#include <NagaiHondaForce.hpp>
Inherits AbstractForce< DIM >.
Inherited by NagaiHondaDifferentialAdhesionForce< 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.
NagaiHondaForce< DIM >::NagaiHondaForce | ( | ) | [inline] |
Constructor.
Definition at line 39 of file NagaiHondaForce.cpp.
NagaiHondaForce< DIM >::~NagaiHondaForce | ( | ) | [inline, virtual] |
Destructor.
Definition at line 49 of file NagaiHondaForce.cpp.
void NagaiHondaForce< DIM >::AddForceContribution | ( | AbstractCellPopulation< DIM > & | rCellPopulation | ) | [inline, virtual] |
Overridden AddForceContribution() method.
Calculates the force on each node in the vertex-based cell population based on the Nagai Honda model.
rCellPopulation | reference to the cell population |
Definition at line 54 of file NagaiHondaForce.cpp.
References EXCEPTION, NagaiHondaForce< DIM >::GetAdhesionParameter(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), VertexBasedCellPopulation< DIM >::GetElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter(), NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), VertexBasedCellPopulation< DIM >::GetNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), VertexBasedCellPopulation< DIM >::GetNumElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexBasedCellPopulation< DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), and VertexBasedCellPopulation< DIM >::rGetMesh().
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.
pNodeA | one node | |
pNodeB | the other node | |
rVertexCellPopulation | reference to the cell population |
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().
double NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter | ( | ) | [inline] |
Definition at line 210 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter.
Referenced by NagaiHondaForce< DIM >::GetAdhesionParameter(), and NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter().
double NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter | ( | ) | [inline] |
Definition at line 204 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter.
Referenced by NagaiHondaForce< DIM >::GetAdhesionParameter(), and NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter().
double NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter | ( | ) | [inline] |
Definition at line 192 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter.
Referenced by NagaiHondaForce< DIM >::AddForceContribution().
double NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter | ( | ) | [inline] |
Definition at line 198 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.
Referenced by NagaiHondaForce< DIM >::AddForceContribution().
void NagaiHondaForce< DIM >::OutputForceParameters | ( | out_stream & | rParamsFile | ) | [inline, virtual] |
Overridden OutputForceParameters() method.
rParamsFile | the file stream to which the parameters are output |
Implements AbstractForce< DIM >.
Reimplemented in NagaiHondaDifferentialAdhesionForce< DIM >.
Definition at line 241 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter, NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter, and NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.
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.
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.
void NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter | ( | double | nagaiHondaCellBoundaryAdhesionEnergyParameter | ) | [inline] |
Set mNagaiHondaCellBoundaryAdhesionEnergyParameter.
nagaiHondaCellBoundaryAdhesionEnergyParameter | the new value of mNagaiHondaCellBoundaryAdhesionEnergyParameter |
Definition at line 234 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaCellBoundaryAdhesionEnergyParameter.
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).
nagaiHondaCellCellAdhesionEnergyEnergyParameter | the new value of mNagaiHondaCellCellAdhesionEnergyParameter |
Definition at line 228 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaCellCellAdhesionEnergyParameter.
void NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter | ( | double | nagaiHondaDeformationEnergyParameter | ) | [inline] |
Set mNagaiHondaDeformationEnergyParameter.
nagaiHondaDeformationEnergyParameter | the new value of mNagaiHondaDeformationEnergyParameter |
Definition at line 216 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaDeformationEnergyParameter.
void NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter | ( | double | nagaiHondaMembraneSurfaceEnergyParameter | ) | [inline] |
Set mNagaiHondaMembraneSurfaceEnergyParameter.
nagaiHondaMembraneSurfaceEnergyParameter | the new value of mNagaiHondaMembraneSurfaceEnergyParameter |
Definition at line 222 of file NagaiHondaForce.cpp.
References NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.
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.
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 108 of file NagaiHondaForce.hpp.
Referenced by NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter().
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().
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 90 of file NagaiHondaForce.hpp.
Referenced by NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter().
double NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter [protected] |
Cell membrane energy parameter. Has units of kg (cell size at equilibrium rest length) s^-2.
Definition at line 95 of file NagaiHondaForce.hpp.
Referenced by NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter(), NagaiHondaForce< DIM >::OutputForceParameters(), NagaiHondaForce< DIM >::serialize(), and NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter().