Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
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#include <SimpleOxygenBasedCellCycleModel.hpp>
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 |
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.
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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().
rModel | the cell cycle model to copy. |
Definition at line 87 of file SimpleOxygenBasedCellCycleModel.cpp.
SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel | ( | ) |
Constructor.
Definition at line 40 of file SimpleOxygenBasedCellCycleModel.cpp.
References SimulationTime::GetTime(), SimulationTime::Instance(), and mCurrentHypoxiaOnsetTime.
Referenced by CreateCellCycleModel().
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virtual |
Overridden builder method to create new copies of this cell-cycle model.
Implements AbstractCellCycleModel.
Reimplemented in StochasticOxygenBasedCellCycleModel.
Definition at line 111 of file SimpleOxygenBasedCellCycleModel.cpp.
References SimpleOxygenBasedCellCycleModel().
double SimpleOxygenBasedCellCycleModel::GetCriticalHypoxicDuration | ( | ) | const |
Definition at line 178 of file SimpleOxygenBasedCellCycleModel.cpp.
References mCriticalHypoxicDuration.
double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxiaOnsetTime | ( | ) | const |
Definition at line 54 of file SimpleOxygenBasedCellCycleModel.cpp.
References mCurrentHypoxiaOnsetTime.
double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxicDuration | ( | ) | const |
Definition at line 49 of file SimpleOxygenBasedCellCycleModel.cpp.
References mCurrentHypoxicDuration.
double SimpleOxygenBasedCellCycleModel::GetHypoxicConcentration | ( | ) | const |
Definition at line 154 of file SimpleOxygenBasedCellCycleModel.cpp.
References mHypoxicConcentration.
double SimpleOxygenBasedCellCycleModel::GetQuiescentConcentration | ( | ) | const |
Definition at line 166 of file SimpleOxygenBasedCellCycleModel.cpp.
References mQuiescentConcentration.
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virtual |
Overridden OutputCellCycleModelParameters() method.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractSimplePhaseBasedCellCycleModel.
Reimplemented in StochasticOxygenBasedCellCycleModel.
Definition at line 195 of file SimpleOxygenBasedCellCycleModel.cpp.
References mCriticalHypoxicDuration, mHypoxicConcentration, mQuiescentConcentration, and AbstractSimplePhaseBasedCellCycleModel::OutputCellCycleModelParameters().
Referenced by StochasticOxygenBasedCellCycleModel::OutputCellCycleModelParameters().
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inlineprivate |
Boost Serialization method for archiving/checkpointing
archive | The boost archive. |
version | The 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.
criticalHypoxicDuration | the new value of mCriticalHypoxicDuration |
Definition at line 183 of file SimpleOxygenBasedCellCycleModel.cpp.
References mCriticalHypoxicDuration.
void SimpleOxygenBasedCellCycleModel::SetCurrentHypoxiaOnsetTime | ( | double | currentHypoxiaOnsetTime | ) |
Set method for mCurrentHypoxiaOnsetTime.
currentHypoxiaOnsetTime | the new value of mCurrentHypoxiaOnsetTime |
Definition at line 189 of file SimpleOxygenBasedCellCycleModel.cpp.
References mCurrentHypoxiaOnsetTime.
void SimpleOxygenBasedCellCycleModel::SetHypoxicConcentration | ( | double | hypoxicConcentration | ) |
Set method for mHypoxicConcentration.
hypoxicConcentration | the new value of mHypoxicConcentration |
Definition at line 159 of file SimpleOxygenBasedCellCycleModel.cpp.
References mHypoxicConcentration.
void SimpleOxygenBasedCellCycleModel::SetQuiescentConcentration | ( | double | quiescentConcentration | ) |
Set method for mQuiescentConcentration.
quiescentConcentration | the new value of mQuiescentConcentration |
Definition at line 171 of file SimpleOxygenBasedCellCycleModel.cpp.
References mQuiescentConcentration.
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virtual |
Overridden UpdateCellCyclePhase() method.
Reimplemented from AbstractSimplePhaseBasedCellCycleModel.
Definition at line 59 of file SimpleOxygenBasedCellCycleModel.cpp.
References SimulationTime::GetTimeStep(), SimulationTime::Instance(), AbstractPhaseBasedCellCycleModel::mCurrentCellCyclePhase, AbstractPhaseBasedCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mQuiescentConcentration, AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateHypoxicDuration().
void SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration | ( | ) |
Method for updating mCurrentHypoxicDuration, called at the start of ReadyToDivide().
Definition at line 116 of file SimpleOxygenBasedCellCycleModel.cpp.
References SimulationTime::GetTime(), SimulationTime::Instance(), RandomNumberGenerator::Instance(), mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, AbstractCellCycleModel::mpCell, and RandomNumberGenerator::ranf().
Referenced by UpdateCellCyclePhase().
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Definition at line 55 of file SimpleOxygenBasedCellCycleModel.hpp.
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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().
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The time when the current period of hypoxia began.
Definition at line 83 of file SimpleOxygenBasedCellCycleModel.hpp.
Referenced by SimpleOxygenBasedCellCycleModel(), GetCurrentHypoxiaOnsetTime(), serialize(), SetCurrentHypoxiaOnsetTime(), and UpdateHypoxicDuration().
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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().
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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().
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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().