#include <TargetAreaLinearGrowthModifier.hpp>

Inheritance diagram for TargetAreaLinearGrowthModifier< DIM >:

Collaboration diagram for TargetAreaLinearGrowthModifier< DIM >:

Public Member Functions
	TargetAreaLinearGrowthModifier ()

virtual	~TargetAreaLinearGrowthModifier ()

void	UpdateTargetAreaOfCell (const CellPtr pCell)

double	GetAgeToStartGrowing ()

void	SetAgeToStartGrowing (double ageToStartGrowing)

double	GetGrowthRate ()

void	SetGrowthRate (double growthRate)

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractTargetAreaModifier< DIM >
	AbstractTargetAreaModifier ()

virtual	~AbstractTargetAreaModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)

double	GetReferenceTargetArea ()

void	SetReferenceTargetArea (double referenceTargetArea)

void	UpdateTargetAreas (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM >
	AbstractCellBasedSimulationModifier ()

virtual	~AbstractCellBasedSimulationModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0

virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0

virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

void	OutputSimulationModifierInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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

Private Attributes
double	mAgeToStartGrowing

double	mGrowthRate

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractTargetAreaModifier< DIM >
double	mReferenceTargetArea

Detailed Description

template<unsigned DIM>
class TargetAreaLinearGrowthModifier< DIM >

A target area modifier class in which the target area of a cell grows linearly, starting from mReferenceTargetArea, over a prescribed duration.

If used with a phase-based cell-cycle model (such as FixedG1GenerationalCellCycleModel), the target area of a cell doubles from the value mReferenceTargetArea over the course of the cell's G2 phase. This rule is based on the description of cell growth and division proposed by Farhadifar et al (The influence of cell mechanics, cell-cell interactions, and proliferation on epithelial packing, Current Biology 17(24):2095-2104, 2007, http://dx.doi.org/10.1016/j.cub.2007.11.049).

If used with a non-phase-based cell-cycle model, the target area of a cell increases linearly at a rate mGrowthRate as soon as the cell's age exceeds mAgeToStartGrowing.

Here mReferenceTargetArea, mAgeToStartGrowing and mGrowthRate are settable member variables. The default value of mReferenceTargetArea is 1.0 and the default value of mAgeToStartGrowing and mGrowthRate is DOUBLE_UNSET.

If mAgeToStartGrowing is set by the user, then mGrowthRate must also be set; note that in this case, these values are used to prescribe target area growth as described earlier, regardless of whether a phase-based cell-cycle model is present.

Definition at line 68 of file TargetAreaLinearGrowthModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

TargetAreaLinearGrowthModifier< DIM >::TargetAreaLinearGrowthModifier ( )

Default constructor.

Definition at line 42 of file TargetAreaLinearGrowthModifier.cpp.

template<unsigned DIM>

TargetAreaLinearGrowthModifier< DIM >::~TargetAreaLinearGrowthModifier ( )

virtual

Destructor.

Definition at line 50 of file TargetAreaLinearGrowthModifier.cpp.

Member Function Documentation

template<unsigned DIM>

double TargetAreaLinearGrowthModifier< DIM >::GetAgeToStartGrowing ( )

Returns: mAgeToStartGrowing.

Definition at line 134 of file TargetAreaLinearGrowthModifier.cpp.

template<unsigned DIM>

double TargetAreaLinearGrowthModifier< DIM >::GetGrowthRate ( )

Returns: mGrowthRate

Definition at line 147 of file TargetAreaLinearGrowthModifier.cpp.

template<unsigned DIM>

void TargetAreaLinearGrowthModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractTargetAreaModifier< DIM >.

Definition at line 160 of file TargetAreaLinearGrowthModifier.cpp.

References AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters().

template<unsigned DIM>

template<class Archive >

void TargetAreaLinearGrowthModifier< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 80 of file TargetAreaLinearGrowthModifier.hpp.

References TargetAreaLinearGrowthModifier< DIM >::mAgeToStartGrowing, and TargetAreaLinearGrowthModifier< DIM >::mGrowthRate.

template<unsigned DIM>

void TargetAreaLinearGrowthModifier< DIM >::SetAgeToStartGrowing ( double ageToStartGrowing )

Set mAgeToStartGrowing.

Parameters

ageToStartGrowing the new value of mAgeToStartGrowing

Definition at line 140 of file TargetAreaLinearGrowthModifier.cpp.

template<unsigned DIM>

void TargetAreaLinearGrowthModifier< DIM >::SetGrowthRate ( double growthRate )

Set mGrowthRate.

Parameters

growthRate the new value of mGrowthRate

Definition at line 153 of file TargetAreaLinearGrowthModifier.cpp.

template<unsigned DIM>

void TargetAreaLinearGrowthModifier< DIM >::UpdateTargetAreaOfCell ( const CellPtr pCell )

virtual

Helper method to update the target area property of an individual cell.

Parameters

pCell pointer to a cell

Todo:: : which cells are apoptotic? if they get apoptotic during G2-phase then this line has to be changed

At division, daughter cells inherit the cell data array from the mother cell. Here, we assign the target area that we want daughter cells to have to cells that we know to divide in this time step.

Todo:: This is a little hack that we might want to clean up in the future.

Implements AbstractTargetAreaModifier< DIM >.

Definition at line 55 of file TargetAreaLinearGrowthModifier.cpp.

References DOUBLE_UNSET, EXCEPTION, AbstractPhaseBasedCellCycleModel::GetG1Duration(), AbstractPhaseBasedCellCycleModel::GetG2Duration(), AbstractPhaseBasedCellCycleModel::GetMDuration(), AbstractPhaseBasedCellCycleModel::GetSDuration(), SimulationTime::GetTime(), and SimulationTime::Instance().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 71 of file TargetAreaLinearGrowthModifier.hpp.

Member Data Documentation

template<unsigned DIM>

double TargetAreaLinearGrowthModifier< DIM >::mAgeToStartGrowing

private

The age of a proliferating cell at which its target area should start growing. Defaults to DOUBLE_UNSET. If this variable is set using SetAgeToStartGrowing(), then it is used regardless of whether a phase-based cell-cycle model is used.

Definition at line 92 of file TargetAreaLinearGrowthModifier.hpp.

Referenced by TargetAreaLinearGrowthModifier< DIM >::serialize().

template<unsigned DIM>

double TargetAreaLinearGrowthModifier< DIM >::mGrowthRate

private

The growth rate of a proliferating cell's target area, when it is growing. Defaults to DOUBLE_UNSET. This variable must be set if mAgeToStartGrowing is set, otherwise an exception is thrown.

Definition at line 99 of file TargetAreaLinearGrowthModifier.hpp.

Referenced by TargetAreaLinearGrowthModifier< DIM >::serialize().

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

cell_based/src/simulation/modifiers/TargetAreaLinearGrowthModifier.hpp
cell_based/src/simulation/modifiers/TargetAreaLinearGrowthModifier.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class TargetAreaLinearGrowthModifier< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class TargetAreaLinearGrowthModifier< DIM >