#include <NagaiHondaDifferentialAdhesionForce.hpp>

Inheritance diagram for NagaiHondaDifferentialAdhesionForce< DIM >:

Collaboration diagram for NagaiHondaDifferentialAdhesionForce< DIM >:

Public Member Functions
	NagaiHondaDifferentialAdhesionForce ()

virtual	~NagaiHondaDifferentialAdhesionForce ()

virtual double	GetAdhesionParameter (Node< DIM > pNodeA, Node< DIM > pNodeB, VertexBasedCellPopulation< DIM > &rVertexCellPopulation)

double	GetNagaiHondaLabelledCellCellAdhesionEnergyParameter ()

double	GetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter ()

double	GetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter ()

void	SetNagaiHondaLabelledCellCellAdhesionEnergyParameter (double labelledCellCellAdhesionEnergyParameter)

void	SetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter (double labelledCellLabelledCellAdhesionEnergyParameter)

void	SetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter (double labelledCellBoundaryAdhesionEnergyParameter)

void	OutputForceParameters (out_stream &rParamsFile)

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

virtual	~NagaiHondaForce ()

virtual void	AddForceContribution (AbstractCellPopulation< DIM > &rCellPopulation)

double	GetNagaiHondaDeformationEnergyParameter ()

double	GetNagaiHondaMembraneSurfaceEnergyParameter ()

double	GetNagaiHondaCellCellAdhesionEnergyParameter ()

double	GetNagaiHondaCellBoundaryAdhesionEnergyParameter ()

void	SetNagaiHondaDeformationEnergyParameter (double nagaiHondaDeformationEnergyParameter)

void	SetNagaiHondaMembraneSurfaceEnergyParameter (double nagaiHondaMembraneSurfaceEnergyParameter)

void	SetNagaiHondaCellCellAdhesionEnergyParameter (double nagaiHondaCellCellAdhesionEnergyEnergyParameter)

void	SetNagaiHondaCellBoundaryAdhesionEnergyParameter (double nagaiHondaCellBoundaryAdhesionEnergyParameter)

void	OutputForceParameters (out_stream &rParamsFile)

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

virtual	~AbstractForce ()

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

void	OutputForceInfo (out_stream &rParamsFile)

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

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	mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

double	mNagaiHondaLabelledCellCellAdhesionEnergyParameter

double	mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from NagaiHondaForce< DIM >
double	mNagaiHondaDeformationEnergyParameter

double	mNagaiHondaMembraneSurfaceEnergyParameter

double	mNagaiHondaCellCellAdhesionEnergyParameter

double	mNagaiHondaCellBoundaryAdhesionEnergyParameter

Detailed Description

template<unsigned DIM>
class NagaiHondaDifferentialAdhesionForce< DIM >

A force class for use in vertex-based simulations, based on a model 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) to include differential adhesion between normal and labelled cells. To include differential adhesion we override the GetAdhesionParameter() method.

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 59 of file NagaiHondaDifferentialAdhesionForce.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NagaiHondaDifferentialAdhesionForce< DIM >::NagaiHondaDifferentialAdhesionForce ( )

Constructor.

Definition at line 40 of file NagaiHondaDifferentialAdhesionForce.cpp.

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

template<unsigned DIM>

NagaiHondaDifferentialAdhesionForce< DIM >::~NagaiHondaDifferentialAdhesionForce ( )

virtual

Destructor.

Definition at line 49 of file NagaiHondaDifferentialAdhesionForce.cpp.

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

Member Function Documentation

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter	(	Node< DIM > *	pNodeA,
		Node< DIM > *	pNodeB,
		VertexBasedCellPopulation< DIM > &	rVertexCellPopulation
	)

virtual

Overridden GetAdhesionParameter() method.

Get the adhesion parameter for the edge between two given nodes. Depends on the type of cells attached to the elements.

Parameters

pNodeA	one node
pNodeB	the other node
rVertexCellPopulation	reference to the cell population

Returns: the adhesion parameter for this edge.

Reimplemented from NagaiHondaForce< DIM >.

Definition at line 54 of file NagaiHondaDifferentialAdhesionForce.cpp.

References AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter(), NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellCellAdhesionEnergyParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter(), and Node< SPACE_DIM >::rGetContainingElementIndices().

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

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter ( )

Returns: mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

Definition at line 143 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter.

Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter(), and NagaiHondaDifferentialAdhesionForce< DIM >::serialize().

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellCellAdhesionEnergyParameter ( )

Returns: mNagaiHondaLabelledCellCellAdhesionEnergyParameter

Definition at line 131 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellCellAdhesionEnergyParameter.

Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter(), and NagaiHondaDifferentialAdhesionForce< DIM >::serialize().

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter ( )

Returns: mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

Definition at line 137 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter.

Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter(), and NagaiHondaDifferentialAdhesionForce< DIM >::serialize().

template<unsigned DIM>

void NagaiHondaDifferentialAdhesionForce< DIM >::OutputForceParameters ( out_stream & rParamsFile )

virtual

Overridden OutputForceParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractForce< DIM >.

Definition at line 167 of file NagaiHondaDifferentialAdhesionForce.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter, NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellCellAdhesionEnergyParameter, NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter, and NagaiHondaForce< DIM >::OutputForceParameters().

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

template<unsigned DIM>

template<class Archive >

void NagaiHondaDifferentialAdhesionForce< 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 93 of file NagaiHondaDifferentialAdhesionForce.hpp.

template<unsigned DIM>

void NagaiHondaDifferentialAdhesionForce< DIM >::SetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter ( double labelledCellBoundaryAdhesionEnergyParameter )

Set mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter.

Parameters

labelledCellBoundaryAdhesionEnergyParameter the new value of mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

Definition at line 161 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter.

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

template<unsigned DIM>

void NagaiHondaDifferentialAdhesionForce< DIM >::SetNagaiHondaLabelledCellCellAdhesionEnergyParameter ( double labelledCellCellAdhesionEnergyParameter )

Set mNagaiHondaLabelledCellCellAdhesionEnergyParameter.

Parameters

labelledCellCellAdhesionEnergyParameter the new value of mNagaiHondaLabelledCellCellAdhesionEnergyParameter

Definition at line 149 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellCellAdhesionEnergyParameter.

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

template<unsigned DIM>

void NagaiHondaDifferentialAdhesionForce< DIM >::SetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter ( double labelledCellLabelledCellAdhesionEnergyParameter )

Set mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter.

Parameters

labelledCellLabelledCellAdhesionEnergyParameter the new value of mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

Definition at line 155 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter.

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

Member Data Documentation

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

private

Cell-boundary adhesion energy parameter for labelled cells. Has units of kg (cell size at equilibrium rest length)^2 s^-2. Takes the default value 1.0.

Definition at line 82 of file NagaiHondaDifferentialAdhesionForce.hpp.

Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::OutputForceParameters(), NagaiHondaDifferentialAdhesionForce< DIM >::serialize(), and NagaiHondaDifferentialAdhesionForce< DIM >::SetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter().

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellCellAdhesionEnergyParameter

private

Cell-cell adhesion energy parameter for labelled and non-labelled cells. Has has units of kg (cell size at equilibrium rest length)^2 s^-2. Takes the default value 1.0.

Definition at line 75 of file NagaiHondaDifferentialAdhesionForce.hpp.

Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellCellAdhesionEnergyParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::OutputForceParameters(), NagaiHondaDifferentialAdhesionForce< DIM >::serialize(), and NagaiHondaDifferentialAdhesionForce< DIM >::SetNagaiHondaLabelledCellCellAdhesionEnergyParameter().

template<unsigned DIM>

double NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

private

Cell-cell adhesion energy parameter for two labelled cells. Has units of kg (cell size at equilibrium rest length)^2 s^-2. Takes the default value 1.0.

Definition at line 68 of file NagaiHondaDifferentialAdhesionForce.hpp.

Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::OutputForceParameters(), NagaiHondaDifferentialAdhesionForce< DIM >::serialize(), and NagaiHondaDifferentialAdhesionForce< DIM >::SetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter().

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

cell_based/src/population/forces/NagaiHondaDifferentialAdhesionForce.hpp
cell_based/src/population/forces/NagaiHondaDifferentialAdhesionForce.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class NagaiHondaDifferentialAdhesionForce< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class NagaiHondaDifferentialAdhesionForce< DIM >