NagaiHondaForce< DIM > Class Template Reference

#include <NagaiHondaForce.hpp>

Inheritance diagram for NagaiHondaForce< DIM >:

Collaboration diagram for NagaiHondaForce< DIM >:

List of all members.

Public Member Functions

NagaiHondaForce ()

~NagaiHondaForce ()

void AddForceContribution (std::vector< c_vector< double, DIM > > &rForces, AbstractCellPopulation< DIM > &rCellPopulation)

double GetAdhesionParameter (Node< DIM > *pNodeA, Node< DIM > *pNodeB)

double GetNagaiHondaDeformationEnergyParameter ()

double GetNagaiHondaMembraneSurfaceEnergyParameter ()

double GetNagaiHondaCellCellAdhesionEnergyParameter ()

double GetNagaiHondaCellBoundaryAdhesionEnergyParameter ()

void SetNagaiHondaDeformationEnergyParameter (double nagaiHondaDeformationEnergyParameter)

void SetNagaiHondaMembraneSurfaceEnergyParameter (double nagaiHondaMembraneSurfaceEnergyParameter)

void SetNagaiHondaCellCellAdhesionEnergyParameter (double nagaiHondaCellCellAdhesionEnergyEnergyParameter)

void SetNagaiHondaCellBoundaryAdhesionEnergyParameter (double nagaiHondaCellBoundaryAdhesionEnergyParameter)

double GetTargetAreaOfCell (const CellPtr pCell) const

double GetMatureCellTargetArea () const

void SetMatureCellTargetArea (double matureCellTargetArea)

void OutputForceParameters (out_stream &rParamsFile)

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Private Attributes

double mNagaiHondaDeformationEnergyParameter

double mNagaiHondaMembraneSurfaceEnergyParameter

double mNagaiHondaCellCellAdhesionEnergyParameter

double mNagaiHondaCellBoundaryAdhesionEnergyParameter

double mMatureCellTargetArea

Friends

class TestForces

class boost::serialization::access

Detailed Description

template<unsigned DIM>
class NagaiHondaForce< DIM >

A force class for use in vertex-based simulations, based on a mechanical model proposed by T. Nagai and H. Honda ("A dynamic cell model for the formation of epithelial tissues", Philosophical Magazine Part B 81:699-719).

Each of the model parameter member variables are rescaled such that mDampingConstantNormal takes the default value 1, whereas Nagai and Honda (who denote the parameter by nu) take the value 0.01.

Definition at line 50 of file NagaiHondaForce.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NagaiHondaForce< DIM >::NagaiHondaForce ( ) [inline]

Constructor.

Definition at line 31 of file NagaiHondaForce.cpp.

template<unsigned DIM>

NagaiHondaForce< DIM >::~NagaiHondaForce ( ) [inline]

Destructor.

Definition at line 42 of file NagaiHondaForce.cpp.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

void NagaiHondaForce< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Serialization of singleton objects must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractForce< DIM >.

Definition at line 83 of file NagaiHondaForce.hpp.

References NagaiHondaForce< DIM >::mMatureCellTargetArea, NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter, and NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.

template<unsigned DIM>

void NagaiHondaForce< DIM >::AddForceContribution	(	std::vector< c_vector< double, DIM > > &	rForces,
		AbstractCellPopulation< DIM > &	rCellPopulation
	)			`[inline, virtual]`

Overridden AddForceContribution() method.

Calculates the force on each node in the vertex-based cell population based on the Nagai Honda model.

Parameters:

	rForces	reference to vector of forces on nodes
	rCellPopulation	reference to the cell population

Implements AbstractForce< DIM >.

Definition at line 47 of file NagaiHondaForce.cpp.

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetAdhesionParameter	(	Node< DIM > *	pNodeA,
		Node< DIM > *	pNodeB
	)			`[inline]`

Get the adhesion parameter for the edge between two given nodes.

Parameters:

	pNodeA	one node
	pNodeB	the other node

Returns:: the adhesion parameter for this edge.

Definition at line 158 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter(), NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter(), and Node< SPACE_DIM >::rGetContainingElementIndices().

Referenced by NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter ( ) [inline]

Returns:: mNagaiHondaDeformationEnergyParameter

Definition at line 187 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter.

Referenced by NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter ( ) [inline]

Returns:: mNagaiHondaMembraneSurfaceEnergyParameter

Definition at line 193 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.

Referenced by NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter ( ) [inline]

Returns:: mCellCellAdhesionEnergyParameter

Definition at line 199 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter.

Referenced by NagaiHondaForce< DIM >::GetAdhesionParameter().

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter ( ) [inline]

Returns:: mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 205 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter.

Referenced by NagaiHondaForce< DIM >::GetAdhesionParameter().

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter ( double nagaiHondaDeformationEnergyParameter ) [inline]

Set mNagaiHondaDeformationEnergyParameter.

Parameters:

nagaiHondaDeformationEnergyParameter

the new value of mNagaiHondaDeformationEnergyParameter

Definition at line 211 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter.

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter ( double nagaiHondaMembraneSurfaceEnergyParameter ) [inline]

Set mNagaiHondaMembraneSurfaceEnergyParameter.

Parameters:

nagaiHondaMembraneSurfaceEnergyParameter

the new value of mNagaiHondaMembraneSurfaceEnergyParameter

Definition at line 217 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaCellCellAdhesionEnergyParameter ( double nagaiHondaCellCellAdhesionEnergyEnergyParameter ) [inline]

Set mNagaiHondaCellCellAdhesionEnergyParameter.

Parameters:

nagaiHondaCellCellAdhesionEnergyEnergyParameter

the new value of mNagaiHondaCellCellAdhesionEnergyParameter

Definition at line 223 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter.

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter ( double nagaiHondaCellBoundaryAdhesionEnergyParameter ) [inline]

Set mNagaiHondaCellBoundaryAdhesionEnergyParameter.

Parameters:

nagaiHondaCellBoundaryAdhesionEnergyParameter

the new value of mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 229 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter.

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetTargetAreaOfCell ( const CellPtr pCell ) const [inline]

Get the target area of a given cell. This grows linearly from 0.5*A to A during the G1 phase of the cell cycle, then remains at A for the rest of the cell cycle, where A denotes the member variable mMatureCellTargetArea.

Parameters:

pCell

the cell

Returns:: the cell's target area

Definition at line 235 of file NagaiHondaForce.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), and NagaiHondaForce< DIM >::mMatureCellTargetArea.

Referenced by NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetMatureCellTargetArea ( ) const [inline]

Returns:: mMatureCellTargetArea

Definition at line 280 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mMatureCellTargetArea.

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetMatureCellTargetArea ( double matureCellTargetArea ) [inline]

Set mMatureCellTargetArea.

Parameters:

matureCellTargetArea

the new value of mMatureCellTargetArea

Definition at line 286 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mMatureCellTargetArea.

template<unsigned DIM>

void NagaiHondaForce< DIM >::OutputForceParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs force parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

rParamsFile

the file stream to which the parameters are output

Implements AbstractForce< DIM >.

Definition at line 293 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mMatureCellTargetArea, NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter, and AbstractForce< DIM >::OutputForceParameters().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractForce< DIM >.

Definition at line 81 of file NagaiHondaForce.hpp.

Member Data Documentation

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter [private]

Cell deformation energy parameter. Has units of kg s^-2 (cell size at equilibrium rest length)^-1.

Definition at line 59 of file NagaiHondaForce.hpp.

Referenced by NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter().

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter [private]

Cell membrane energy parameter. Has units of kg (cell size at equilibrium rest length) s^-2.

Definition at line 64 of file NagaiHondaForce.hpp.

Referenced by NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter().

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter [private]

Cell-cell adhesion energy parameter. Has has units of kg (cell size at equilibrium rest length)^2 s^-2.

Definition at line 69 of file NagaiHondaForce.hpp.

Referenced by NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaCellCellAdhesionEnergyParameter().

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter [private]

Cell-boundary adhesion energy parameter. Has units of kg (cell size at equilibrium rest length)^2 s^-2.

Definition at line 74 of file NagaiHondaForce.hpp.

Referenced by NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter().

template<unsigned DIM>

double NagaiHondaForce< DIM >::mMatureCellTargetArea [private]

Non-dimensional target area of a mature (fully-grown) Cell.

Definition at line 79 of file NagaiHondaForce.hpp.

Referenced by NagaiHondaForce< DIM >::GetMatureCellTargetArea(), NagaiHondaForce< DIM >::GetTargetAreaOfCell(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetMatureCellTargetArea().

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

cell_based/src/population/mechanics/NagaiHondaForce.hpp
cell_based/src/population/mechanics/NagaiHondaForce.cpp


Public Member Functions
	NagaiHondaForce ()
	~NagaiHondaForce ()
void	AddForceContribution (std::vector< c_vector< double, DIM > > &rForces, AbstractCellPopulation< DIM > &rCellPopulation)
double	GetAdhesionParameter (Node< DIM > pNodeA, Node< DIM > pNodeB)
double	GetNagaiHondaDeformationEnergyParameter ()
double	GetNagaiHondaMembraneSurfaceEnergyParameter ()
double	GetNagaiHondaCellCellAdhesionEnergyParameter ()
double	GetNagaiHondaCellBoundaryAdhesionEnergyParameter ()
void	SetNagaiHondaDeformationEnergyParameter (double nagaiHondaDeformationEnergyParameter)
void	SetNagaiHondaMembraneSurfaceEnergyParameter (double nagaiHondaMembraneSurfaceEnergyParameter)
void	SetNagaiHondaCellCellAdhesionEnergyParameter (double nagaiHondaCellCellAdhesionEnergyEnergyParameter)
void	SetNagaiHondaCellBoundaryAdhesionEnergyParameter (double nagaiHondaCellBoundaryAdhesionEnergyParameter)
double	GetTargetAreaOfCell (const CellPtr pCell) const
double	GetMatureCellTargetArea () const
void	SetMatureCellTargetArea (double matureCellTargetArea)
void	OutputForceParameters (out_stream &rParamsFile)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mNagaiHondaDeformationEnergyParameter
double	mNagaiHondaMembraneSurfaceEnergyParameter
double	mNagaiHondaCellCellAdhesionEnergyParameter
double	mNagaiHondaCellBoundaryAdhesionEnergyParameter
double	mMatureCellTargetArea
Friends
class	TestForces
class	boost::serialization::access

NagaiHondaForce< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class NagaiHondaForce< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class NagaiHondaForce< DIM >