Chaste  Release::2018.1
Alarcon2004OxygenBasedCellCycleOdeSystem Class Reference

#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>

+ Inheritance diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:
+ Collaboration diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

Public Member Functions

 Alarcon2004OxygenBasedCellCycleOdeSystem (double oxygenConcentration, bool isLabelled, std::vector< double > stateVariables=std::vector< double >())
 
 ~Alarcon2004OxygenBasedCellCycleOdeSystem ()
 
void Init ()
 
void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
 
bool CalculateStoppingEvent (double time, const std::vector< double > &rY)
 
void SetIsLabelled (bool isLabelled)
 
bool IsLabelled () const
 
double GetOxygenConcentration () const
 
- Public Member Functions inherited from AbstractOdeSystem
 AbstractOdeSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractOdeSystem ()
 
virtual double CalculateRootFunction (double time, const std::vector< double > &rY)
 
bool GetUseAnalyticJacobian ()
 
const std::vector< double > & rGetConstStateVariables () const
 
- Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
 AbstractParameterisedSystem (unsigned numberOfStateVariables)
 
std::vector< double > & rGetStateVariables ()
 
std::vector< doubleGetStateVariables ()
 
void SetStateVariables (const std::vector< double > &rStateVariables)
 
double GetStateVariable (unsigned index) const
 
double GetStateVariable (const std::string &rName) const
 
void SetStateVariable (unsigned index, double newValue)
 
void SetStateVariable (const std::string &rName, double newValue)
 
virtual void VerifyStateVariables ()
 
void SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)
 
void SetDefaultInitialCondition (unsigned index, double initialCondition)
 
std::vector< doubleGetInitialConditions () const
 
void ResetToInitialConditions ()
 
double GetParameter (unsigned index) const
 
double GetParameter (const std::string &rName) const
 
void SetParameter (const std::string &rName, double value)
 
void SetParameter (unsigned index, double value)
 
double GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
double GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
void SetAnyVariable (unsigned index, double value)
 
void SetAnyVariable (const std::string &rName, double value)
 
virtual std::vector< doubleComputeDerivedQuantities (double time, const std::vector< double > &rState)
 
std::vector< doubleComputeDerivedQuantitiesFromCurrentState (double time)
 
- Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
 AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractUntemplatedParameterisedSystem ()
 
boost::shared_ptr< const
AbstractOdeSystemInformation
GetSystemInformation () const
 
std::string GetSystemName () const
 
unsigned GetNumberOfAttributes () const
 
bool HasAttribute (const std::string &rName) const
 
double GetAttribute (const std::string &rName) const
 
unsigned GetNumberOfStateVariables () const
 
const std::vector< std::string > & rGetStateVariableNames () const
 
const std::vector< std::string > & rGetStateVariableUnits () const
 
unsigned GetStateVariableIndex (const std::string &rName) const
 
bool HasStateVariable (const std::string &rName) const
 
std::string GetStateVariableUnits (unsigned index) const
 
unsigned GetNumberOfParameters () const
 
const std::vector< std::string > & rGetParameterNames () const
 
const std::vector< std::string > & rGetParameterUnits () const
 
unsigned GetParameterIndex (const std::string &rName) const
 
bool HasParameter (const std::string &rName) const
 
std::string GetParameterUnits (unsigned index) const
 
unsigned GetNumberOfDerivedQuantities () const
 
const std::vector< std::string > & rGetDerivedQuantityNames () const
 
const std::vector< std::string > & rGetDerivedQuantityUnits () const
 
unsigned GetDerivedQuantityIndex (const std::string &rName) const
 
bool HasDerivedQuantity (const std::string &rName) const
 
std::string GetDerivedQuantityUnits (unsigned index) const
 
unsigned GetAnyVariableIndex (const std::string &rName) const
 
bool HasAnyVariable (const std::string &rName) const
 
std::string GetAnyVariableUnits (unsigned index) const
 
std::string GetAnyVariableUnits (const std::string &rName) const
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 

Private Attributes

double ma1
 
double ma2
 
double ma3
 
double ma4
 
double mb3
 
double mb4
 
double mc1
 
double mc2
 
double md1
 
double md2
 
double mJ3
 
double mJ4
 
double mEta
 
double mMstar
 
double mB
 
double mxThreshold
 
double myThreshold
 
double mOxygenConcentration
 
bool mIsLabelled
 

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string DumpState (const std::string &rMessage)
 
std::string DumpState (const std::string &rMessage, std::vector< double >Y)
 
std::string DumpState (const std::string &rMessage, std::vector< double >Y, double time)
 
void CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)
 
- Protected Attributes inherited from AbstractOdeSystem
bool mUseAnalyticJacobian
 
- Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< doublemStateVariables
 
std::vector< doublemParameters
 
- Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned mNumberOfStateVariables
 
boost::shared_ptr
< AbstractOdeSystemInformation
mpSystemInfo
 

Detailed Description

Represents the Alarcon et al. (2004) system of ODEs (see ticket #461). [doi:10.1016/j.jtbi.2004.04.016]

The variables are

0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. P = oxygen concentration

Definition at line 59 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleOdeSystem::Alarcon2004OxygenBasedCellCycleOdeSystem ( double  oxygenConcentration,
bool  isLabelled,
std::vector< double stateVariables = std::vector<double>() 
)

Constructor.

Parameters
oxygenConcentrationis a non-dimensional oxygen concentration value between 0 and 1
isLabelledwhether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)
stateVariablesoptional initial conditions for state variables (only used in archiving)

State variables

0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. oxygenConcentration

Definition at line 39 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References Init(), ma1, mc1, mIsLabelled, mMstar, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mxThreshold, myThreshold, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

Alarcon2004OxygenBasedCellCycleOdeSystem::~Alarcon2004OxygenBasedCellCycleOdeSystem ( )

Destructor.

Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

Member Function Documentation

bool Alarcon2004OxygenBasedCellCycleOdeSystem::CalculateStoppingEvent ( double  time,
const std::vector< double > &  rY 
)
virtual

Calculate whether the conditions for the cell cycle to finish have been met.

Parameters
timeat which to calculate whether the stopping event has occurred
rYvalue of the solution vector used to evaluate the RHS.
Returns
whether or not stopping conditions have been met

Reimplemented from AbstractOdeSystem.

Definition at line 158 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mxThreshold, and myThreshold.

void Alarcon2004OxygenBasedCellCycleOdeSystem::EvaluateYDerivatives ( double  time,
const std::vector< double > &  rY,
std::vector< double > &  rDY 
)
virtual

Compute the RHS of the Alarcon et al. (2004) system of ODEs.

Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].

Parameters
timeused to evaluate the RHS.
rYvalue of the solution vector used to evaluate the RHS.
rDYfilled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 109 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References ma1, ma2, ma3, ma4, mB, mb3, mb4, mc1, mc2, md1, md2, mEta, mIsLabelled, mJ3, mJ4, and mMstar.

double Alarcon2004OxygenBasedCellCycleOdeSystem::GetOxygenConcentration ( ) const
void Alarcon2004OxygenBasedCellCycleOdeSystem::Init ( )

Initialise parameter values.

Definition at line 91 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References ma2, ma3, ma4, mB, mb3, mb4, mc2, md1, md2, mEta, mJ3, mJ4, and mMstar.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem().

bool Alarcon2004OxygenBasedCellCycleOdeSystem::IsLabelled ( ) const
Returns
mIsLabelled.

Definition at line 198 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

template<class Archive >
void Alarcon2004OxygenBasedCellCycleOdeSystem::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Serialize the object and its member variables.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 116 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

void Alarcon2004OxygenBasedCellCycleOdeSystem::SetIsLabelled ( bool  isLabelled)

Set mIsLabelled.

Parameters
isLabelledwhether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)

Definition at line 193 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

Member Data Documentation

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma1
private

Constants for the Alarcon et al. (2004) modelDimensionless parameter a_1.

Definition at line 68 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma2
private

Dimensionless parameter a_2.

Definition at line 70 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma3
private

Dimensionless parameter a_3.

Definition at line 72 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma4
private

Dimensionless parameter a_4.

Definition at line 74 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mB
private

Dimensionless parameter B.

Definition at line 96 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mb3
private

Dimensionless parameter b_3.

Definition at line 76 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mb4
private

Dimensionless parameter b_4.

Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mc1
private

Dimensionless parameter c_1.

Definition at line 80 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mc2
private

Dimensionless parameter c_2.

Definition at line 82 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::md1
private

Dimensionless parameter d_1.

Definition at line 84 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::md2
private

Dimensionless parameter d_2.

Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mEta
private

Dimensionless parameter eta.

Definition at line 92 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

bool Alarcon2004OxygenBasedCellCycleOdeSystem::mIsLabelled
private

Whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system).

Definition at line 106 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), EvaluateYDerivatives(), IsLabelled(), and SetIsLabelled().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mJ3
private

Dimensionless parameter J_3.

Definition at line 88 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mJ4
private

Dimensionless parameter J_4.

Definition at line 90 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mMstar
private

Dimensionless parameter m_star.

Definition at line 94 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mOxygenConcentration
private

The oxygen concentration (this affects the ODE system).

Definition at line 103 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by GetOxygenConcentration().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mxThreshold
private

Dimensionless parameter x_THR.

Definition at line 98 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().

double Alarcon2004OxygenBasedCellCycleOdeSystem::myThreshold
private

Dimensionless parameter y_THR.

Definition at line 100 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().


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