Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
DeltaNotchEdgeOdeSystem Class Reference

#include <DeltaNotchEdgeOdeSystem.hpp>

+ Inheritance diagram for DeltaNotchEdgeOdeSystem:
+ Collaboration diagram for DeltaNotchEdgeOdeSystem:

Public Member Functions

 DeltaNotchEdgeOdeSystem (std::vector< double > stateVariables=std::vector< double >())
 
 ~DeltaNotchEdgeOdeSystem ()
 
void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
 
- Public Member Functions inherited from AbstractOdeSystem
 AbstractOdeSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractOdeSystem ()
 
virtual bool CalculateStoppingEvent (double time, const std::vector< double > &rY)
 
virtual double CalculateRootFunction (double time, const std::vector< double > &rY)
 
bool GetUseAnalyticJacobian ()
 
const std::vector< double > & rGetConstStateVariables () const
 
- Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
 AbstractParameterisedSystem (unsigned numberOfStateVariables)
 
std::vector< double > & rGetStateVariables ()
 
std::vector< doubleGetStateVariables ()
 
void SetStateVariables (const std::vector< double > &rStateVariables)
 
double GetStateVariable (unsigned index) const
 
double GetStateVariable (const std::string &rName) const
 
void SetStateVariable (unsigned index, double newValue)
 
void SetStateVariable (const std::string &rName, double newValue)
 
virtual void VerifyStateVariables ()
 
void SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)
 
void SetDefaultInitialCondition (unsigned index, double initialCondition)
 
std::vector< doubleGetInitialConditions () const
 
void ResetToInitialConditions ()
 
double GetParameter (unsigned index) const
 
double GetParameter (const std::string &rName) const
 
void SetParameter (const std::string &rName, double value)
 
void SetParameter (unsigned index, double value)
 
double GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
double GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
void SetAnyVariable (unsigned index, double value)
 
void SetAnyVariable (const std::string &rName, double value)
 
virtual std::vector< doubleComputeDerivedQuantities (double time, const std::vector< double > &rState)
 
std::vector< doubleComputeDerivedQuantitiesFromCurrentState (double time)
 
- Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
 AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractUntemplatedParameterisedSystem ()
 
boost::shared_ptr< const AbstractOdeSystemInformationGetSystemInformation () const
 
std::string GetSystemName () const
 
unsigned GetNumberOfAttributes () const
 
bool HasAttribute (const std::string &rName) const
 
double GetAttribute (const std::string &rName) const
 
unsigned GetNumberOfStateVariables () const
 
const std::vector< std::string > & rGetStateVariableNames () const
 
const std::vector< std::string > & rGetStateVariableUnits () const
 
unsigned GetStateVariableIndex (const std::string &rName) const
 
bool HasStateVariable (const std::string &rName) const
 
std::string GetStateVariableUnits (unsigned index) const
 
unsigned GetNumberOfParameters () const
 
const std::vector< std::string > & rGetParameterNames () const
 
const std::vector< std::string > & rGetParameterUnits () const
 
unsigned GetParameterIndex (const std::string &rName) const
 
bool HasParameter (const std::string &rName) const
 
std::string GetParameterUnits (unsigned index) const
 
unsigned GetNumberOfDerivedQuantities () const
 
const std::vector< std::string > & rGetDerivedQuantityNames () const
 
const std::vector< std::string > & rGetDerivedQuantityUnits () const
 
unsigned GetDerivedQuantityIndex (const std::string &rName) const
 
bool HasDerivedQuantity (const std::string &rName) const
 
std::string GetDerivedQuantityUnits (unsigned index) const
 
unsigned GetAnyVariableIndex (const std::string &rName) const
 
bool HasAnyVariable (const std::string &rName) const
 
std::string GetAnyVariableUnits (unsigned index) const
 
std::string GetAnyVariableUnits (const std::string &rName) const
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string DumpState (const std::string &rMessage)
 
std::string DumpState (const std::string &rMessage, std::vector< double > Y)
 
std::string DumpState (const std::string &rMessage, std::vector< double > Y, double time)
 
void CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)
 
- Protected Attributes inherited from AbstractOdeSystem
bool mUseAnalyticJacobian
 
- Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< doublemStateVariables
 
std::vector< doublemParameters
 
- Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned mNumberOfStateVariables
 
boost::shared_ptr< AbstractOdeSystemInformationmpSystemInfo
 

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). Here, however, we include edge based model: Delta and Notch interactions between each cell are modelled directly. We use similar ODE system as by Collier et al., except that we modify terms corresponding to means of neighbour concentrations of Delta/Notch. In this ODE model, concentration of edge Delta/Notch depend on intracellular (interior) concentrations

Definition at line 58 of file DeltaNotchEdgeOdeSystem.hpp.

Constructor & Destructor Documentation

◆ DeltaNotchEdgeOdeSystem()

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

Default constructor.

Parameters
stateVariablesoptional initial conditions for state variables (only used in archiving)

The state variables are as follows:

0 - Notch concentration for this cell edge 1 - Delta concentration for this cell edge

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 39 of file DeltaNotchEdgeOdeSystem.cpp.

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

◆ ~DeltaNotchEdgeOdeSystem()

DeltaNotchEdgeOdeSystem::~DeltaNotchEdgeOdeSystem ( )

Destructor.

Definition at line 67 of file DeltaNotchEdgeOdeSystem.cpp.

Member Function Documentation

◆ EvaluateYDerivatives()

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

Notch in this edge is inhibited by Delta in neighbouring edge. Cytoplasmic Notch is trafficked into this junction. The type of interactions of Delta and Notch in this edge are similar to interior SRN model

Parameters
timeused to evaluate the RHS.
rYvalue of the solution vector used to evaluate the RHS.
rDYfilled in with the resulting derivatives (using Collier et al. system of equations).

Implements AbstractOdeSystem.

Definition at line 71 of file DeltaNotchEdgeOdeSystem.cpp.

References AbstractParameterisedSystem< std::vector< double > >::mParameters.

◆ serialize()

template<class Archive >
void DeltaNotchEdgeOdeSystem::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 70 of file DeltaNotchEdgeOdeSystem.hpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access
friend

Definition at line 62 of file DeltaNotchEdgeOdeSystem.hpp.


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