CryptSimulation1d Class Reference

#include <CryptSimulation1d.hpp>

Collaboration diagram for CryptSimulation1d:

Public Member Functions
	CryptSimulation1d (AbstractTissue< 1 > &rTissue, std::vector< AbstractForce< 1 > * > forceCollection, bool deleteTissueAndForceCollection=false, bool initialiseCells=true)
void	ApplyTissueBoundaryConditions (const std::vector< c_vector< double, 1 > > &rOldLocations)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
c_vector< double, 1 >	CalculateCellDivisionVector (TissueCell &rParentCell)
Private Attributes
MeshBasedTissue< 1 > *	mpStaticCastTissue
Friends
class	TestCryptSimulation1d
class	boost::serialization::access

Detailed Description

A 1D crypt simulation object. The model is a simplified version of a 2D crypt model developed by Meineke et al (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 45 of file CryptSimulation1d.hpp.

Constructor & Destructor Documentation

CryptSimulation1d::CryptSimulation1d	(	AbstractTissue< 1 > &	rTissue,
		std::vector< AbstractForce< 1 > * >	forceCollection,
		bool	deleteTissueAndForceCollection = `false`,
		bool	initialiseCells = `true`
	)

Constructor.

Parameters:

	rTissue	A tissue facade class (contains a mesh and cells)
	forceCollection	The mechanics to use in the simulation
	deleteTissueAndForceCollection	Whether to delete the tissue and force collection on destruction to free up memory
	initialiseCells	whether to initialise cells (set to false when loading from an archive)

Definition at line 33 of file CryptSimulation1d.cpp.

References TissueConfig::Instance(), mpStaticCastTissue, TissueSimulation< 1 >::mrTissue, and TissueConfig::SetSpringStiffness().

Member Function Documentation

void CryptSimulation1d::ApplyTissueBoundaryConditions ( const std::vector< c_vector< double, 1 > > & rOldLocations )

Overridden ApplyTissueBoundaryConditions() method.

If an instance of WntConcentration is not set up, then stem cells at the bottom of the crypt are pinned. Any cell that has moved below the bottom of the crypt is moved back up.

Parameters:

rOldLocations

the node locations at the previous time step

If WntConcentration is not set up then stem cells must be pinned, so we reset the location of each stem cell.

Definition at line 102 of file CryptSimulation1d.cpp.

References AbstractTissue< DIM >::GetLocationIndexUsingCell(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), mpStaticCastTissue, TissueSimulation< 1 >::mrTissue, Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

c_vector< double, 1 > CryptSimulation1d::CalculateCellDivisionVector ( TissueCell & rParentCell ) [private, virtual]

Calculates the new locations of a dividing cell's cell centres. Moves the dividing node a bit and returns co-ordinates for the new node. It does this by picking a random direction (0->2PI) and placing the parent and daughter in opposing directions on this axis.

Parameters:

rParentCell

the parent cell