Owen2011OxygenBasedCellCycleOdeSystem Class Reference

#include <Owen2011OxygenBasedCellCycleOdeSystem.hpp>

Inheritance diagram for Owen2011OxygenBasedCellCycleOdeSystem:

Collaboration diagram for Owen2011OxygenBasedCellCycleOdeSystem:

Public Member Functions
	Owen2011OxygenBasedCellCycleOdeSystem (units::quantity< unit::concentration > oxygenConcentration, boost::shared_ptr< AbstractCellMutationState > mutation_state, std::vector< double > stateVariables=std::vector< double >())
	~Owen2011OxygenBasedCellCycleOdeSystem ()
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)
units::quantity< unit::concentration >	GetOxygenConcentration () const
boost::shared_ptr< AbstractCellMutationState >	GetMutationState () const
void	SetMutationState (boost::shared_ptr< AbstractCellMutationState > pMutationState)

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

Private Attributes
units::quantity< unit::pressure >	mCphi
units::quantity< unit::time >	mTmin
units::quantity< unit::rate >	mk7
units::quantity< unit::rate >	mk7dash
units::quantity< unit::pressure >	mCp53
units::quantity< unit::rate >	mk8
units::quantity< unit::rate >	mk8doubledash
units::quantity< unit::dimensionless >	mJ5
units::quantity< unit::rate >	mk8dash
units::quantity< unit::pressure >	mCVEGF
units::quantity< unit::concentration >	mOxygenConcentration
boost::shared_ptr< AbstractCellMutationState >	pmMutationState
units::quantity< unit::time >	mReferenceTimeScale
units::quantity< unit::concentration >	mReferenceConcentrationScale
units::quantity< unit::solubility >	mReferenceSolubility

Friends
class	boost::serialization::access

Detailed Description

Represents the Owen (2011) system of ODEs.

The variables are 0. phi = Cell-cycle phase 1. p53 = p53 concentration 2. VEGF = VEGF concentration 3. O2 = Oxygen concentration

Definition at line 58 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

Owen2011OxygenBasedCellCycleOdeSystem::Owen2011OxygenBasedCellCycleOdeSystem	(	units::quantity< unit::concentration >	oxygenConcentration,
		boost::shared_ptr< AbstractCellMutationState >	mutation_state,
		std::vector< double >	stateVariables = std::vector<double>()
	)

Constructor.

Parameters

oxygenConcentration	the oxygen concentration
mutation_state	the cell mutation state
stateVariables	optional initial conditions for state variables (only used in archiving)

Definition at line 48 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

References mCp53, mCphi, mCVEGF, mJ5, mk7, mk7dash, mk8, mk8dash, mk8doubledash, mOxygenConcentration, Owen11Parameters::mpCellVegfProductionRate, GenericParameters::mpGasConcentrationAtStp, Owen11Parameters::mpMaxCellVegfProductionRate, Owen11Parameters::mpMinimumCellCyclePeriodCancer, Owen11Parameters::mpMinimumCellCyclePeriodNormal, Owen11Parameters::mpOxygenPartialPressureAtHalfMaxCycleRateCancer, Owen11Parameters::mpOxygenPartialPressureAtHalfMaxCycleRateNormal, Owen11Parameters::mpOxygenTensionForHalfMaxP53Degradation, Owen11Parameters::mpOxygenTensionForHalfMaxVegfDegradation, Secomb04Parameters::mpOxygenVolumetricSolubility, Owen11Parameters::mpP53EffectOnVegfProduction, Owen11Parameters::mpP53MaxDegradationRate, Owen11Parameters::mpP53ProductionRateConstant, Owen11Parameters::mpVegfEffectOnVegfProduction, mReferenceConcentrationScale, mReferenceSolubility, mTmin, and pmMutationState.

Referenced by serialize().

Owen2011OxygenBasedCellCycleOdeSystem::~Owen2011OxygenBasedCellCycleOdeSystem

(

)

Destructor.

Definition at line 99 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

Referenced by serialize().

Member Function Documentation

bool Owen2011OxygenBasedCellCycleOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)

Calculate whether the conditions for the cell cycle to finish have been met.

Parameters

time	at which to calculate whether the stopping event has occurred
rY	value of the solution vector used to evaluate the RHS.

Returns

whether or not stopping conditions have been met

Definition at line 104 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

Referenced by serialize().

void Owen2011OxygenBasedCellCycleOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)

Compute the RHS of the Owen (2011) 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 Owen (2011) system of equations).

Definition at line 109 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

References mCp53, mCphi, mCVEGF, mJ5, mk7, mk7dash, mk8, mk8dash, mk8doubledash, mOxygenConcentration, mReferenceConcentrationScale, mReferenceSolubility, mReferenceTimeScale, mTmin, and pmMutationState.

Referenced by serialize().

boost::shared_ptr< AbstractCellMutationState > Owen2011OxygenBasedCellCycleOdeSystem::GetMutationState

(

)

const

Get the cell's mutation state.

Returns

the cell's mutation state.

Definition at line 146 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

References pmMutationState.

Referenced by serialize().

units::quantity< unit::concentration > Owen2011OxygenBasedCellCycleOdeSystem::GetOxygenConcentration

(

)

const

Return the oxygen concentration

Returns

mOxygenConcentration.

Definition at line 151 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

References mOxygenConcentration.

Referenced by serialize().

template<class Archive >

void Owen2011OxygenBasedCellCycleOdeSystem::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 147 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

References CalculateStoppingEvent(), EvaluateYDerivatives(), GetMutationState(), GetOxygenConcentration(), Owen2011OxygenBasedCellCycleOdeSystem(), SetMutationState(), and ~Owen2011OxygenBasedCellCycleOdeSystem().

void Owen2011OxygenBasedCellCycleOdeSystem::SetMutationState

(

boost::shared_ptr< AbstractCellMutationState >

pMutationState

)

Set the cell's mutation state.

Parameters

pMutationState

the cell's new mutation state

Definition at line 174 of file Owen2011OxygenBasedCellCycleOdeSystem.cpp.

References pmMutationState.

Referenced by serialize().

Member Data Documentation

units::quantity<unit::pressure> Owen2011OxygenBasedCellCycleOdeSystem::mCp53

private

Oxygen partial pressure for half-max p53 degradation

Definition at line 86 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::pressure> Owen2011OxygenBasedCellCycleOdeSystem::mCphi

private

Partial pressure at half max rate

Definition at line 66 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::pressure> Owen2011OxygenBasedCellCycleOdeSystem::mCVEGF

private

Parameter with units of mmHg

Definition at line 111 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::dimensionless> Owen2011OxygenBasedCellCycleOdeSystem::mJ5

private

Parameter with units of —-

Definition at line 101 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::rate> Owen2011OxygenBasedCellCycleOdeSystem::mk7

private

p53 production rate constant

Definition at line 76 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::rate> Owen2011OxygenBasedCellCycleOdeSystem::mk7dash

private

p53 production rate constant

Definition at line 81 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::rate> Owen2011OxygenBasedCellCycleOdeSystem::mk8

private

Parameter with units of min^-1

Definition at line 91 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::rate> Owen2011OxygenBasedCellCycleOdeSystem::mk8dash

private

Parameter with units of min^-1

Definition at line 106 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::rate> Owen2011OxygenBasedCellCycleOdeSystem::mk8doubledash

private

Parameter with units of min^-1

Definition at line 96 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::concentration> Owen2011OxygenBasedCellCycleOdeSystem::mOxygenConcentration

private

The oxygen concentration (this affects the ODE system).

Definition at line 116 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), GetOxygenConcentration(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::concentration> Owen2011OxygenBasedCellCycleOdeSystem::mReferenceConcentrationScale

private

The reference concentration scale

Definition at line 131 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::solubility> Owen2011OxygenBasedCellCycleOdeSystem::mReferenceSolubility

private

The reference solubility

Definition at line 136 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

units::quantity<unit::time> Owen2011OxygenBasedCellCycleOdeSystem::mReferenceTimeScale

private

The reference time scale

Definition at line 126 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives().

units::quantity<unit::time> Owen2011OxygenBasedCellCycleOdeSystem::mTmin

private

Minimum cycle time

Definition at line 71 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Owen2011OxygenBasedCellCycleOdeSystem().

boost::shared_ptr<AbstractCellMutationState> Owen2011OxygenBasedCellCycleOdeSystem::pmMutationState

private

Mutation state.

Definition at line 121 of file Owen2011OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), GetMutationState(), Owen2011OxygenBasedCellCycleOdeSystem(), and SetMutationState().

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

• projects/MicrovesselChaste/src/ode/Owen2011OxygenBasedCellCycleOdeSystem.hpp
• projects/MicrovesselChaste/src/ode/Owen2011OxygenBasedCellCycleOdeSystem.cpp