Chaste Release::3.1
Public Member Functions | Private Member Functions | Private Attributes | Friends
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 ()
virtual ~NagaiHondaForce ()
void AddForceContribution (std::vector< c_vector< double, DIM > > &rForces, AbstractCellPopulation< DIM > &rCellPopulation)
virtual double GetAdhesionParameter (Node< DIM > *pNodeA, Node< DIM > *pNodeB, VertexBasedCellPopulation< DIM > &rVertexCellPopulation)
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 57 of file NagaiHondaForce.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
NagaiHondaForce< DIM >::NagaiHondaForce ( )

Constructor.

Definition at line 39 of file NagaiHondaForce.cpp.

template<unsigned DIM>
NagaiHondaForce< DIM >::~NagaiHondaForce ( ) [virtual]

Destructor.

Definition at line 50 of file NagaiHondaForce.cpp.

Member Function Documentation

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

Overridden AddForceContribution() method.

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

Parameters:
rForcesreference to vector of forces on nodes
rCellPopulationreference to the cell population

Definition at line 55 of file NagaiHondaForce.cpp.

References EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), VertexBasedCellPopulation< DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), VertexBasedCellPopulation< DIM >::GetNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexBasedCellPopulation< DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPerimeterGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), and VertexBasedCellPopulation< DIM >::rGetMesh().

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:
pNodeAone node
pNodeBthe other node
rVertexCellPopulationreference 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().

template<unsigned DIM>
double NagaiHondaForce< DIM >::GetMatureCellTargetArea ( ) const
Returns:
mMatureCellTargetArea

Definition at line 294 of file NagaiHondaForce.cpp.

template<unsigned DIM>
double NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter ( )
Returns:
mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 219 of file NagaiHondaForce.cpp.

template<unsigned DIM>
double NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter ( )
Returns:
mCellCellAdhesionEnergyParameter

Definition at line 213 of file NagaiHondaForce.cpp.

template<unsigned DIM>
double NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter ( )
Returns:
mNagaiHondaDeformationEnergyParameter

Definition at line 201 of file NagaiHondaForce.cpp.

template<unsigned DIM>
double NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter ( )
Returns:
mNagaiHondaMembraneSurfaceEnergyParameter

Definition at line 207 of file NagaiHondaForce.cpp.

template<unsigned DIM>
double NagaiHondaForce< DIM >::GetTargetAreaOfCell ( const CellPtr  pCell) const

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:
pCellthe cell
Returns:
the cell's target area

Definition at line 249 of file NagaiHondaForce.cpp.

References SimulationTime::GetTime(), and SimulationTime::Instance().

template<unsigned DIM>
void NagaiHondaForce< DIM >::OutputForceParameters ( out_stream &  rParamsFile) [virtual]

Overridden OutputForceParameters() method.

Parameters:
rParamsFilethe file stream to which the parameters are output

Implements AbstractForce< DIM >.

Reimplemented in NagaiHondaDifferentialAdhesionForce< DIM >.

Definition at line 307 of file NagaiHondaForce.cpp.

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

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

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

Serialize the object.

Parameters:
archivethe archive
versionthe current version of this class

Reimplemented from AbstractForce< DIM >.

Reimplemented in NagaiHondaDifferentialAdhesionForce< DIM >.

Definition at line 90 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 >::SetMatureCellTargetArea ( double  matureCellTargetArea)

Set mMatureCellTargetArea.

Parameters:
matureCellTargetAreathe new value of mMatureCellTargetArea

Definition at line 300 of file NagaiHondaForce.cpp.

template<unsigned DIM>
void NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter ( double  nagaiHondaCellBoundaryAdhesionEnergyParameter)

Set mNagaiHondaCellBoundaryAdhesionEnergyParameter.

Parameters:
nagaiHondaCellBoundaryAdhesionEnergyParameterthe new value of mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 243 of file NagaiHondaForce.cpp.

template<unsigned DIM>
void NagaiHondaForce< DIM >::SetNagaiHondaCellCellAdhesionEnergyParameter ( double  nagaiHondaCellCellAdhesionEnergyEnergyParameter)

Set mNagaiHondaCellCellAdhesionEnergyParameter.

Parameters:
nagaiHondaCellCellAdhesionEnergyEnergyParameterthe new value of mNagaiHondaCellCellAdhesionEnergyParameter

Definition at line 237 of file NagaiHondaForce.cpp.

template<unsigned DIM>
void NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter ( double  nagaiHondaDeformationEnergyParameter)

Set mNagaiHondaDeformationEnergyParameter.

Parameters:
nagaiHondaDeformationEnergyParameterthe new value of mNagaiHondaDeformationEnergyParameter

Definition at line 225 of file NagaiHondaForce.cpp.

template<unsigned DIM>
void NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter ( double  nagaiHondaMembraneSurfaceEnergyParameter)

Set mNagaiHondaMembraneSurfaceEnergyParameter.

Parameters:
nagaiHondaMembraneSurfaceEnergyParameterthe new value of mNagaiHondaMembraneSurfaceEnergyParameter

Definition at line 231 of file NagaiHondaForce.cpp.

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractForce< DIM >.

Reimplemented in NagaiHondaDifferentialAdhesionForce< DIM >.

Definition at line 88 of file NagaiHondaForce.hpp.

Member Data Documentation

template<unsigned DIM>
double NagaiHondaForce< DIM >::mMatureCellTargetArea [private]

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

Definition at line 86 of file NagaiHondaForce.hpp.

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

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 81 of file NagaiHondaForce.hpp.

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

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 76 of file NagaiHondaForce.hpp.

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

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 66 of file NagaiHondaForce.hpp.

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

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 71 of file NagaiHondaForce.hpp.

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

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