#include <NagaiHondaForce.hpp>
Inheritance diagram for NagaiHondaForce< DIM >: Collaboration diagram for NagaiHondaForce< DIM >: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< DIM >::NagaiHondaForce | ( | ) |
Constructor.
Definition at line 39 of file NagaiHondaForce.cpp.
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virtual |
Destructor.
Definition at line 52 of file NagaiHondaForce.cpp.
Member Function Documentation
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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 57 of file NagaiHondaForce.cpp.
References EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::GetCellUsingLocationIndex(), VertexBasedCellPopulation< SPACE_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(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), VertexBasedCellPopulation< SPACE_DIM >::GetNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), VertexBasedCellPopulation< SPACE_DIM >::GetNumElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexBasedCellPopulation< SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), and VertexBasedCellPopulation< SPACE_DIM >::rGetMesh().
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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 166 of file NagaiHondaForce.cpp.
References Node< SPACE_DIM >::rGetContainingElementIndices().
| double NagaiHondaForce< DIM >::GetNagaiHondaCellBoundaryAdhesionEnergyParameter | ( | ) |
- Returns
- mNagaiHondaCellBoundaryAdhesionEnergyParameter
Definition at line 213 of file NagaiHondaForce.cpp.
| double NagaiHondaForce< DIM >::GetNagaiHondaCellCellAdhesionEnergyParameter | ( | ) |
- Returns
- mCellCellAdhesionEnergyParameter
Definition at line 207 of file NagaiHondaForce.cpp.
| double NagaiHondaForce< DIM >::GetNagaiHondaDeformationEnergyParameter | ( | ) |
- Returns
- mNagaiHondaDeformationEnergyParameter
Definition at line 195 of file NagaiHondaForce.cpp.
| double NagaiHondaForce< DIM >::GetNagaiHondaMembraneSurfaceEnergyParameter | ( | ) |
- Returns
- mNagaiHondaMembraneSurfaceEnergyParameter
Definition at line 201 of file NagaiHondaForce.cpp.
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virtual |
Overridden OutputForceParameters() method.
- Parameters
-
rParamsFile the file stream to which the parameters are output
Implements AbstractForce< DIM >.
Definition at line 243 of file NagaiHondaForce.cpp.
References AbstractForce< ELEMENT_DIM, SPACE_DIM >::OutputForceParameters().
Referenced by NagaiHondaDifferentialAdhesionForce< DIM >::OutputForceParameters().
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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, and NagaiHondaForce< DIM >::mNagaiHondaMembraneSurfaceEnergyParameter.
| void NagaiHondaForce< DIM >::SetNagaiHondaCellBoundaryAdhesionEnergyParameter | ( | double | nagaiHondaCellBoundaryAdhesionEnergyParameter | ) |
Set mNagaiHondaCellBoundaryAdhesionEnergyParameter.
- Parameters
-
nagaiHondaCellBoundaryAdhesionEnergyParameter the new value of mNagaiHondaCellBoundaryAdhesionEnergyParameter
Definition at line 237 of file NagaiHondaForce.cpp.
| 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 231 of file NagaiHondaForce.cpp.
| void NagaiHondaForce< DIM >::SetNagaiHondaDeformationEnergyParameter | ( | double | nagaiHondaDeformationEnergyParameter | ) |
Set mNagaiHondaDeformationEnergyParameter.
- Parameters
-
nagaiHondaDeformationEnergyParameter the new value of mNagaiHondaDeformationEnergyParameter
Definition at line 219 of file NagaiHondaForce.cpp.
| void NagaiHondaForce< DIM >::SetNagaiHondaMembraneSurfaceEnergyParameter | ( | double | nagaiHondaMembraneSurfaceEnergyParameter | ) |
Set mNagaiHondaMembraneSurfaceEnergyParameter.
- Parameters
-
nagaiHondaMembraneSurfaceEnergyParameter the new value of mNagaiHondaMembraneSurfaceEnergyParameter
Definition at line 225 of file NagaiHondaForce.cpp.
Member Data Documentation
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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 >::serialize().
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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 103 of file NagaiHondaForce.hpp.
Referenced by NagaiHondaForce< DIM >::serialize().
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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 >::serialize().
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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 >::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
