NagaiHondaForce< DIM > Class Template Reference

#include <NagaiHondaForce.hpp>

Inheritance diagram for NagaiHondaForce< DIM >:

Collaboration diagram for NagaiHondaForce< DIM >:

Public Member Functions
	NagaiHondaForce ()
virtual	~NagaiHondaForce ()
virtual void	AddForceContribution (AbstractCellPopulation< DIM > &rCellPopulation)
virtual double	GetAdhesionParameter (Node< DIM > *pNodeA, Node< DIM > *pNodeB, VertexBasedCellPopulation< DIM > &rVertexCellPopulation)
double	GetNagaiHondaDeformationEnergyParameter ()
double	GetNagaiHondaMembraneSurfaceEnergyParameter ()
double	GetNagaiHondaCellCellAdhesionEnergyParameter ()
double	GetNagaiHondaCellBoundaryAdhesionEnergyParameter ()
double	GetNagaiHondaTargetAreaParameter ()
void	SetNagaiHondaDeformationEnergyParameter (double nagaiHondaDeformationEnergyParameter)
void	SetNagaiHondaMembraneSurfaceEnergyParameter (double nagaiHondaMembraneSurfaceEnergyParameter)
void	SetNagaiHondaCellCellAdhesionEnergyParameter (double nagaiHondaCellCellAdhesionEnergyEnergyParameter)
void	SetNagaiHondaCellBoundaryAdhesionEnergyParameter (double nagaiHondaCellBoundaryAdhesionEnergyParameter)
void	SetNagaiHondaTargetAreaParameter (double nagaiHondaTargetAreaParameter)
void	OutputForceParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractForce< DIM >
	AbstractForce ()
virtual	~AbstractForce ()
virtual void	AddForceContribution (AbstractCellPopulation< ELEMENT_DIM, SPACE_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

Protected Attributes
double	mNagaiHondaDeformationEnergyParameter
double	mNagaiHondaMembraneSurfaceEnergyParameter
double	mNagaiHondaCellCellAdhesionEnergyParameter
double	mNagaiHondaCellBoundaryAdhesionEnergyParameter
double	mNagaiHondaTargetAreaParameter

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

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). In contrast to the force proposed by Nagai and Honda this force has an additional force term implemented that scales with the perimeter of a cell to simulate the surface membrane energy. This particular perimeter force term in turn differs from the one proposed by Farhadifar et al (2007) in the sense that it employs a target perimeter.

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 61 of file NagaiHondaForce.hpp.

Constructor & Destructor Documentation

NagaiHondaForce()

template<unsigned DIM>

NagaiHondaForce< DIM >::NagaiHondaForce

(

)

Constructor.

Definition at line 39 of file NagaiHondaForce.cpp.

~NagaiHondaForce()

template<unsigned DIM>

NagaiHondaForce< DIM >::~NagaiHondaForce ( )

virtual

Destructor.

Definition at line 53 of file NagaiHondaForce.cpp.

Member Function Documentation

AddForceContribution()

template<unsigned DIM>

void NagaiHondaForce< DIM >::AddForceContribution ( AbstractCellPopulation< DIM > &  rCellPopulation )

virtual

Overridden AddForceContribution() method.

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

Parameters

rCellPopulation

reference to the cell population

Definition at line 58 of file NagaiHondaForce.cpp.

References Node< SPACE_DIM >::AddAppliedForceContribution(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), VertexBasedCellPopulation< DIM >::GetElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexBasedCellPopulation< DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), VertexBasedCellPopulation< DIM >::GetNumElements(), VertexBasedCellPopulation< DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), Node< SPACE_DIM >::rGetContainingElementIndices(), and VertexBasedCellPopulation< DIM >::rGetMesh().

GetAdhesionParameter()

template<unsigned DIM>

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

virtual

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

Parameters

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

Returns

the adhesion parameter for this edge.

Reimplemented in NagaiHondaDifferentialAdhesionForce< DIM >.

Definition at line 172 of file NagaiHondaForce.cpp.

References Node< SPACE_DIM >::rGetContainingElementIndices().

GetNagaiHondaCellBoundaryAdhesionEnergyParameter()

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter

(

)

Returns

mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 219 of file NagaiHondaForce.cpp.

GetNagaiHondaCellCellAdhesionEnergyParameter()

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter

(

)

Returns

mCellCellAdhesionEnergyParameter

Definition at line 213 of file NagaiHondaForce.cpp.

GetNagaiHondaDeformationEnergyParameter()

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter

(

)

Returns

mNagaiHondaDeformationEnergyParameter

Definition at line 201 of file NagaiHondaForce.cpp.

GetNagaiHondaMembraneSurfaceEnergyParameter()

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter

(

)

Returns

mNagaiHondaMembraneSurfaceEnergyParameter

Definition at line 207 of file NagaiHondaForce.cpp.

GetNagaiHondaTargetAreaParameter()

template<unsigned DIM>

double NagaiHondaForce< DIM >::GetNagaiHondaTargetAreaParameter

(

)

Returns

mNagaiHondaTargetAreaParameter

Definition at line 225 of file NagaiHondaForce.cpp.

OutputForceParameters()

template<unsigned DIM>

void NagaiHondaForce< 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 261 of file NagaiHondaForce.cpp.

References AbstractForce< ELEMENT_DIM, SPACE_DIM >::OutputForceParameters().

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

serialize()

template<unsigned DIM>

template<class Archive >

void NagaiHondaForce< 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 76 of file NagaiHondaForce.hpp.

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

SetNagaiHondaCellBoundaryAdhesionEnergyParameter()

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter

(

double

nagaiHondaCellBoundaryAdhesionEnergyParameter

)

Set mNagaiHondaCellBoundaryAdhesionEnergyParameter.

Parameters

nagaiHondaCellBoundaryAdhesionEnergyParameter

the new value of mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 249 of file NagaiHondaForce.cpp.

SetNagaiHondaCellCellAdhesionEnergyParameter()

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaCellCellAdhesionEnergyParameter

(

double

nagaiHondaCellCellAdhesionEnergyEnergyParameter

)

Set mNagaiHondaCellCellAdhesionEnergyParameter. This parameter corresponds to 1/2 of the sigma parameter in the forces by Nagai et al. (2007).

Parameters

nagaiHondaCellCellAdhesionEnergyEnergyParameter

the new value of mNagaiHondaCellCellAdhesionEnergyParameter

Definition at line 243 of file NagaiHondaForce.cpp.

SetNagaiHondaDeformationEnergyParameter()

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter

(

double

nagaiHondaDeformationEnergyParameter

)

Set mNagaiHondaDeformationEnergyParameter.

Parameters

nagaiHondaDeformationEnergyParameter

the new value of mNagaiHondaDeformationEnergyParameter

Definition at line 231 of file NagaiHondaForce.cpp.

SetNagaiHondaMembraneSurfaceEnergyParameter()

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter

(

double

nagaiHondaMembraneSurfaceEnergyParameter

)

Set mNagaiHondaMembraneSurfaceEnergyParameter.

Parameters

nagaiHondaMembraneSurfaceEnergyParameter

the new value of mNagaiHondaMembraneSurfaceEnergyParameter

Definition at line 237 of file NagaiHondaForce.cpp.

SetNagaiHondaTargetAreaParameter()

template<unsigned DIM>

void NagaiHondaForce< DIM >::SetNagaiHondaTargetAreaParameter

(

double

nagaiHondaTargetAreaParameter

)

Set mNagaiHondaTargetAreaParameter.

Parameters

nagaiHondaTargetAreaParameter

the new value of mNagaiHondaTargetAreaParameter

Definition at line 255 of file NagaiHondaForce.cpp.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Definition at line 67 of file NagaiHondaForce.hpp.

TestForces

template<unsigned DIM>

friend class TestForces

friend

Definition at line 63 of file NagaiHondaForce.hpp.

Member Data Documentation

mNagaiHondaCellBoundaryAdhesionEnergyParameter

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter

protected

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

Definition at line 109 of file NagaiHondaForce.hpp.

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

mNagaiHondaCellCellAdhesionEnergyParameter

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter

protected

Cell-cell adhesion energy parameter. Has has units of kg (cell size at equilibrium rest length)^2 s^-2. This parameter corresponds to 1/2 of the sigma parameter introduced in the original paper. This slight difference comes from the fact that when we apply the forces to a particular node, each edge is visited twice - and hence the force originating from that edge is applied twice.

Definition at line 104 of file NagaiHondaForce.hpp.

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

mNagaiHondaDeformationEnergyParameter

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter

protected

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

Definition at line 91 of file NagaiHondaForce.hpp.

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

mNagaiHondaMembraneSurfaceEnergyParameter

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter

protected

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

Definition at line 96 of file NagaiHondaForce.hpp.

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

mNagaiHondaTargetAreaParameter

template<unsigned DIM>

double NagaiHondaForce< DIM >::mNagaiHondaTargetAreaParameter

protected

Target area parameter. Has units of (cell size at equilibrium rest length)^2.

Note: If a subclass of AbstractTargetAreaModifier is present in the cell-based simulation, then we use the CellData item "target area" stored in each Cell in the force calculation instead of this parameter value.

Definition at line 118 of file NagaiHondaForce.hpp.

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

---

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

• cell_based/src/population/forces/NagaiHondaForce.hpp
• cell_based/src/population/forces/NagaiHondaForce.cpp