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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <DeltaNotchEdgeSrnModel.hpp>
Protected Member Functions | |
DeltaNotchEdgeSrnModel (const DeltaNotchEdgeSrnModel &rModel) | |
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void | Initialise (AbstractOdeSystem *pOdeSystem) |
AbstractOdeSrnModel (const AbstractOdeSrnModel &rModel) | |
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AbstractSrnModel (const AbstractSrnModel &rModel) | |
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CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler) | |
bool | SolveOdeToTime (double currentTime) |
virtual void | AdjustOdeParameters (double currentTime) |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
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std::vector< double > | mInitialConditions |
unsigned | mStateSize |
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CellPtr | mpCell |
double | mSimulatedToTime |
unsigned | mEdgeLocalIndex = UNSIGNED_UNSET |
bool | mIsEdgeBasedModel = false |
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double | mDt |
AbstractOdeSystem * | mpOdeSystem |
boost::shared_ptr< AbstractCellCycleModelOdeSolver > | mpOdeSolver |
double | mLastTime |
bool | mFinishedRunningOdes |
A subclass of AbstractOdeSrnModel that includes a Delta-Notch ODE system in the sub-cellular reaction network. This SRN model represents a membrane/ cortex of a single junction of a cell. This class of models can be used together with DeltaNotchInteriorSrn models. The ODE model used here is an attempt to use previous work (see DeltaNotchSrnModel class) for more detailed description of Delta-Notch interactions involving edge quantities (this or neighbour edge information) and potentially coupling with cytoplasmic concentrations (DeltaNotchInteriorSrn class).
Definition at line 55 of file DeltaNotchEdgeSrnModel.hpp.
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protected |
Protected copy-constructor for use by CreateSrnModel(). The only way for external code to create a copy of a SRN model is by calling that method, to ensure that a model of the correct subclass is created.
This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.
This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent SRN model will have had ResetForDivision() called just before CreateSrnModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().
rModel | the SRN model to copy. |
Definition at line 56 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractUntemplatedParameterisedSystem::GetNumberOfParameters(), CellCycleModelOdeHandler::GetOdeSystem(), AbstractParameterisedSystem< VECTOR >::GetParameter(), CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and AbstractParameterisedSystem< VECTOR >::SetParameter().
DeltaNotchEdgeSrnModel::DeltaNotchEdgeSrnModel | ( | boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() | ) |
Default constructor calls base class.
pOdeSolver | An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers) |
Definition at line 38 of file DeltaNotchEdgeSrnModel.cpp.
References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().
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virtual |
Here we add Delta/Notch when junctions merge via common vertex deletion Override the method declared in AbstractSrnModel class
pMergedEdgeSrn | Pointer to an SRN |
Reimplemented from AbstractSrnModel.
Definition at line 200 of file DeltaNotchEdgeSrnModel.cpp.
References AddSrnQuantities().
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virtual |
Here we assume that when a neighbouring junctions shrinks, 25% of its Delta/Notch concentration is added to this edge Override the method declared in AbstractSrnModel class
pShrunkEdgeSrn | Pointer to an SRN |
Reimplemented from AbstractSrnModel.
Definition at line 191 of file DeltaNotchEdgeSrnModel.cpp.
References AddSrnQuantities().
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virtual |
Adds Delta/Notch from the input SRN model to this model. Override the method declared in AbstractSrnModel class
pOtherSrn | Pointer to an SRN |
scale | scale factor |
Reimplemented from AbstractSrnModel.
Definition at line 179 of file DeltaNotchEdgeSrnModel.cpp.
References GetDelta(), GetNotch(), SetDelta(), and SetNotch().
Referenced by AddMergedEdgeSrn(), and AddShrunkEdgeSrn().
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Overridden builder method to create new copies of this SRN model.
Implements AbstractSrnModel.
Definition at line 82 of file DeltaNotchEdgeSrnModel.cpp.
double DeltaNotchEdgeSrnModel::GetDelta | ( | ) |
Definition at line 142 of file DeltaNotchEdgeSrnModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by AddSrnQuantities().
double DeltaNotchEdgeSrnModel::GetInteriorDelta | ( | ) | const |
The value of interior Delta is stored as parameters in this model, which is retrieved by this method
Definition at line 161 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.
double DeltaNotchEdgeSrnModel::GetInteriorNotch | ( | ) | const |
The value of interior Notch is stored as parameters in this model, which is retrieved by this method
Definition at line 167 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.
double DeltaNotchEdgeSrnModel::GetNeighbouringDelta | ( | ) | const |
Definition at line 155 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.
double DeltaNotchEdgeSrnModel::GetNotch | ( | ) |
Definition at line 129 of file DeltaNotchEdgeSrnModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by DeltaNotchInteriorSrnModel::AddShrunkEdgeToInterior(), and AddSrnQuantities().
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virtual |
Initialise the SRN model at the start of a simulation.
This overridden method sets up a new Delta-Notch ODE system.
Reimplemented from AbstractOdeSrnModel.
Definition at line 96 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractOdeSrnModel::Initialise().
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This method is called when a new edge is created (e.g. after cell division or T1 swap)
Reimplemented from AbstractSrnModel.
Definition at line 101 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::SetParameter(), and AbstractParameterisedSystem< VECTOR >::SetStateVariable().
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Output SRN model parameters to file.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractOdeSrnModel.
Definition at line 173 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractOdeSrnModel::OutputSrnModelParameters().
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inlineprivate |
Archive the SRN model and member variables.
archive | the archive |
version | the current version of this class |
Definition at line 68 of file DeltaNotchEdgeSrnModel.hpp.
void DeltaNotchEdgeSrnModel::SetDelta | ( | double | value | ) |
Set the Delta level in this edge.
value | the new Delta level in this edge |
Definition at line 149 of file DeltaNotchEdgeSrnModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by AddSrnQuantities().
void DeltaNotchEdgeSrnModel::SetNotch | ( | double | value | ) |
Set the Notch level in this edge.
value | the new Notch level in this edge |
Definition at line 136 of file DeltaNotchEdgeSrnModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by AddSrnQuantities().
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virtual |
Overridden SimulateToTime() method for custom behaviour. Updates parameters (such as neighbour or interior Delta/Notch) and runs the simulation to current time
Reimplemented from AbstractOdeSrnModel.
Definition at line 87 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractOdeSrnModel::SimulateToCurrentTime(), and UpdateDeltaNotch().
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By default, Edge concentrations are split according to the lengths of two new edges , when an edge is split, relative to the original edge they are created from. Override the method declared in AbstractSrnModel class
relativePosition | position of the node splitting the two new edges relative to the original edge, used when splitting Edge concentrations |
Reimplemented from AbstractSrnModel.
Definition at line 206 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractOdeSrnModel::ScaleSrnVariables().
void DeltaNotchEdgeSrnModel::UpdateDeltaNotch | ( | ) |
Update the levels of Delta and Notch of neighbouring edge sensed by this edge That is, fetch neighbour values from CellEdgeData object, storing the sensed information, into this model
Definition at line 114 of file DeltaNotchEdgeSrnModel.cpp.
References AbstractSrnModel::GetEdgeLocalIndex(), AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetParameter().
Referenced by SimulateToCurrentTime().
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friend |
Needed for serialization.
Definition at line 60 of file DeltaNotchEdgeSrnModel.hpp.