Chaste  Release::2017.1
SimpleOxygenBasedCellCycleModel Class Reference

#include <SimpleOxygenBasedCellCycleModel.hpp>

+ Inheritance diagram for SimpleOxygenBasedCellCycleModel:
+ Collaboration diagram for SimpleOxygenBasedCellCycleModel:

Public Member Functions

 SimpleOxygenBasedCellCycleModel ()
 
void UpdateCellCyclePhase ()
 
void UpdateHypoxicDuration ()
 
double GetCurrentHypoxicDuration () const
 
double GetCurrentHypoxiaOnsetTime () const
 
AbstractCellCycleModelCreateCellCycleModel ()
 
double GetHypoxicConcentration () const
 
void SetHypoxicConcentration (double hypoxicConcentration)
 
double GetQuiescentConcentration () const
 
void SetQuiescentConcentration (double quiescentConcentration)
 
double GetCriticalHypoxicDuration () const
 
void SetCriticalHypoxicDuration (double criticalHypoxicDuration)
 
void SetCurrentHypoxiaOnsetTime (double currentHypoxiaOnsetTime)
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
 AbstractSimplePhaseBasedCellCycleModel ()
 
virtual ~AbstractSimplePhaseBasedCellCycleModel ()
 
virtual void ResetForDivision ()
 
void InitialiseDaughterCell ()
 
virtual void Initialise ()
 
- Public Member Functions inherited from AbstractPhaseBasedCellCycleModel
 AbstractPhaseBasedCellCycleModel ()
 
virtual ~AbstractPhaseBasedCellCycleModel ()
 
virtual bool ReadyToDivide ()
 
CellCyclePhase GetCurrentCellCyclePhase () const
 
virtual double GetG1Duration () const
 
double GetStemCellG1Duration () const
 
double GetTransitCellG1Duration () const
 
double GetSG2MDuration () const
 
virtual double GetSDuration () const
 
virtual double GetG2Duration () const
 
virtual double GetMDuration () const
 
virtual void SetStemCellG1Duration (double stemCellG1Duration)
 
virtual void SetTransitCellG1Duration (double transitCellG1Duration)
 
void SetSDuration (double sDuration)
 
void SetG2Duration (double g2Duration)
 
void SetMDuration (double mDuration)
 
virtual double GetAverageTransitCellCycleTime ()
 
virtual double GetAverageStemCellCycleTime ()
 
double GetMinimumGapDuration () const
 
void SetMinimumGapDuration (double minimumGapDuration)
 
- Public Member Functions inherited from AbstractCellCycleModel
 AbstractCellCycleModel ()
 
virtual ~AbstractCellCycleModel ()
 
void SetCell (CellPtr pCell)
 
CellPtr GetCell ()
 
virtual void SetBirthTime (double birthTime)
 
void SetDimension (unsigned dimension)
 
unsigned GetDimension () const
 
double GetBirthTime () const
 
double GetAge ()
 
virtual bool CanCellTerminallyDifferentiate ()
 
void OutputCellCycleModelInfo (out_stream &rParamsFile)
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 

Protected Member Functions

 SimpleOxygenBasedCellCycleModel (const SimpleOxygenBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
virtual void SetG1Duration ()
 
 AbstractSimplePhaseBasedCellCycleModel (const AbstractSimplePhaseBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
 AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractCellCycleModel
 AbstractCellCycleModel (const AbstractCellCycleModel &rModel)
 

Protected Attributes

double mCurrentHypoxicDuration
 
double mCurrentHypoxiaOnsetTime
 
double mHypoxicConcentration
 
double mQuiescentConcentration
 
double mCriticalHypoxicDuration
 
- Protected Attributes inherited from AbstractPhaseBasedCellCycleModel
CellCyclePhase mCurrentCellCyclePhase
 
double mG1Duration
 
double mMinimumGapDuration
 
double mStemCellG1Duration
 
double mTransitCellG1Duration
 
double mSDuration
 
double mG2Duration
 
double mMDuration
 
- Protected Attributes inherited from AbstractCellCycleModel
CellPtr mpCell
 
double mBirthTime
 
bool mReadyToDivide
 
unsigned mDimension
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Detailed Description

Simple oxygen-based cell-cycle model.

A simple oxygen-dependent cell-cycle model that inherits from AbstractSimplePhaseBasedCellCycleModel. The duration of G1 phase depends on the local oxygen concentration. A prolonged period of acute hypoxia leads to the cell being labelled as apoptotic. This model allows for quiescence imposed by transient periods of hypoxia, followed by reoxygenation.

Definition at line 51 of file SimpleOxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel ( const SimpleOxygenBasedCellCycleModel rModel)
protected

Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters
rModelthe cell cycle model to copy.

Definition at line 87 of file SimpleOxygenBasedCellCycleModel.cpp.

SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel ( )

Member Function Documentation

AbstractCellCycleModel * SimpleOxygenBasedCellCycleModel::CreateCellCycleModel ( )
virtual

Overridden builder method to create new copies of this cell-cycle model.

Returns
new cell-cycle model

Implements AbstractCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 111 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimpleOxygenBasedCellCycleModel().

double SimpleOxygenBasedCellCycleModel::GetCriticalHypoxicDuration ( ) const
Returns
mCriticalHypoxicDuration

Definition at line 178 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxiaOnsetTime ( ) const
Returns
mCurrentHypoxiaOnsetTime

Definition at line 54 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxicDuration ( ) const
Returns
mCurrentHypoxicDuration

Definition at line 49 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetHypoxicConcentration ( ) const
Returns
mHypoxicConcentration

Definition at line 154 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

double SimpleOxygenBasedCellCycleModel::GetQuiescentConcentration ( ) const
Returns
mQuiescentConcentration

Definition at line 166 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual
template<class Archive >
void SimpleOxygenBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Boost Serialization method for archiving/checkpointing

Parameters
archiveThe boost archive.
versionThe current version of this class.

Definition at line 62 of file SimpleOxygenBasedCellCycleModel.hpp.

References mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, and mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::SetCriticalHypoxicDuration ( double  criticalHypoxicDuration)

Set method for mCriticalHypoxicDuration.

Parameters
criticalHypoxicDurationthe new value of mCriticalHypoxicDuration

Definition at line 183 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

void SimpleOxygenBasedCellCycleModel::SetCurrentHypoxiaOnsetTime ( double  currentHypoxiaOnsetTime)

Set method for mCurrentHypoxiaOnsetTime.

Parameters
currentHypoxiaOnsetTimethe new value of mCurrentHypoxiaOnsetTime

Definition at line 189 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

void SimpleOxygenBasedCellCycleModel::SetHypoxicConcentration ( double  hypoxicConcentration)

Set method for mHypoxicConcentration.

Parameters
hypoxicConcentrationthe new value of mHypoxicConcentration

Definition at line 159 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

void SimpleOxygenBasedCellCycleModel::SetQuiescentConcentration ( double  quiescentConcentration)

Set method for mQuiescentConcentration.

Parameters
quiescentConcentrationthe new value of mQuiescentConcentration

Definition at line 171 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration ( )

Member Data Documentation

double SimpleOxygenBasedCellCycleModel::mCriticalHypoxicDuration
protected

Non-dimensionalized critical hypoxic duration. Has units of hours.

Definition at line 103 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetCriticalHypoxicDuration(), OutputCellCycleModelParameters(), serialize(), SetCriticalHypoxicDuration(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mCurrentHypoxiaOnsetTime
protected

The time when the current period of hypoxia began.

Definition at line 83 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetCurrentHypoxiaOnsetTime(), serialize(), SetCurrentHypoxiaOnsetTime(), SimpleOxygenBasedCellCycleModel(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mCurrentHypoxicDuration
protected

How long the current period of hypoxia has lasted. Has units of hours.

Definition at line 78 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetCurrentHypoxicDuration(), serialize(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mHypoxicConcentration
protected

Non-dimensionalized oxygen concentration below which cells are considered to be hypoxic. A prolonged period of hypoxia causes the cell to become apoptotic.

Definition at line 90 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetHypoxicConcentration(), OutputCellCycleModelParameters(), serialize(), SetHypoxicConcentration(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mQuiescentConcentration
protected

Non-dimensionalized oxygen concentration below which cells are considered to be quiescent and slow their progress through the G1 phase of the cell cycle.

Definition at line 97 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetQuiescentConcentration(), OutputCellCycleModelParameters(), serialize(), SetQuiescentConcentration(), and UpdateCellCyclePhase().


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