Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
NagaiHondaDifferentialAdhesionForce< DIM > Class Template Reference

#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 ()
 
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
 

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
 
double mNagaiHondaTargetAreaParameter
 

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

◆ NagaiHondaDifferentialAdhesionForce()

◆ ~NagaiHondaDifferentialAdhesionForce()

Destructor.

Definition at line 49 of file NagaiHondaDifferentialAdhesionForce.cpp.

Member Function Documentation

◆ GetAdhesionParameter()

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
pNodeAone node
pNodeBthe other node
rVertexCellPopulationreference 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, SPACE_DIM >::GetCellUsingLocationIndex(), and Node< SPACE_DIM >::rGetContainingElementIndices().

◆ GetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter()

template<unsigned DIM>
double NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter ( )
Returns
mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

Definition at line 143 of file NagaiHondaDifferentialAdhesionForce.cpp.

◆ GetNagaiHondaLabelledCellCellAdhesionEnergyParameter()

template<unsigned DIM>
double NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellCellAdhesionEnergyParameter ( )
Returns
mNagaiHondaLabelledCellCellAdhesionEnergyParameter

Definition at line 131 of file NagaiHondaDifferentialAdhesionForce.cpp.

◆ GetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter()

template<unsigned DIM>
double NagaiHondaDifferentialAdhesionForce< DIM >::GetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter ( )
Returns
mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

Definition at line 137 of file NagaiHondaDifferentialAdhesionForce.cpp.

◆ OutputForceParameters()

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

Overridden OutputForceParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Implements AbstractForce< DIM >.

Definition at line 167 of file NagaiHondaDifferentialAdhesionForce.cpp.

References NagaiHondaForce< DIM >::OutputForceParameters().

◆ 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
archiveThe boost archive.
versionThe current version of this class.

Definition at line 93 of file NagaiHondaDifferentialAdhesionForce.hpp.

References NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter, NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellCellAdhesionEnergyParameter, and NagaiHondaDifferentialAdhesionForce< DIM >::mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter.

◆ SetNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter()

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

Set mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter.

Parameters
labelledCellBoundaryAdhesionEnergyParameterthe new value of mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

Definition at line 161 of file NagaiHondaDifferentialAdhesionForce.cpp.

◆ SetNagaiHondaLabelledCellCellAdhesionEnergyParameter()

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

Set mNagaiHondaLabelledCellCellAdhesionEnergyParameter.

Parameters
labelledCellCellAdhesionEnergyParameterthe new value of mNagaiHondaLabelledCellCellAdhesionEnergyParameter

Definition at line 149 of file NagaiHondaDifferentialAdhesionForce.cpp.

◆ SetNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter()

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

Set mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter.

Parameters
labelledCellLabelledCellAdhesionEnergyParameterthe new value of mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

Definition at line 155 of file NagaiHondaDifferentialAdhesionForce.cpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

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

Definition at line 84 of file NagaiHondaDifferentialAdhesionForce.hpp.

Member Data Documentation

◆ mNagaiHondaLabelledCellBoundaryAdhesionEnergyParameter

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 >::serialize().

◆ mNagaiHondaLabelledCellCellAdhesionEnergyParameter

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 >::serialize().

◆ mNagaiHondaLabelledCellLabelledCellAdhesionEnergyParameter

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 >::serialize().


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