LinearSpringWithVariableSpringConstantsForce< DIM > Class Template Reference

#include <LinearSpringWithVariableSpringConstantsForce.hpp>

Inheritance diagram for LinearSpringWithVariableSpringConstantsForce< DIM >:

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Collaboration diagram for LinearSpringWithVariableSpringConstantsForce< DIM >:

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List of all members.

Public Member Functions

 LinearSpringWithVariableSpringConstantsForce ()
 ~LinearSpringWithVariableSpringConstantsForce ()
void SetEdgeBasedSpringConstant (bool useEdgeBasedSpringConstant)
void SetMutantSprings (bool useMutantSprings, double mutantMutantMultiplier=2, double normalMutantMultiplier=1.5)
void SetBetaCateninSprings (bool useBCatSprings)
void SetApoptoticSprings (bool useApoptoticSprings)
double VariableSpringConstantMultiplicationFactor (unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< DIM > &rCellPopulation, bool isCloserThanRestLength)
void AddForceContribution (std::vector< c_vector< double, DIM > > &rForces, AbstractCellPopulation< DIM > &rCellPopulation)
double GetBetaCatSpringScaler ()
void SetBetaCatSpringScaler (double betaCatSpringScaler)
double GetApoptoticSpringTensionStiffness ()
void SetApoptoticSpringTensionStiffness (double apoptoticSpringTensionStiffness)
double GetApoptoticSpringCompressionStiffness ()
void SetApoptoticSpringCompressionStiffness (double apoptoticSpringCompressionStiffness)
virtual void OutputForceParameters (out_stream &rParamsFile)

Protected Attributes

bool mUseEdgeBasedSpringConstant
bool mUseMutantSprings
double mMutantMutantMultiplier
double mNormalMutantMultiplier
bool mUseBCatSprings
bool mUseApoptoticSprings
double mBetaCatSpringScaler
double mApoptoticSpringTensionStiffness
double mApoptoticSpringCompressionStiffness

Private Member Functions

template<class Archive>
void serialize (Archive &archive, const unsigned int version)

Friends

class TestLinearSpringWithVariableSpringConstantsForce
class boost::serialization::access

Detailed Description

template<unsigned DIM>
class LinearSpringWithVariableSpringConstantsForce< DIM >

A subclass of GeneralisedLinearSpringForce with variable spring constants.

Definition at line 44 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 36 of file LinearSpringWithVariableSpringConstantsForce.cpp.

template<unsigned DIM>
LinearSpringWithVariableSpringConstantsForce< DIM >::~LinearSpringWithVariableSpringConstantsForce (  )  [inline]

Destructor.

Definition at line 51 of file LinearSpringWithVariableSpringConstantsForce.cpp.

Member Function Documentation

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

Archive the object and its member variables.

Parameters:
archive the archive
version the current version of this class

Reimplemented from GeneralisedLinearSpringForce< DIM >.

Definition at line 59 of file LinearSpringWithVariableSpringConstantsForce.hpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringCompressionStiffness, LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringTensionStiffness, LinearSpringWithVariableSpringConstantsForce< DIM >::mBetaCatSpringScaler, LinearSpringWithVariableSpringConstantsForce< DIM >::mMutantMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mNormalMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseApoptoticSprings, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseBCatSprings, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseEdgeBasedSpringConstant, and LinearSpringWithVariableSpringConstantsForce< DIM >::mUseMutantSprings.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetEdgeBasedSpringConstant ( bool  useEdgeBasedSpringConstant  )  [inline]

Set whether to use an edge-based spring constant.

Parameters:
useEdgeBasedSpringConstant whether to use an edge-based spring constant

Definition at line 56 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mUseEdgeBasedSpringConstant.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetMutantSprings ( bool  useMutantSprings,
double  mutantMutantMultiplier = 2,
double  normalMutantMultiplier = 1.5 
) [inline]

Use different spring strengths depending on two cells: Normal-normal, Normal-mutant, mutant-mutant

Parameters:
useMutantSprings whether to use mutant springs
mutantMutantMultiplier the multiplier for springs connecting two mutant cells
normalMutantMultiplier the multiplier for springs connecting a mutant cell with a normal cell

Definition at line 63 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mMutantMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mNormalMutantMultiplier, and LinearSpringWithVariableSpringConstantsForce< DIM >::mUseMutantSprings.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetBetaCateninSprings ( bool  useBCatSprings  )  [inline]

Use the amount of beta-catenin on an edge to find spring constant.

Parameters:
useBCatSprings whether to use beta-catenin-dependent spring stiffness

Definition at line 71 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mUseBCatSprings.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetApoptoticSprings ( bool  useApoptoticSprings  )  [inline]

Set spring stiffness to be dependent on whether cells are apoptotic

Parameters:
useApoptoticSprings whether to have apoptosis-dependent spring stiffness

Definition at line 77 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mUseApoptoticSprings.

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor ( unsigned  nodeAGlobalIndex,
unsigned  nodeBGlobalIndex,
AbstractCellPopulation< DIM > &  rCellPopulation,
bool  isCloserThanRestLength 
) [inline, virtual]

Return a multiplication factor for the spring constant, which may depend on whether the given pair of neighbouring cells are e.g. undergoing apoptosis, have mutations, or experience variable levels of beta catenin.

Parameters:
nodeAGlobalIndex index of one neighbouring node
nodeBGlobalIndex index of the other neighbouring node
rCellPopulation the cell population
isCloserThanRestLength whether the neighbouring nodes lie closer than the rest length of their connecting spring
Returns:
the multiplication factor.

Reimplemented from GeneralisedLinearSpringForce< DIM >.

Definition at line 83 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), GeneralisedLinearSpringForce< DIM >::GetMeinekeSpringStiffness(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel(), MeshBasedCellPopulation< DIM >::GetSurfaceAreaOfVoronoiElement(), MeshBasedCellPopulation< DIM >::GetVoronoiEdgeLength(), AbstractCellPopulation< DIM >::IsMeshBasedCellPopulation(), LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringCompressionStiffness, LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringTensionStiffness, LinearSpringWithVariableSpringConstantsForce< DIM >::mBetaCatSpringScaler, LinearSpringWithVariableSpringConstantsForce< DIM >::mMutantMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mNormalMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseApoptoticSprings, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseBCatSprings, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseEdgeBasedSpringConstant, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseMutantSprings, and GeneralisedLinearSpringForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution ( std::vector< c_vector< double, DIM > > &  rForces,
AbstractCellPopulation< DIM > &  rCellPopulation 
) [inline, virtual]

Overridden AddForceContribution method.

Parameters:
rForces reference to vector of forces on nodes
rCellPopulation reference to the cell population

Reimplemented from AbstractTwoBodyInteractionForce< DIM >.

Definition at line 203 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), EXCEPTION, MeshBasedCellPopulation< DIM >::SpringsBegin(), and MeshBasedCellPopulation< DIM >::SpringsEnd().

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::GetBetaCatSpringScaler (  )  [inline]

Returns:
mBetaCatSpringScaler

Definition at line 229 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mBetaCatSpringScaler.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetBetaCatSpringScaler ( double  betaCatSpringScaler  )  [inline]

Set mBetaCatSpringScaler.

Parameters:
betaCatSpringScaler the new value of mBetaCatSpringScaler

Definition at line 235 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mBetaCatSpringScaler.

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::GetApoptoticSpringTensionStiffness (  )  [inline]

Returns:
mApoptoticSpringTensionStiffness

Definition at line 242 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringTensionStiffness.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetApoptoticSpringTensionStiffness ( double  apoptoticSpringTensionStiffness  )  [inline]

Set mApoptoticSpringTensionStiffness.

Parameters:
apoptoticSpringTensionStiffness the new value of mApoptoticSpringTensionStiffness

Definition at line 248 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringTensionStiffness.

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::GetApoptoticSpringCompressionStiffness (  )  [inline]

Returns:
mApoptoticSpringCompressionStiffness

Definition at line 255 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringCompressionStiffness.

template<unsigned DIM>
void LinearSpringWithVariableSpringConstantsForce< DIM >::SetApoptoticSpringCompressionStiffness ( double  apoptoticSpringCompressionStiffness  )  [inline]

Set mApoptoticSpringCompressionStiffness.

Parameters:
apoptoticSpringCompressionStiffness the new value of mApoptoticSpringCompressionStiffness

Definition at line 261 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringCompressionStiffness.

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

Outputs force parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
rParamsFile the file stream to which the parameters are output

Reimplemented from GeneralisedLinearSpringForce< DIM >.

Definition at line 268 of file LinearSpringWithVariableSpringConstantsForce.cpp.

References LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringCompressionStiffness, LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringTensionStiffness, LinearSpringWithVariableSpringConstantsForce< DIM >::mBetaCatSpringScaler, LinearSpringWithVariableSpringConstantsForce< DIM >::mMutantMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mNormalMutantMultiplier, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseApoptoticSprings, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseBCatSprings, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseEdgeBasedSpringConstant, LinearSpringWithVariableSpringConstantsForce< DIM >::mUseMutantSprings, and GeneralisedLinearSpringForce< DIM >::OutputForceParameters().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from GeneralisedLinearSpringForce< DIM >.

Definition at line 51 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Member Data Documentation

template<unsigned DIM>
bool LinearSpringWithVariableSpringConstantsForce< DIM >::mUseEdgeBasedSpringConstant [protected]

Whether to use spring constant proportional to cell-cell contact length/area (defaults to false).

Definition at line 78 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetEdgeBasedSpringConstant(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
bool LinearSpringWithVariableSpringConstantsForce< DIM >::mUseMutantSprings [protected]

Whether to use different stiffnesses depending on whether either cell is a mutant.

Definition at line 81 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetMutantSprings(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::mMutantMutantMultiplier [protected]

Multiplier for spring stiffness if mutant.

Definition at line 84 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetMutantSprings(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::mNormalMutantMultiplier [protected]

Multiplier for spring stiffness if mutant.

Definition at line 87 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetMutantSprings(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
bool LinearSpringWithVariableSpringConstantsForce< DIM >::mUseBCatSprings [protected]

Use springs which are dependent on beta-catenin levels.

Definition at line 90 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetBetaCateninSprings(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
bool LinearSpringWithVariableSpringConstantsForce< DIM >::mUseApoptoticSprings [protected]

Use springs which are dependent on whether cells are apoptotic.

Definition at line 93 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetApoptoticSprings(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::mBetaCatSpringScaler [protected]

Scaling factor for beta catenin to spring strength.

Definition at line 96 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::GetBetaCatSpringScaler(), LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetBetaCatSpringScaler(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringTensionStiffness [protected]

Non-dimensionalized 'stiffness' of a apoptotic cell under tension.

Definition at line 99 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::GetApoptoticSpringTensionStiffness(), LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetApoptoticSpringTensionStiffness(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
double LinearSpringWithVariableSpringConstantsForce< DIM >::mApoptoticSpringCompressionStiffness [protected]

Non-dimensionalized 'stiffness' of a apoptotic cell under compression.

Definition at line 102 of file LinearSpringWithVariableSpringConstantsForce.hpp.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::GetApoptoticSpringCompressionStiffness(), LinearSpringWithVariableSpringConstantsForce< DIM >::OutputForceParameters(), LinearSpringWithVariableSpringConstantsForce< DIM >::serialize(), LinearSpringWithVariableSpringConstantsForce< DIM >::SetApoptoticSpringCompressionStiffness(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

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