DeltaNotchOdeSystem Class Reference

#include <DeltaNotchOdeSystem.hpp>

Inherits AbstractOdeSystem.

Collaboration diagram for DeltaNotchOdeSystem:

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List of all members.

Public Member Functions
	DeltaNotchOdeSystem (double meanDelta=0.0, std::vector< double > stateVariables=std::vector< double >())
	~DeltaNotchOdeSystem ()
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

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Detailed Description

Represents the Delta-Notch ODE system described by Collier et al, "Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling" (Journal of Theoretical Biology 183:429-446, 1996).

Definition at line 47 of file DeltaNotchOdeSystem.hpp.

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Constructor & Destructor Documentation

DeltaNotchOdeSystem::DeltaNotchOdeSystem	(	double	meanDelta = 0.0,
		std::vector< double >	stateVariables = std::vector<double>()
	)

Todo:

extract model parameters as member variables

Default constructor.

Parameters:

	meanDelta	the average of the levels of Delta in the surrounding cells (defaults to zero)
	stateVariables	optional initial conditions for state variables (only used in archiving)

The state variables are as follows:

0 - Notch concentration for this cell 1 - Delta concentration for this cell 2 - average Delta concentration for this cell's immediate neighbours

We store the last state variable so that it can be written to file at each time step alongside the others, and visualized.

Definition at line 32 of file DeltaNotchOdeSystem.cpp.

References AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

DeltaNotchOdeSystem::~DeltaNotchOdeSystem

(

)

Destructor.

Definition at line 58 of file DeltaNotchOdeSystem.cpp.

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Member Function Documentation

void DeltaNotchOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)			[virtual]

Compute the RHS of the Alarcon et al. (2004) system of ODEs.

Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].

Parameters:

	time	used to evaluate the RHS.
	rY	value of the solution vector used to evaluate the RHS.
	rDY	filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 62 of file DeltaNotchOdeSystem.cpp.

template<class Archive >

void DeltaNotchOdeSystem::serialize	(	Archive &	archive,
		const unsigned int	version
	)			[inline, private]

Serialize the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 59 of file DeltaNotchOdeSystem.hpp.

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

• cell_based/src/odes/DeltaNotchOdeSystem.hpp
• cell_based/src/odes/DeltaNotchOdeSystem.cpp