Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <DeltaNotchEdgeOdeSystem.hpp>
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< double > | GetStateVariables () |
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< double > | GetInitialConditions () 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< double > | ComputeDerivedQuantities (double time, const std::vector< double > &rState) |
std::vector< double > | ComputeDerivedQuantitiesFromCurrentState (double time) |
Public Member Functions inherited from AbstractUntemplatedParameterisedSystem | |
AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractUntemplatedParameterisedSystem () |
boost::shared_ptr< const AbstractOdeSystemInformation > | GetSystemInformation () 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< double > | mStateVariables |
std::vector< double > | mParameters |
Protected Attributes inherited from AbstractUntemplatedParameterisedSystem | |
unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
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.
DeltaNotchEdgeOdeSystem::DeltaNotchEdgeOdeSystem | ( | std::vector< double > | stateVariables = std::vector<double>() | ) |
Default constructor.
stateVariables | optional 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 | ( | ) |
Destructor.
Definition at line 67 of file DeltaNotchEdgeOdeSystem.cpp.
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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
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 Collier et al. system of equations). |
Implements AbstractOdeSystem.
Definition at line 71 of file DeltaNotchEdgeOdeSystem.cpp.
References AbstractParameterisedSystem< std::vector< double > >::mParameters.
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inlineprivate |
Serialize the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 70 of file DeltaNotchEdgeOdeSystem.hpp.
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friend |
Definition at line 62 of file DeltaNotchEdgeOdeSystem.hpp.