TysonNovak2001OdeSystem Class Reference

#include <TysonNovak2001OdeSystem.hpp>

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List of all members.

Public Member Functions

 TysonNovak2001OdeSystem (std::vector< double > stateVariables=std::vector< double >())
 ~TysonNovak2001OdeSystem ()
void Init ()
void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
bool CalculateStoppingEvent (double time, const std::vector< double > &rY)
double CalculateRootFunction (double time, const std::vector< double > &rY)
virtual void AnalyticJacobian (const std::vector< double > &rSolutionGuess, double **jacobian, double time, double timeStep)

Private Member Functions

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

Private Attributes

double mK1
double mK2d
double mK2dd
double mK2ddd
double mCycB_threshold
double mK3d
double mK3dd
double mK4d
double mK4
double mJ3
double mJ4
double mK5d
double mK5dd
double mK6
double mJ5
unsigned mN
double mK7
double mK8
double mJ7
double mJ8
double mMad
double mK9
double mK10
double mK11
double mK12d
double mK12dd
double mK12ddd
double mKeq
double mK13
double mK14
double mK15d
double mK15dd
double mK16d
double mK16dd
double mJ15
double mJ16
double mMu
double mMstar

Friends

class boost::serialization::access

Detailed Description

Represents the Tyson & Novak (2001) system of ODEs. [doi:10.1006/jtbi.2001.2293]

Definition at line 43 of file TysonNovak2001OdeSystem.hpp.

Constructor & Destructor Documentation

TysonNovak2001OdeSystem::TysonNovak2001OdeSystem ( std::vector< double >  stateVariables = std::vector<double>()  ) 

Constructor.

Parameters:
stateVariables optional initial conditions for state variables (only used in archiving)

Definition at line 32 of file TysonNovak2001OdeSystem.cpp.

References Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), AbstractParameterisedSystem< std::vector< double > >::mpSystemInfo, and AbstractOdeSystem::SetStateVariables().

TysonNovak2001OdeSystem::~TysonNovak2001OdeSystem (  ) 

Destructor.

Definition at line 45 of file TysonNovak2001OdeSystem.cpp.

Member Function Documentation

template<class Archive>
void TysonNovak2001OdeSystem::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 136 of file TysonNovak2001OdeSystem.hpp.

void TysonNovak2001OdeSystem::Init (  ) 

Initialise parameter values.

Definition at line 50 of file TysonNovak2001OdeSystem.cpp.

References mCycB_threshold, mJ15, mJ16, mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK11, mK12d, mK12dd, mK12ddd, mK13, mK14, mK15d, mK15dd, mK16d, mK16dd, mK2d, mK2dd, mK2ddd, mK3d, mK3dd, mK4, mK4d, mK5d, mK5dd, mK6, mK7, mK8, mK9, mKeq, mMad, mMstar, mMu, and mN.

Referenced by TysonNovak2001OdeSystem().

void TysonNovak2001OdeSystem::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).

1. [CycB] 2. [Cdh1] 3. [Cdc20T] 4. [Cdc20A] 5. [IEP] 6. m - mass of the cell

Implements AbstractOdeSystem.

Definition at line 93 of file TysonNovak2001OdeSystem.cpp.

References mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5d, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, and mN.

Referenced by CalculateRootFunction(), and CalculateStoppingEvent().

bool TysonNovak2001OdeSystem::CalculateStoppingEvent ( double  time,
const std::vector< double > &  rY 
) [virtual]

Calculate whether the conditions for the cell cycle to finish have been met. (Used by Chaste solvers to find whether or not to stop solving)

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

Reimplemented from AbstractOdeSystem.

Definition at line 216 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

double TysonNovak2001OdeSystem::CalculateRootFunction ( double  time,
const std::vector< double > &  rY 
) [virtual]

Calculate whether the conditions for the cell cycle to finish have been met. (Used by CVODE solver to find exact stopping position)

Parameters:
time at which to calculate whether the stopping event has occurred
rY value of the solution vector used to evaluate the RHS.
Returns:
How close we are to the root of the stopping condition

Reimplemented from AbstractOdeSystem.

Definition at line 226 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

void TysonNovak2001OdeSystem::AnalyticJacobian ( const std::vector< double > &  rSolutionGuess,
double **  jacobian,
double  time,
double  timeStep 
) [virtual]

Compute the Jacobian of the ODE system.

Parameters:
rSolutionGuess initial guess for the solution vector.
jacobian the Jacobian of the ODE system.
time at which to calculate the Jacobian.
timeStep used to calculate the Jacobian.

Implements AbstractOdeSystemWithAnalyticJacobian.

Definition at line 153 of file TysonNovak2001OdeSystem.cpp.

References mJ3, mJ4, mJ5, mJ7, mJ8, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, and mN.

Member Data Documentation

double TysonNovak2001OdeSystem::mK1 [private]

Parameters for the Tyson & Novak (2001) model. Dimensional parameter k_1.

Definition at line 52 of file TysonNovak2001OdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK2d [private]

Dimensional parameter k_2'.

Definition at line 54 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK2dd [private]

Dimensional parameter k_2''.

Definition at line 56 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK2ddd [private]

Dimensional parameter k_2'''.

Definition at line 58 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mCycB_threshold [private]

Dimensionless parameter [CycB]_threshold.

Definition at line 60 of file TysonNovak2001OdeSystem.hpp.

Referenced by CalculateRootFunction(), CalculateStoppingEvent(), and Init().

double TysonNovak2001OdeSystem::mK3d [private]

Dimensional parameter k_3'.

Definition at line 62 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK3dd [private]

Dimensional parameter k_3''.

Definition at line 64 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK4d [private]

Dimensional parameter k_4'.

Definition at line 66 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK4 [private]

Dimensional parameter k_4.

Definition at line 68 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ3 [private]

Dimensionless parameter J_3.

Definition at line 70 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ4 [private]

Dimensionless parameter J_4.

Definition at line 72 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK5d [private]

Dimensional parameter k_5'.

Definition at line 74 of file TysonNovak2001OdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK5dd [private]

Dimensional parameter k_5''.

Definition at line 76 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK6 [private]

Dimensional parameter k_6.

Definition at line 78 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ5 [private]

Dimensionless parameter J_5.

Definition at line 80 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

unsigned TysonNovak2001OdeSystem::mN [private]

Dimensionless parameter n.

Definition at line 82 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK7 [private]

Dimensional parameter k_7.

Definition at line 84 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK8 [private]

Dimensional parameter k_8.

Definition at line 86 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ7 [private]

Dimensionless parameter J_7.

Definition at line 88 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ8 [private]

Dimensionless parameter J_8.

Definition at line 90 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mMad [private]

Dimensionless parameter [Mad].

Definition at line 92 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK9 [private]

Dimensional parameter k_9.

Definition at line 94 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK10 [private]

Dimensional parameter k_10.

Definition at line 96 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK11 [private]

Dimensional parameter k_11.

Definition at line 98 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK12d [private]

Dimensional parameter k_12'.

Definition at line 100 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK12dd [private]

Dimensional parameter k_12''.

Definition at line 102 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK12ddd [private]

Dimensional parameter k_12'''.

Definition at line 104 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mKeq [private]

Dimensionless parameter K_eq.

Definition at line 106 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK13 [private]

Dimensional parameter k_13.

Definition at line 108 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK14 [private]

Dimensional parameter k_14.

Definition at line 110 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK15d [private]

Dimensional parameter k_15'.

Definition at line 112 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK15dd [private]

Dimensional parameter k_15''.

Definition at line 114 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK16d [private]

Dimensional parameter k_16'.

Definition at line 116 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK16dd [private]

Dimensional parameter k_16''.

Definition at line 118 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mJ15 [private]

Dimensionless parameter J_15.

Definition at line 120 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mJ16 [private]

Dimensionless parameter J_16.

Definition at line 122 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mMu [private]

Dimensional parameter mu.

Definition at line 124 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mMstar [private]

Dimensionless parameter m_star.

Definition at line 126 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

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