/**
* Constructor.
*
* @param a the value of the parameter mA
*/
OdeSystemForCoupledHeatEquationWithSource(double a)
: AbstractOdeSystemForCoupledPdeSystem(1,1),
mA(a)
{
mpSystemInfo = OdeSystemInformation<OdeSystemForCoupledHeatEquationWithSource>::Instance();
SetStateVariables(GetInitialConditions());
}
MyOdeSystem(std::vector<double> stateVariables=std::vector<double>()) : AbstractOdeSystem(2)
{
mpSystemInfo = OdeSystemInformation<MyOdeSystem>::Instance();
if (stateVariables != std::vector<double>())
{
SetStateVariables(stateVariables);
}
}
TysonNovak2001OdeSystem::TysonNovak2001OdeSystem(std::vector<double> stateVariables)
: AbstractOdeSystemWithAnalyticJacobian(6)
{
mpSystemInfo = OdeSystemInformation<TysonNovak2001OdeSystem>::Instance();
Init();
if (stateVariables != std::vector<double>())
{
SetStateVariables(stateVariables);
}
}
Alarcon2004OxygenBasedCellCycleOdeSystem::Alarcon2004OxygenBasedCellCycleOdeSystem(double oxygenConcentration,
bool isLabelled,
std::vector<double> stateVariables)
: AbstractOdeSystem(6),
mOxygenConcentration(oxygenConcentration),
mIsLabelled(isLabelled)
{
mpSystemInfo.reset(new CellwiseOdeSystemInformation<Alarcon2004OxygenBasedCellCycleOdeSystem>);
/**
* State variables
*
* 0. x = Cdh1-APC complexes
* 1. y = cyclin-CDK
* 2. z = p27
* 3. m = mass
* 4. u = RBNP
* 5. oxygenConcentration
*/
Init(); // set up parameters
// Parameter values are taken from the Alarcon et al. (2004) paper
if (mIsLabelled) // labelled "cancer" cells
{
ma1 = 0.04;
mc1 = 0.007;
mxThreshold = 0.004;
myThreshold = 0.05;
}
else // normal cells
{
ma1 = 0.05;
mc1 = 0.1;
mxThreshold = 0.004;
myThreshold = 0.2;
}
// Cell-specific initial conditions
SetDefaultInitialCondition(3, 0.5*mMstar);
SetDefaultInitialCondition(5, oxygenConcentration);
if (stateVariables != std::vector<double>())
{
SetStateVariables(stateVariables);
}
}
Mirams2010WntOdeSystem::Mirams2010WntOdeSystem(double wntLevel,
boost::shared_ptr<AbstractCellMutationState> pMutationState,
std::vector<double> stateVariables)
: AbstractOdeSystem(3),
mpMutationState(pMutationState),
mWntLevel(wntLevel)
{
mpSystemInfo.reset(new CellwiseOdeSystemInformation<Mirams2010WntOdeSystem>);
/**
* State variables.
*
* 0. b1 = Beta-Catenin (1st allele's copy)
* 1. b2 = Beta-Catenin (2nd allele's copy)
* 2. wntLevel
*/
Init(); // set up parameter values
// Set up rough guesses for the initial steady states in this Wnt conc.
double b1 = 0;
double b2 = 0;
b1 = (mA/2.0) / (((wntLevel + mB)/(mC*wntLevel + mD)) + mF);
if (!mpMutationState)
{
// No mutations specified
}
else if (mpMutationState->IsType<BetaCateninOneHitCellMutationState>())
{
b2 = (mA/2.0)/mF;
}
else
{
b2 = (mA/2.0) / (((wntLevel + mB)/(mC*wntLevel + mD)) + mF);
}
SetDefaultInitialCondition(0, b1);
SetDefaultInitialCondition(1, b2);
SetDefaultInitialCondition(2, wntLevel);
if (stateVariables != std::vector<double>())
{
SetStateVariables(stateVariables);
}
}
WntCellCycleOdeSystem::WntCellCycleOdeSystem(double wntLevel,
boost::shared_ptr<AbstractCellMutationState> pMutationState,
std::vector<double> stateVariables)
: AbstractOdeSystem(9),
mpMutationState(pMutationState),
mWntLevel(wntLevel)
{
mpSystemInfo.reset(new CellwiseOdeSystemInformation<WntCellCycleOdeSystem>);
/**
* State variables.
*
* 0. r = pRb
* 1. e = E2F1 (This is the S-phase indicator)
* 2. i = CycD (inactive)
* 3. j = CycD (active)
* 4. p = pRb-p
* 5. c = APC (Active)
* 6. b1 = Beta-Catenin (1st allele's copy)
* 7. b2 = Beta-Catenin (2nd allele's copy)
* 8. wntLevel
*/
Init(); // set up parameter values
// Set up a Wnt signalling pathway in a steady state
double destruction_level = ma5d/(ma4d*wntLevel+ma5d);
double beta_cat_level_1 = -1.0;
double beta_cat_level_2 = -1.0;
if (!mpMutationState)
{
// No mutations specified
}
else if (mpMutationState && mpMutationState->IsType<ApcOneHitCellMutationState>())
{
// APC +/- : only half are active
beta_cat_level_1 = 0.5*ma2d/(ma2d+0.5*ma3d*destruction_level);
beta_cat_level_2 = 0.5*ma2d/(ma2d+0.5*ma3d*destruction_level);
}
else if (mpMutationState && mpMutationState->IsType<ApcTwoHitCellMutationState>())
{
// APC -/-
destruction_level = 0.0; // no active destruction complex
beta_cat_level_1 = 0.5; // fully active beta-catenin
beta_cat_level_2 = 0.5; // fully active beta-catenin
}
else if (mpMutationState && mpMutationState->IsType<BetaCateninOneHitCellMutationState>())
{
// Beta-cat delta 45
beta_cat_level_1 = 0.5*ma2d/(ma2d+ma3d*destruction_level);
beta_cat_level_2 = 0.5;
}
else
{
// healthy cells
beta_cat_level_1 = 0.5*ma2d/(ma2d+ma3d*destruction_level);
beta_cat_level_2 = 0.5*ma2d/(ma2d+ma3d*destruction_level);
}
// Cell-specific initial conditions
SetDefaultInitialCondition(5, destruction_level);
SetDefaultInitialCondition(6, beta_cat_level_1);
SetDefaultInitialCondition(7, beta_cat_level_2);
SetDefaultInitialCondition(8, wntLevel);
if (stateVariables != std::vector<double>())
{
SetStateVariables(stateVariables);
}
}
void FSDEMatViscoT::TakeParameterList(const ParameterListT& list)
{
/* inherited */
FSSolidMatT::TakeParameterList(list);
fMu = list.GetParameter("mu");
fElectricPermittivity = list.GetParameter("epsilon");
fNrig = list.GetParameter("Nrig");
fLambda = list.GetParameter("lambda");
/* write into vector to pass to C code for stress/modulus calculations */
fParams.Dimension(3);
fParams[0] = fMu;
fParams[1] = fLambda;
fParams[2] = fElectricPermittivity;
fParams[3] = fNrig;
/* dimension work space */
fTangentMechanical.Dimension(kStressDim);
fTangentMechanicalElec.Dimension(kStressDim);
fStress.Dimension(kNumDOF);
fTangentElectrical.Dimension(kNumDOF);
fTangentElectromechanical.Dimension(kStressDim, kNumDOF);
fElectricDisplacement.Dimension(kNumDOF);
fElectricField.Dimension(kNumDOF);
/* Code from RGSplitT2.cpp */
StringT caller = "FSDEMatViscoT::TakeParameterList";
int num_neq = list.NumLists("rg_neq_potential");
int num_shear_visc = list.NumLists("rg_shear_viscosity");
int num_bulk_visc = list.NumLists("rg_bulk_viscosity");
if (num_neq != num_shear_visc || num_neq != num_bulk_visc)
ExceptionT::GeneralFail("FSDEMatViscoT::TakeParameterList",
"number of matrix viscosity functions does not match number of matrix nonequilibrium potentials");
fNumProcess = list.NumLists("rg_shear_viscosity");
/* inherited from RGViscoelasticityT.cpp */
/* Default Dimension state variable arrays - from RGViscoelasticityT.cpp */
if (fNumProcess > 0) SetStateVariables(fNumProcess);
fPot.Dimension(fNumProcess+1);
fVisc_s.Dimension(fNumProcess);
fVisc_b.Dimension(fNumProcess);
/* For some reason, dimensioning these in TakeParameterList works better */
fF_M.Dimension(NumSD());
fF_T_inv.Dimension(NumSD());
fF3D.Dimension(3);
fInverse.Dimension(3);
fb.Dimension(3);
fbe.Dimension(3);
fb_tr.Dimension(3);
fEigs_dev.Dimension(3);
fEigs.Dimension(3);
fEigs_e.Dimension(3);
fEigs_tr.Dimension(3);
ftau_EQ.Dimension(3);
ftau_NEQ.Dimension(3);
fStressNEQ.Dimension(NumSD());
fStress3D.Dimension(3);
fDtauDe_EQ.Dimension(3);
fDtauDe_NEQ.Dimension(3);
fiKAB.Dimension(3);
fCalg.Dimension(3);
fModulus3D.Dimension(6);
fModMat.Dimension(6);
fModulusNEQ.Dimension(dSymMatrixT::NumValues(NumSD()));
const ParameterListT& eq_pot = list.GetListChoice(*this, "rg_eq_potential");
if(eq_pot.Name() == "neo-hookean")
fPot[0] = new NeoHookean;
else if(eq_pot.Name() == "mooney-rivlin")
fPot[0] = new MooneyRivlin;
else if(eq_pot.Name() == "veronda-westmann")
fPot[0] = new VWPotentialT;
else if(eq_pot.Name() == "fung-potential")
fPot[0] = new FungPotentialT;
else if(eq_pot.Name() == "arruda-boyce")
fPot[0] = new ArrudaBoyce;
else
ExceptionT::GeneralFail(caller, "no such potential");
if (!fPot[0]) ExceptionT::GeneralFail(caller, "could not construct \"%s\"", eq_pot.Name().Pointer());
fPot[0]->TakeParameterList(eq_pot);
for (int i = 0; i < fNumProcess; i++)
{
const ParameterListT& pot_neq = list.GetListChoice(*this, "rg_neq_potential",i);
if(pot_neq.Name() == "mooney-rivlin")
fPot[i+1] = new MooneyRivlin;
else if(pot_neq.Name() == "neo-hookean")
fPot[i+1] = new NeoHookean;
else if(pot_neq.Name() == "veronda-westmann")
fPot[i+1] = new VWPotentialT;
else if(pot_neq.Name() == "fung-potential")
fPot[i+1] = new FungPotentialT;
else if(pot_neq.Name() == "arruda-boyce")
fPot[i+1] = new ArrudaBoyce;
else
ExceptionT::GeneralFail(caller, "no such potential");
if (!fPot[i+1]) ExceptionT::GeneralFail(caller, "could not construct \"%s\"", pot_neq.Name().Pointer());
fPot[i+1]->TakeParameterList(pot_neq);
const ParameterListT& shear_visc = list.GetListChoice(*this, "rg_shear_viscosity", i);
if (shear_visc.Name() == "linear_exponential")
fVisc_s[i] = new LinearExponentialT;
#ifdef __DEVELOPMENT__
else if (shear_visc.Name() == "scaled-csch")
fVisc_s[i] = new ScaledCsch;
#endif
else
ExceptionT::GeneralFail(caller, "no such potential");
if (!fVisc_s[i]) throw ExceptionT::kOutOfMemory;
fVisc_s[i]->TakeParameterList(shear_visc);
const ParameterListT& bulk_visc = list.GetListChoice(*this, "rg_bulk_viscosity", i);
if (bulk_visc.Name() == "linear_exponential")
fVisc_b[i] = new LinearExponentialT;
#ifdef __DEVELOPMENT__
else if (bulk_visc.Name() == "scaled-csch")
fVisc_b[i] = new ScaledCsch;
#endif
else
ExceptionT::GeneralFail(caller, "no such potential");
if (!fVisc_b[i]) throw ExceptionT::kOutOfMemory;
fVisc_b[i]->TakeParameterList(bulk_visc);
}
/* set dimension of workspaces */
// Initialize();
}
void AbstractParameterisedSystem<VECTOR>::ResetToInitialConditions()
{
VECTOR inits = GetInitialConditions();
SetStateVariables(inits);
DeleteVector(inits);
}
