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Session 9: s imulating transport processes and cell-cell signalling in Chaste

Session 9: s imulating transport processes and cell-cell signalling in Chaste. Cell-based Chaste workshop Friday 6 th January 2012. Summary of Delta-Notch model. In many developing tissues a fine-grained mixture of cell types is generated through cell-cell interactions

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Session 9: s imulating transport processes and cell-cell signalling in Chaste

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  1. Session 9: simulating transport processes and cell-cell signalling in Chaste Cell-based Chaste workshop Friday 6thJanuary 2012

  2. Summary of Delta-Notch model • In many developing tissues a fine-grained mixture of cell types is generated through cell-cell interactions • This occurs within a population of cells that are initially equivalent in their developmental potential • The mechanism is based on lateral inhibition • Extensive genetic and biochemical studies have identified Notchas the receptor and the product of Delta as the corresponding ligand expressed in the cell delivering inhibition

  3. Summary of Delta-Notch model • Collier et al. (1996) model

  4. Implementation • Create a suitable cell population, e.g. a VertexBasedCellPopulation, using a DeltaNotchCellCycleModel • Overridden UpdateCellCyclePhase() method updates the current level of mean Delta among nearest neighbours according to CellwiseData, and uses this to solve the Delta/Notch ODE system over one mechanics timestep • Set up CellwiseData • Create a DeltaNotchOffLatticeSimulation • Overridden PostSolve() method computes, for each cell, the current level of Delta, Notch, and mean Delta among nearest neighbours, and stores these in CellwiseData

  5. Summary of nutrient transport model

  6. Summary of nutrient transport model

  7. Implementation • Hierarchy of classes • PDE class, e.g. CellwiseSourcePde • Boundary condition class, e.g. ConstBoundaryCondition • These are associated in a PdeAndBoundaryConditions object • One or more PdeAndBoundaryConditionsobjects, together with the cell population, are associated in a CellBasedPdeHandler • Use AbstractCellBasedSimulation::mpCellBasedPdeHandler • Call SetCellBasedPdeHandler() on the simulation object • The PDE handler will call SolvePdeAndWriteResultsToFile() within PostSolve() • PDE solution is stored in CellwiseData • Set up CellwiseData at start of simulation • Use a cell-cycle model such as SimpleOxygenBasedCellCycleModel, which has access to the PDE solution via CellwiseData

  8. Implementation • Documentation and further details of the class hierarchy are available on the wiki. • You will find the tutorials for this session here: • UserTutorials/RunningDeltaNotchSimulations • UserTutorials/RunningTumourSpheroidSimulations • These will guide you through the implementation of these models. • Further exercises are also suggested for those who are interested.

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