Alarcon2004OxygenBasedCellCycleOdeSystem Class Reference

#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>

Inheritance diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

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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 51 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.


Constructor & Destructor Documentation

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

Constructor.

Parameters:
oxygenConcentration is a non-dimensional oxygen concentration value between 0 and 1
isLabelled whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)
stateVariables optional 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

Todo:
should this be 0.004??

Definition at line 31 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

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

Alarcon2004OxygenBasedCellCycleOdeSystem::~Alarcon2004OxygenBasedCellCycleOdeSystem (  ) 

Destructor.

Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.


Member Function Documentation

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

Serialize the object and its member variables.

Parameters:
archive the archive
version the current version of this class

Definition at line 108 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

void Alarcon2004OxygenBasedCellCycleOdeSystem::Init (  ) 

Initialise parameter values.

Definition at line 83 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

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

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem().

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:
time used to evaluate the RHS.
rY value of the solution vector used to evaluate the RHS.
rDY filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 101 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

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

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:
time at which to calculate whether the stopping event has occurred
rY value of the solution vector used to evaluate the RHS.
Returns:
whether or not stopping conditions have been met

Reimplemented from AbstractOdeSystem.

Definition at line 150 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mxThreshold, and myThreshold.

void Alarcon2004OxygenBasedCellCycleOdeSystem::SetIsLabelled ( bool  isLabelled  ) 

Set mIsLabelled.

Parameters:
isLabelled whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)

Definition at line 185 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

bool Alarcon2004OxygenBasedCellCycleOdeSystem::IsLabelled (  )  const

Get method for mIsLabelled.

Definition at line 190 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

double Alarcon2004OxygenBasedCellCycleOdeSystem::GetOxygenConcentration (  )  const

Get method for mOxygenConcentration.

Definition at line 195 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mOxygenConcentration.


Member Data Documentation

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

Definition at line 60 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

Dimensionless parameter a_2.

Definition at line 62 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter a_3.

Definition at line 64 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter a_4.

Definition at line 66 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter b_3.

Definition at line 68 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter b_4.

Definition at line 70 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter c_1.

Definition at line 72 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

Dimensionless parameter c_2.

Definition at line 74 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter d_1.

Definition at line 76 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter d_2.

Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter J_3.

Definition at line 80 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter J_4.

Definition at line 82 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter eta.

Definition at line 84 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter m_star.

Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

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

Dimensionless parameter B.

Definition at line 88 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

Dimensionless parameter x_THR.

Definition at line 90 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().

Dimensionless parameter y_THR.

Definition at line 92 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().

The oxygen concentration (this affects the ODE system).

Definition at line 95 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by GetOxygenConcentration().

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

Definition at line 98 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

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


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

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