NagaiHondaForce< DIM > Class Template Reference

#include <NagaiHondaForce.hpp>

Inherits AbstractForce< DIM >.

Inherited by NagaiHondaDifferentialAdhesionForce< DIM >.

Collaboration diagram for NagaiHondaForce< DIM >:

List of all members.

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 ()
void SetNagaiHondaDeformationEnergyParameter (double nagaiHondaDeformationEnergyParameter)
void SetNagaiHondaMembraneSurfaceEnergyParameter (double nagaiHondaMembraneSurfaceEnergyParameter)
void SetNagaiHondaCellCellAdhesionEnergyParameter (double nagaiHondaCellCellAdhesionEnergyEnergyParameter)
void SetNagaiHondaCellBoundaryAdhesionEnergyParameter (double nagaiHondaCellBoundaryAdhesionEnergyParameter)
void OutputForceParameters (out_stream &rParamsFile)

Protected Attributes

double mNagaiHondaDeformationEnergyParameter
double mNagaiHondaMembraneSurfaceEnergyParameter
double mNagaiHondaCellCellAdhesionEnergyParameter
double mNagaiHondaCellBoundaryAdhesionEnergyParameter

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

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

Constructor.

Definition at line 39 of file NagaiHondaForce.cpp.

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

Destructor.

Definition at line 49 of file NagaiHondaForce.cpp.


Member Function Documentation

template<unsigned DIM>
void NagaiHondaForce< DIM >::AddForceContribution ( AbstractCellPopulation< DIM > &  rCellPopulation  )  [inline, virtual]
template<unsigned DIM>
double NagaiHondaForce< DIM >::GetAdhesionParameter ( Node< DIM > *  pNodeA,
Node< DIM > *  pNodeB,
VertexBasedCellPopulation< DIM > &  rVertexCellPopulation 
) [inline, 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 163 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 >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter (  )  [inline]
template<unsigned DIM>
double NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter (  )  [inline]
template<unsigned DIM>
double NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter (  )  [inline]
Returns:
mNagaiHondaDeformationEnergyParameter

Definition at line 192 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 198 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.

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

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

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.

Reimplemented from AbstractForce< DIM >.

Reimplemented in NagaiHondaDifferentialAdhesionForce< DIM >.

Definition at line 76 of file NagaiHondaForce.hpp.

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

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

Set mNagaiHondaCellBoundaryAdhesionEnergyParameter.

Parameters:
nagaiHondaCellBoundaryAdhesionEnergyParameter the new value of mNagaiHondaCellBoundaryAdhesionEnergyParameter

Definition at line 234 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter.

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

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

Parameters:
nagaiHondaCellCellAdhesionEnergyEnergyParameter the new value of mNagaiHondaCellCellAdhesionEnergyParameter

Definition at line 228 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter.

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

Set mNagaiHondaDeformationEnergyParameter.

Parameters:
nagaiHondaDeformationEnergyParameter the new value of mNagaiHondaDeformationEnergyParameter

Definition at line 216 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 222 of file NagaiHondaForce.cpp.

References NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.


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 67 of file NagaiHondaForce.hpp.


Member Data Documentation

template<unsigned DIM>
double NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter [protected]
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 Lambda parameter in forces proposed by Farhadifar et al (2007). 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 103 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 >::mNagaiHondaDeformationEnergyParameter [protected]
template<unsigned DIM>
double NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter [protected]

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

Generated by  doxygen 1.6.2