// Real velocity = (pk0 * (PO2-base) - pk1 * dammy);
Real velocity = ((pk0 - pk1)*(PO2-base));
setFlux(velocity);
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real delta1 = (1.0 + F6P->getMolarConc()*1000.0 / KPFK_F6P) * (1.0 + ATP->getMolarConc()*1000.0 / KPFK_ATP)+ ADP->getMolarConc()*1000.0 / KPFK_ADP + FBP->getMolarConc()*1000.0 / KPFK_FBP * (1.0 + ADP->getMolarConc()*1000.0 / KPFK_ADP);
Real delta2 = (1.0 + F6P->getMolarConc()*1000.0 / KPFK_F6P2) * (1.0 + ATP->getMolarConc()*1000.0 / KPFK_ATP2)+ ADP->getMolarConc()*1000.0 / KPFK_ADP2 + FBP->getMolarConc()*1000.0 / KPFK_FBP2 * (1.0 + ADP->getMolarConc()*1000.0 / KPFK_ADP2);
Real alpha = KPFK_F6P * KPFK_ATP / KPFK_F6P2 / KPFK_ATP2;
Real L = Lo_PFK * pow(((1.0+ATP->getMolarConc()*1000.0/KPFK_iATP) / (1.0 + d_PFK * ATP->getMolarConc()*1000.0/KPFK_iATP)) * ((1.0 + e_PFK * AMP->getMolarConc()*1000.0/KPFK_aAMP) / (1.0 + AMP->getMolarConc()*1000.0/KPFK_aAMP)), 4);
Real VPFK_maxr = VPFK_maxf->getValue() * KPFK_ADP * KPFK_FBP / KPFK_ATP / KPFK_F6P / KPFK_eq;
Real PFK_a = (1.0 + alpha * L * pow(delta2/delta1, 3))*(VPFK_maxf->getValue() * ATP->getMolarConc()*1000.0 * F6P->getMolarConc()*1000.0 /(KPFK_ATP * KPFK_F6P) - VPFK_maxr * ADP->getMolarConc()*1000.0 * FBP->getMolarConc()*1000.0 /(KPFK_ADP * KPFK_FBP));
Real PFK_b = delta1 * (1.0 + L * pow(delta2/delta1, 4));
setFlux( GX->getValue() * _SizeN_A * PFK_a / PFK_b / 60000.0 /1000.0);
// setFlux(PFK_a / PFK_b );
//V_PFK.setValue(PFK_a / PFK_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire(){
Real velocity = 1;
Real ActCo = E0.getVariable()->getValue();
if( ActCo == 0 ){
velocity = ConstAct;
}
else{
Real IN = 1000 * S0.getVariable()->getMolarConc();
Real EX = 1000 * P0.getVariable()->getMolarConc();
velocity = Vm * ( ( IN / ( Km + IN ) )- ( EX / ( Km + EX ) ) );
velocity *= N_A * S0.getVariable()->getSuperSystem()->getSize();
velocity *= ActCo / 1000 / 1000 / 3600;
velocity *= SW;
}
setFlux( velocity );
}
virtual void fire(){
Real velocity = 1;
Real ActCo = E0.getVariable()->getValue();
if( ActCo == 0 ){
velocity = ConstAct;
}
else{
Real A = 1000 * S0.getVariable()->getMolarConc();
Real B = 1000 * S1.getVariable()->getMolarConc();
Real C = 1000 * S2.getVariable()->getMolarConc();
Real M = A * B * C / (alpha * KmA * KmB * KmC);
Real N = 1 + A / KmA + A * B / (KmA * KmB) + A * C / (KmA * KmC) +
A * B * C/ (alpha * KmA * KmB * KmC);
velocity *= Vmf * N_A * S0.getVariable()->getSuperSystem()->getSize();
velocity *= M / N;
velocity *= ActCo / 1000 / 1000 / 3600;
}
setFlux( velocity );
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VGPA_maxr = VGPA_maxf->getValue() * KGPA_GLYb * KGPA_iG1P / KGPA_iGLYf / KGPA_Pi / KGPA_eq;
Real GPA_a= VGPA_maxf->getValue() * (GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / KGPA_iGLYf / KGPA_Pi ) - VGPA_maxr * (GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0 / KGPA_GLYb / KGPA_iG1P);
Real GPA_b= 1.0 + GLY->getMolarConc()*1000.0 / KGPA_iGLYf + Pi->getMolarConc()*1000.0 / KGPA_iPi + GLY->getMolarConc()*1000.0 / KGPA_iGLYb + G1P->getMolarConc()*1000.0 / KGPA_iG1P + GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGPA_GLYf * KGPA_iPi) + GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0 /(KGPA_GLYb * KGPA_iG1P) ;
Real V_GPA = GPA_a / GPA_b;
Real VGPB_maxr = VGPB_maxf->getValue() * KGPB_iGLYb * KGPB_G1P / KGPB_iGLYf / KGPB_Pi / KGPB_eq;
Real GPB_a = (pow(AMP->getMolarConc()*1000.0, nH_GPB)/ KGPB_AMP) * (VGPB_maxf->getValue() * (GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 /(KGPB_iGLYf * KGPB_Pi)) - VGPB_maxr * (GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0/(KGPB_iGLYb * KGPB_G1P)));
Real GPB_b = (1.0 + pow(AMP->getMolarConc()*1000.0, nH_GPB)/ KGPB_AMP) * ( 1.0 + GLY->getMolarConc()*1000.0 / KGPB_iGLYf + Pi->getMolarConc()*1000.0 / KGPB_iPi + GLY->getMolarConc()*1000.0 / KGPB_iGLYb + G1P->getMolarConc()*1000.0 / KGPB_iG1P + GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGPB_iGLYf * KGPB_Pi) + GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0 /(KGPB_iGLYb * KGPB_G1P) );
Real V_GPB = GPB_a / GPB_b;
setFlux( GX->getValue() * _SizeN_A * ( V_GPA * frac_a->getValue() + V_GPB * frac_b->getValue()) / 60000.0 / 1000.0);
// setFlux( V_GPA * frac_a->getValue() + V_GPB * frac_b->getValue());
// setFlux(GPB_a / GPB_b );
// setFlux(GPA_a / GPA_b );
//V_GPA.setValue(GPA_a / GPA_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire()
{
Real L = ( pow( pow( 10, -1 * E0.getValue() ) / Ka, n ) *
pow( 1 + E1.getMolarConc() / KTATP, 4 ) *
pow( 1 + E2.getMolarConc() / KTMg, 4 ) *
pow( 1 + E3.getMolarConc() / KTB23PG, 4 ) ) /
( pow( 1 + ( S0.getMolarConc() / KmFru6P ) + ( P0.getMolarConc() / KmFru16P2 ), 4 ) *
pow( 1 + E4.getMolarConc() / KRAMP, 4 ) *
pow( 1 + E5.getMolarConc() / KRPhos, 4 ) *
pow( 1 + E6.getMolarConc() / KRGlc16P2, 4 ) );
Real pfkrd = 1 + ( S0.getMolarConc() / KmFru6P ) +
( S1.getMolarConc() / KmMgATP ) +
( ( S0.getMolarConc() * S1.getMolarConc() ) / ( KmFru6P * KmMgATP ) ) +
( P0.getMolarConc() / KmFru16P2 ) +
( P1.getMolarConc() / KmMgADP ) +
( ( P0.getMolarConc() * P1.getMolarConc() ) / ( KmFru16P2 * KmMgADP ) );
Real velocity = ( C0.getMolarConc() / ( ( 1 + L ) * pfkrd ) ) *
( ( kcatf * S0.getMolarConc() * S1.getMolarConc() ) / ( KmFru6P * KmMgATP ) -
//note: use book model.
( kcatf * P0.getMolarConc() * P1.getMolarConc() ) / ( KmFru16P2 * KmMgADP ) );
velocity = velocity * getSuperSystem()->getSize() * N_A * E7.getValue()/1000;
Real GG = E8.getMolarConc()/E9.getMolarConc();
velocity *= GG/(K_GSSG + GG);
setFlux( velocity );
}
virtual void fire()
{
Real aVelocity( k );
aVelocity *= C0.getValue();
setFlux( aVelocity );
}
virtual void fire()
{
Real velocity = k8* S0.getMolarConc() - k9 * P0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux( velocity );
}
virtual void fire()
{
Real E( C0.getMolarConc() );
Real V( -1 * V1 * E );
V /= K1 + E;
V *= 1E-018 * N_A;
setFlux( V );
}
virtual void fire()
{
Real velocity = theK1 * S0.getMolarConc() * S1.getMolarConc() - k2 * P0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
velocity = velocity * E1.getValue() / 1000;
setFlux( velocity );
}
virtual void fire()
{
Real velocity = Kma * S0.getMolarConc() -
Kmd * P0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
velocity = velocity * E0.getValue() / 1000;
setFlux( velocity );
}
virtual void fire()
{
Real velocity = k * S0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
if(velocity < 0)
{
velocity = 0;
}
setFlux( velocity );
}
virtual void fire()
{
Real pgmrd = 1 + ( S0.getMolarConc() / KmP3GA ) +
( P0.getMolarConc() / KmP2GA );
Real velocity = ( PGM / pgmrd ) *
( ( ( kcatf * S0.getMolarConc() ) / KmP3GA ) -
( ( kcatr * P0.getMolarConc() ) / KmP2GA ) );
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux( velocity );
}
virtual void fire()
{
const Real S( S0.getVariable()->getMolarConc() );
const Real P( P0.getVariable()->getMolarConc() );
const Real KmP_S( KmP * S );
const Real KmS_P( KmS * P );
Real velocity( KcF * KmP_S );
velocity -= KcR * KmS_P;
velocity *= C0.getVariable()->getValue();
velocity /= KmS_P + KmP_S + KmSP;
setFlux( velocity );
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VPGLM_maxr = VPGLM_maxf->getValue() * KPGLM_G6P / KPGLM_G1P / KPGLM_eq;
Real PGLM_a = VPGLM_maxf->getValue() * G1P->getMolarConc()*1000.0 / KPGLM_G1P - VPGLM_maxr * G6P->getMolarConc()*1000.0 / KPGLM_G6P;
Real PGLM_b = 1.0 + G1P->getMolarConc()*1000.0 / KPGLM_G1P + G6P->getMolarConc()*1000.0 / KPGLM_G6P;
setFlux( GX->getValue() * _SizeN_A * PGLM_a / PGLM_b / 60000.0 /1000.0);
// setFlux(PGLM_a / PGLM_b );
//V_PGLM.setValue(PGLM_a / PGLM_b / unit);
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire()
{
double currTime(getStepper()->getCurrentTime());
//std::cout << theVariableReferenceVector[0].getVariable()->getID() << std::endl;
if(currTime > 1000)
{
double currValue(theVariableReferenceVector[0].getValue());
double diffValue(currValue-prevValue);
if(diffValue*diffValue >=
theVariableReferenceVector[0].getCoefficient()*
theVariableReferenceVector[0].getCoefficient()
&& currValue != prevValue)
{
double interval(currTime-prevTime);
totalInterval += interval;
++intervalCnt;
std::cout << currTime << " " << getID() << " averageInterval:"
<< totalInterval/intervalCnt << std::endl;
prevTime = currTime;
prevValue = currValue;
}
}
else
{
prevTime = currTime;
}
Real velocity( k * N_A );
velocity *= getSuperSystem()->getSize();
for( VariableReferenceVector::const_iterator s(
theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
VariableReference const& aVariableReference( *s );
Integer aCoefficient( aVariableReference.getCoefficient() );
do
{
++aCoefficient;
velocity *= aVariableReference.getVariable()->getMolarConc();
}
while( aCoefficient != 0 );
}
setFlux(velocity);
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
// Real VPGI_maxf = VPGI_maxr * KPGI_G6P * KPGI_eq / KPGI_F6P;
Real VPGI_maxf = VPGI_maxr->getValue() * KPGI_G6P * KPGI_eq / KPGI_F6P;
// Real PGI_a = VPGI_maxf * G6P->getValue() / KPGI_G6P - VPGI_maxr * F6P->getValue() / KPGI_F6P;
Real PGI_a = VPGI_maxf * G6P->getMolarConc()*1000.0 / KPGI_G6P - VPGI_maxr->getValue() * F6P->getMolarConc()*1000.0 / KPGI_F6P;
Real PGI_b = 1.0 + G6P->getMolarConc()*1000.0 / KPGI_G6P + F6P->getMolarConc()*1000.0 / KPGI_F6P;
setFlux( GX->getValue() * _SizeN_A * PGI_a / PGI_b / 60000.0 / 1000.0);
// setFlux(PGI_a / PGI_b );
//V_PGI.setValue(PGI_a / PGI_b / unit);
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
void MassActionProcess::fire()
{
if(theSpace == 0)
{
Species* aSpecies(NULL);
for(VariableReferenceVector::iterator
i(theVariableReferenceVector.begin());
i != theVariableReferenceVector.end(); ++i)
{
Variable* aVariable((*i).getVariable());
aSpecies = theSpatiocyteStepper->getSpecies(aVariable);
if(aSpecies != NULL)
{
break;
}
}
if(aSpecies->getIsVolume())
{
theSpace = aSpecies->getCompartment()->actualVolume;
cout << "Mass Action Volume:" << theSpace << endl;
}
else
{
theSpace = aSpecies->getCompartment()->actualArea;
cout << "Mass Action Area:" << theSpace << endl;
}
}
double velocity(k);
velocity *= theSpace;
for(VariableReferenceVector::iterator
s(theVariableReferenceVector.begin());
s != theZeroVariableReferenceIterator; ++s)
{
VariableReference aVariableReference(*s);
long int aCoefficient(aVariableReference.getCoefficient());
do
{
++aCoefficient;
velocity *= aVariableReference.getVariable()->getValue()/theSpace;
}
while(aCoefficient != 0);
}
setFlux(velocity);
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VGAPDH_maxr = VGAPDH_maxf->getValue() * KGAPDH_13BPG * KGAPDH_NADH / KGAPDH_GAP / KGAPDH_NAD / KGAPDH_Pi / KGAPDH_eq;
Real GAPDH_a = VGAPDH_maxf->getValue() * GAP->getMolarConc()*1000.0 * NAD->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGAPDH_GAP * KGAPDH_NAD * KGAPDH_Pi) - VGAPDH_maxr * BPG13->getMolarConc()*1000.0 * NADH->getMolarConc()*1000.0 / (KGAPDH_13BPG * KGAPDH_NADH);
Real GAPDH_b = 1.0 + GAP->getMolarConc()*1000.0 / KGAPDH_GAP + NAD->getMolarConc()*1000.0 / KGAPDH_NAD + Pi->getMolarConc()*1000.0 / KGAPDH_Pi + GAP->getMolarConc()*1000.0 * NAD->getMolarConc()*1000.0 / (KGAPDH_GAP * KGAPDH_NAD) + GAP->getMolarConc()*1000.0 * NAD->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGAPDH_GAP * KGAPDH_NAD * KGAPDH_Pi) + BPG13->getMolarConc()*1000.0 / KGAPDH_13BPG + NADH->getMolarConc()*1000.0 / KGAPDH_NADH + BPG13->getMolarConc()*1000.0 * NADH->getMolarConc()*1000.0/(KGAPDH_13BPG * KGAPDH_NADH);
setFlux( GX->getValue() * _SizeN_A * GAPDH_a / GAPDH_b / 60000.0 /1000.0);
// setFlux(GAPDH_a / GAPDH_b );
//V_GAPDH.setValue(GAPDH_a / GAPDH_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire(){
Real velocity = 1;
Real ActCo = E0.getVariable()->getValue();
Real PYR = 1000000 * S0.getVariable()->getMolarConc();
Real NADH = 1000000 * S1.getVariable()->getMolarConc();
Real LAC = 1000000 * P0.getVariable()->getMolarConc();
Real NAD = 1000000 * P1.getVariable()->getMolarConc();
Real pH = E1.getVariable()->getValue();
Real NADHi = NADH/KiNADH;
Real NADi = NAD/KiNAD;
Real PYRai = PYR/KiaPYR;
Real PYRbi = PYR/KibPYR;
Real PYRm = PYR/KmPYR;
Real LACm = LAC/KmLAC;
Real LACi = LAC/KiLAC;
Real NADHmi = KmNADH/KiNADH;
Real NADmi = KmNAD/KiNAD;
Real L = (Kcatf * NADHi * PYRm ) - (Kcatr * NADi * LACm);
Real MM = 1 + PYRm*NADHmi + LACm*NADmi;
Real M = MM *(1+ PYRbi) + NADHi + NADi + NADHi*PYRm +
NADHi*LACm*NADmi + NADi*LACm*NADHmi + LACm*NADi + NADHi*PYRm*LACi +
PYRai*LACm*NADi;
velocity *= L/M;
velocity *= C0.getVariable()->getValue();
velocity *= ActCo / 1000;
setFlux( velocity );
}
virtual void fire()
{
boost::python::handle<> aHandle(
PyEval_EvalCode(
reinterpret_cast< PyCodeObject* >( theCompiledExpression.get() ),
theGlobalNamespace.ptr(), theLocalNamespace.ptr() ) );
boost::python::object aResultObject( aHandle );
// do not use extract<double> for efficiency
if( ! PyFloat_Check( aResultObject.ptr() ) )
{
THROW_EXCEPTION_INSIDE( SimulationError,
asString() + ": "
"The expression gave a non-float object." );
}
const Real aFlux( PyFloat_AS_DOUBLE( aResultObject.ptr() ) );
setFlux( aFlux );
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VCK_maxf = VCK_maxr->getValue() / KCK_iATP / KCK_Cr / KCK_eq * KCK_iADP * KCK_PCr;
// Real VCK_maxf = VCK_maxr->getValue() * KCK_iATP * KCK_Cr * KCK_eq / KCK_iADP / KCK_PCr; ducky 140414
Real CK_a = VCK_maxr->getValue() * ATP->getMolarConc()*1000.0 * Cr->getMolarConc()*1000.0 / (KCK_iATP * KCK_Cr) - VCK_maxf * ADP->getMolarConc()*1000.0 * PCr->getMolarConc()*1000.0 / (KCK_iADP * KCK_PCr);
Real CK_b = 1.0 + ADP->getMolarConc()*1000.0 / KCK_iADP + PCr->getMolarConc()*1000.0 / KCK_iPCr + ADP->getMolarConc()*1000.0 * PCr->getMolarConc()*1000.0 / (KCK_iADP * KCK_PCr) + ATP->getMolarConc()*1000.0 / KCK_iATP + Cr->getMolarConc()*1000.0 / KCK_Cr + ATP->getMolarConc()*1000.0 * Cr->getMolarConc()*1000.0 / (KCK_iATP * KCK_Cr);
setFlux(GX->getValue() * _SizeN_A * CK_a / CK_b / 60000.0 /1000.0);
// Real V_CK = 16.05 * PCr->getMolarConc()*1000.0 * ADP->getMolarConc()*1000.0 - 9.67e-6 * ATP->getMolarConc()*1000.0 * Cr->getMolarConc()*1000.0;
// setFlux(V_CK * _SizeN_A / 60000.0 / 1000.0);
// setFlux(CK_a / CK_b );
//V_CK.setValue(CK_a / CK_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire()
{
Real velocity( k * N_A );
velocity *= getSuperSystem()->getSize();
for( VariableReferenceVector::const_iterator
s( theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
VariableReference aVariableReference( *s );
Integer aCoefficient( aVariableReference.getCoefficient() );
do {
++aCoefficient;
velocity *= aVariableReference.getMolarConc();
} while( aCoefficient != 0 );
}
setFlux(velocity);
}
virtual void fire()
{
Real Gln_o( Gln_o1->getMolarConc() );
Real Gln_i( Gln_i2->getMolarConc() );
Real Na_o( Na_o3->getMolarConc() );
Real Na_i( Na_i4->getMolarConc() );
Real His_o( His_o5->getMolarConc() );
Real His_i( His_i6->getMolarConc() );
//Real size(getSuperSystem()->getSize());
Real velocityf = ( (Vmax * Gln_o * Na_o) /
( (Gln_o + Km_Gln * (His_o/Ki_His + 1) ) * (Na_o + Km_Na) ) );
velocityf *= Gln_o1->getSuperSystem()->getSize()*N_A;
Real velocityr = ( (Vmax * Gln_i * Na_i) /
( (Gln_i + Km_Gln * (His_i/Ki_His + 1) ) * (Na_i + Km_Na) ) );
velocityr *= Gln_i2->getSuperSystem()->getSize()*N_A;
Real velocity = velocityf - velocityr;
//std::cout <<"velocity="<<velocity<<"\n";
setFlux(velocity);
}
virtual void fire()
{
Real S0Concentration = S0.getMolarConc();
Real S1Concentration = S1.getMolarConc();
Real P0Concentration = P0.getMolarConc();
Real P1Concentration = P1.getMolarConc();
Real Denom =
+ KcR * KmS1 * S0Concentration
+ KcR * KmS0 * S1Concentration
+ KmP1 * P0Concentration * KcF_Keq_Inv
+ KmP0 * P1Concentration * KcF_Keq_Inv
+ KcR * S0Concentration * S1Concentration
+ KmP1 * S0Concentration * P0Concentration * KcF_Keq_Inv / KiS0
+ P0Concentration * P1Concentration * KcF_Keq_Inv
+ KcR * KmS0 * S1Concentration * P1Concentration / KiP1;
Real velocity = KcF * KcR * C0.getValue()
* ( S0Concentration * S1Concentration
- P0Concentration * P1Concentration / Keq ) / Denom;
setFlux( velocity );
}
virtual void fire(){
Real velocity = 1;
Real ActCo = E0.getVariable()->getValue();
if( ActCo == 0 ){
velocity = ConstAct;
}
else{
velocity = C0.getVariable()->getValue();
Real A = S0.getVariable()->getMolarConc();
Real B = S1.getVariable()->getMolarConc();
Real P = P0.getVariable()->getMolarConc();
Real Q = P1.getVariable()->getMolarConc();
Real R = P2.getVariable()->getMolarConc();
Real D = D1 + D2 * A + D3 * B + D4 * P + D5 * R + D6 * A * B
+ D7 * A * P + D8 * B * R + D9 * P * Q + D10 * P * R + D11 * Q * R
+ D12 * A * B * P + D13 * A * B * Q + D14 * A * P * Q
+ D15 * B * Q * R + D16 * P * Q * R + D17 * A * B * P * Q
+ D18 * B * P * Q * R;
velocity *= ( N1 * A * B - N2 * P * Q * R ) / D;
velocity *= ActCo / 1000;
}
setFlux( velocity );
}
virtual void fire()
{
Real AS( AS1->getMolarConc() );
Real Fum( Fum2->getMolarConc() );
Real Arg( Arg3->getMolarConc() );
Real ASL( ASL4->getMolarConc() );
Real size(ASL4->getSuperSystem()->getSize());
Real velocity = ( (k1 * k3 * k5 * AS) - (k2 * k4 * k6 * Fum * Arg) ) * ASL;
// -> M/s^3
Real DENOM = ( k5 * (k2 + k3) ) + ( AS * k1 * (k3 + k5) )
+ ( Fum * k2 * k4 ) + ( Arg * k6 * (k2 + k3) )
+ ( Fum * Arg * k4 * k6 ) + ( AS * Fum * k1 * k4 );
// -> 1/s^2
velocity /= DENOM;
velocity*=size*N_A;
//std::cout <<"velocity="<<velocity<<"\n";
setFlux(velocity);
}
