Chaste  Build::
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< AbstractCellMutationStateGetMutationState () 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< AbstractCellMutationStatepmMutationState
 
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 ( )

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
timeat which to calculate whether the stopping event has occurred
rYvalue 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
timeused to evaluate the RHS.
rYvalue of the solution vector used to evaluate the RHS.
rDYfilled 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
archivethe archive
versionthe 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
pMutationStatethe 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

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