Chaste Release::3.1
Alarcon2004OxygenBasedCellCycleOdeSystem Class Reference

#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>

Inheritance diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:
Collaboration diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

List of all members.

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

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

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

Get method for mOxygenConcentration.

Definition at line 203 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mOxygenConcentration.

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

Get method for mIsLabelled.

Definition at line 198 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

template<class Archive >
void Alarcon2004OxygenBasedCellCycleOdeSystem::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

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

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

Definition at line 68 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

Dimensionless parameter a_2.

Definition at line 70 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter a_3.

Definition at line 72 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter a_4.

Definition at line 74 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter B.

Definition at line 96 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter b_3.

Definition at line 76 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter b_4.

Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter c_2.

Definition at line 82 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter d_1.

Definition at line 84 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter d_2.

Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter eta.

Definition at line 92 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

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().

Dimensionless parameter J_3.

Definition at line 88 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter J_4.

Definition at line 90 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

The oxygen concentration (this affects the ODE system).

Definition at line 103 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by GetOxygenConcentration().


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