Title here
Summary here
This tutorial was generated from the file projects/CellBasedComparison2017/test/TestMorphogenMonolayerLiteratePaper.hpp at revision r27522. Note that the code is given in full at the bottom of the page.
Long-range Signalling Example
On this wiki page we describe in detail the code that is used to run this example from the paper.
The easiest way to visualize these simulations is with Paraview.
Code overview
The first thing to do is to include the necessary header files.
#include <cxxtest/TestSuite.h>
// Must be included before other cell_based headers
#include "CellBasedSimulationArchiver.hpp"
#include "SmartPointers.hpp"
#include "AbstractCellBasedWithTimingsTestSuite.hpp"
#include "DefaultCellProliferativeType.hpp"
#include "CellIdWriter.hpp"
#include "CellAgesWriter.hpp"
#include "VoronoiDataWriter.hpp"
#include "CellMutationStatesWriter.hpp"
#include "ParabolicGrowingDomainPdeModifier.hpp"
#include "MorphogenCellwiseSourceParabolicPde.hpp"
#include "VolumeTrackingModifier.hpp"
#include "MorphogenDependentCellCycleModel.hpp"
#include "CellDataItemWriter.hpp"
#include "OffLatticeSimulation.hpp"
#include "OnLatticeSimulation.hpp"
#include "CellsGenerator.hpp"
#include "RandomCellKiller.hpp"
#include "MeshBasedCellPopulationWithGhostNodes.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "RepulsionForce.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "HoneycombVertexMeshGenerator.hpp"
#include "NagaiHondaForce.hpp"
#include "SimpleTargetAreaModifier.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "PottsMeshGenerator.hpp"
#include "VolumeConstraintPottsUpdateRule.hpp"
#include "AdhesionPottsUpdateRule.hpp"
#include "SurfaceAreaConstraintPottsUpdateRule.hpp"
#include "CaBasedCellPopulation.hpp"
#include "DiffusionCaUpdateRule.hpp"
#include "ShovingCaBasedDivisionRule.hpp"
#include "AdhesionCaSwitchingUpdateRule.hpp"
#include "PetscSetupAndFinalize.hpp"This is where you can set parameters to be used in all the simulations.
static const double M_TIME_FOR_SIMULATION = 100; //100
static const double M_NUM_CELLS_ACROSS = 10; // 10
static const double M_UPTAKE_RATE = 0.01; // S in paper
static const double M_DIFFUSION_CONSTANT = 1e-4; // D in paper
static const double M_DUDT_COEFFICIENT = 1.0; // Not used in paper so 1
class TestMorphogenMonolayerLiteratePaper : public AbstractCellBasedWithTimingsTestSuite
{
private:This is a helper method to generate cells and is used in all simulations.
void GenerateCells(unsigned num_cells, std::vector<CellPtr>& rCells)
{
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DefaultCellProliferativeType, p_transit_type);
RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
for (unsigned i=0; i<num_cells; i++)
{
//UniformlyDistributedCellCycleModel* p_cycle_model = new UniformlyDistributedCellCycleModel();
MorphogenDependentCellCycleModel* p_cycle_model = new MorphogenDependentCellCycleModel();
p_cycle_model->SetDimension(2);
p_cycle_model->SetCurrentMass(0.5*(p_gen->ranf()+1.0));
p_cycle_model->SetMorphogenInfluence(10.0);
CellPtr p_cell(new Cell(p_state, p_cycle_model));
p_cell->SetCellProliferativeType(p_transit_type);
// Note the first few recorded ages will be too short as cells start with some mass.
//p_cell->SetBirthTime(0.0);
p_cell->SetBirthTime(-20);
p_cell->InitialiseCellCycleModel();
// Initial Condition for Morphogen PDE
p_cell->GetCellData()->SetItem("morphogen",0.0);
// Set Target Area so dont need to use a growth model in vertex simulations
p_cell->GetCellData()->SetItem("target area", 1.0);
rCells.push_back(p_cell);
}
}
public:CA
Simulate reaction diffusion on a growing a population of cells in the Cellular Automaton model.
void TestCaBasedMorphogenMonolayer()
{
// Create a simple 2D PottsMesh
unsigned domain_wide = 20*M_NUM_CELLS_ACROSS;
PottsMeshGenerator<2> generator(domain_wide, 0, 0, domain_wide, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
p_mesh->Translate(-(double)domain_wide*0.5 + 0.5,-(double)domain_wide*0.5 + 0.5);
// Specify where cells lie, i.e only within the specified initial radius
std::vector<unsigned> location_indices;
for (AbstractMesh<2, 2>::NodeIterator node_iter = p_mesh->GetNodeIteratorBegin();
node_iter != p_mesh->GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
c_vector<double,2> node_location = node_iter->rGetLocation();
if (norm_2(node_location)<0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
location_indices.push_back(node_index);
}
}
std::vector<CellPtr> cells;
GenerateCells(location_indices.size(),cells);
// Create cell population
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
// Set population to output all data to results files
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
// Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Ca");
simulator.SetDt(1/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Add Division Rule
boost::shared_ptr<AbstractCaBasedDivisionRule<2> > p_division_rule(new ShovingCaBasedDivisionRule<2>());
cell_population.SetCaBasedDivisionRule(p_division_rule);
// Add switching Update Rule to smooth out the edge of the monolayer note no Temp as don't want random switches
MAKE_PTR(AdhesionCaSwitchingUpdateRule<2u>, p_switching_update_rule);
p_switching_update_rule->SetCellCellAdhesionEnergyParameter(0.1);
p_switching_update_rule->SetCellBoundaryAdhesionEnergyParameter(0.2);
p_switching_update_rule->SetTemperature(0.0); //
simulator.AddUpdateRule(p_switching_update_rule);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}CP
Simulate reaction diffusion on a growing a population of cells in the Cellular Potts model.
void TestPottsBasedMorphogenMonolayer()
{
unsigned cell_width = 4;
unsigned domain_width = M_NUM_CELLS_ACROSS*cell_width*20;
PottsMeshGenerator<2> generator(domain_width, 2*M_NUM_CELLS_ACROSS, cell_width, domain_width, 2*M_NUM_CELLS_ACROSS, cell_width);
PottsMesh<2>* p_mesh = generator.GetMesh();
p_mesh->Translate(-(double)domain_width*0.5+0.5,-(double)domain_width*0.5+0.5);
//p_mesh->Scale(0.25,0.25); // Not scaling
//Remove all elements outside the specified initial radius
for (PottsMesh<2>::PottsElementIterator elem_iter = p_mesh->GetElementIteratorBegin();
elem_iter != p_mesh->GetElementIteratorEnd();
++elem_iter)
{
unsigned elem_index = elem_iter->GetIndex();
c_vector<double,2> element_centre = p_mesh->GetCentroidOfElement(elem_index);
if (norm_2(element_centre)>0.5*M_NUM_CELLS_ACROSS *cell_width + 1e-5)
{
p_mesh->DeleteElement(elem_index);
}
}
p_mesh->RemoveDeletedElements();
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumElements(),cells);
PottsBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.SetTemperature(0.1);
cell_population.SetNumSweepsPerTimestep(1);
// Set population to output all data to results files
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
// Set the Temperature
cell_population.SetTemperature(0.1); //Default is 0.1
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Potts");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Create update rules and pass to the simulation
MAKE_PTR(VolumeConstraintPottsUpdateRule<2>, p_volume_constraint_update_rule);
p_volume_constraint_update_rule->SetMatureCellTargetVolume(16); // i.e 4x4 cells
p_volume_constraint_update_rule->SetDeformationEnergyParameter(0.1);
simulator.AddUpdateRule(p_volume_constraint_update_rule);
MAKE_PTR(SurfaceAreaConstraintPottsUpdateRule<2>, p_surface_constraint_update_rule);
p_surface_constraint_update_rule->SetMatureCellTargetSurfaceArea(16); // i.e 4x4 cells
p_surface_constraint_update_rule->SetDeformationEnergyParameter(0.01);
simulator.AddUpdateRule(p_surface_constraint_update_rule);
MAKE_PTR(AdhesionPottsUpdateRule<2>, p_adhesion_update_rule);
p_adhesion_update_rule->SetCellCellAdhesionEnergyParameter(0.1);
p_adhesion_update_rule->SetCellBoundaryAdhesionEnergyParameter(0.2);
simulator.AddUpdateRule(p_adhesion_update_rule);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,(double)cell_width*(double)cell_width*M_DIFFUSION_CONSTANT,M_UPTAKE_RATE, 8.0));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}OS
Simulate reaction diffusion on a growing a population of cells in the Overlapping Spheres model.
void TestNodeBasedMorphogenMonolayer()
{
HoneycombMeshGenerator generator(2.0*M_NUM_CELLS_ACROSS, 3.0*M_NUM_CELLS_ACROSS,0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
p_generating_mesh->Translate(-M_NUM_CELLS_ACROSS,-sqrt(3.0)*M_NUM_CELLS_ACROSS);
//Remove all elements outside the specified initial radius
for (AbstractMesh<2, 2>::NodeIterator node_iter = p_generating_mesh->GetNodeIteratorBegin();
node_iter != p_generating_mesh->GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
c_vector<double,2> node_location = node_iter->rGetLocation();
if (norm_2(node_location)>0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
p_generating_mesh->DeleteNodePriorToReMesh(node_index);
}
}
p_generating_mesh->ReMesh();
double cut_off_length = 1.5; //this is the default
NodesOnlyMesh<2>* p_mesh = new NodesOnlyMesh<2>;
p_mesh->ConstructNodesWithoutMesh(*p_generating_mesh, cut_off_length);
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumNodes(),cells);
NodeBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Node");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetMeinekeSpringStiffness(50.0);
p_linear_force->SetCutOffLength(cut_off_length);
simulator.AddForce(p_linear_force);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
delete p_mesh; // to stop memory leaks
}VT
Simulate reaction diffusion on a growing a population of cells in the Voronoi Tesselation model.
void TestMeshBasedMorphogenMonolayer()
{
HoneycombMeshGenerator generator(2.0*M_NUM_CELLS_ACROSS,3.0*M_NUM_CELLS_ACROSS);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
p_mesh->Translate(-(double)M_NUM_CELLS_ACROSS*0.5,-sqrt(3)*M_NUM_CELLS_ACROSS);
//Remove all elements outside the specified initial radius
for (AbstractMesh<2, 2>::NodeIterator node_iter = p_mesh->GetNodeIteratorBegin();
node_iter != p_mesh->GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
c_vector<double,2> node_location = node_iter->rGetLocation();
if (norm_2(node_location)>0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
p_mesh->DeleteNodePriorToReMesh(node_index);
}
}
p_mesh->ReMesh();
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumNodes(),cells);
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set population to output all data to results files
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variabl name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
cell_population.SetWriteVtkAsPoints(true);
cell_population.AddPopulationWriter<VoronoiDataWriter>();
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Mesh");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetMeinekeSpringStiffness(50.0);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}VM
Simulate reaction diffusion on a growing a population of cells in the Cell Vertex model.
void TestVertexBasedMorphogenMonolayer()
{
// Create Mesh
HoneycombVertexMeshGenerator generator(2.0*M_NUM_CELLS_ACROSS, 3.0*M_NUM_CELLS_ACROSS);
MutableVertexMesh<2,2>* p_mesh = generator.GetMesh();
p_mesh->SetCellRearrangementThreshold(0.1);
p_mesh->Translate(-M_NUM_CELLS_ACROSS,-sqrt(3.0)*M_NUM_CELLS_ACROSS+ sqrt(3.0)/6.0);
//Remove all elements outside the specified initial radius
for (VertexMesh<2,2>::VertexElementIterator elem_iter = p_mesh->GetElementIteratorBegin();
elem_iter != p_mesh->GetElementIteratorEnd();
++elem_iter)
{
unsigned elem_index = elem_iter->GetIndex();
c_vector<double,2> element_centre = p_mesh->GetCentroidOfElement(elem_index);
if (norm_2(element_centre)>0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
p_mesh->DeleteElementPriorToReMesh(elem_index);
}
}
p_mesh->ReMesh();
// Create Cells
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumElements(),cells);
// Create Population
VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
// Create Simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Vertex");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Create Forces and pass to simulation NOTE: these are not the default ones and chosen to give a stable growing monolayer
MAKE_PTR(NagaiHondaForce<2>, p_force);
p_force->SetNagaiHondaDeformationEnergyParameter(50.0);
p_force->SetNagaiHondaMembraneSurfaceEnergyParameter(1.0);
p_force->SetNagaiHondaCellCellAdhesionEnergyParameter(1.0);
p_force->SetNagaiHondaCellBoundaryAdhesionEnergyParameter(10.0);
simulator.AddForce(p_force);
// Create Modifiers and pass to simulation
// Create a pde modifier and pass it to the simulation
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}
};Code
The full code is given below
File name TestMorphogenMonolayerLiteratePaper.hpp
#include <cxxtest/TestSuite.h>
// Must be included before other cell_based headers
#include "CellBasedSimulationArchiver.hpp"
#include "SmartPointers.hpp"
#include "AbstractCellBasedWithTimingsTestSuite.hpp"
#include "DefaultCellProliferativeType.hpp"
#include "CellIdWriter.hpp"
#include "CellAgesWriter.hpp"
#include "VoronoiDataWriter.hpp"
#include "CellMutationStatesWriter.hpp"
#include "ParabolicGrowingDomainPdeModifier.hpp"
#include "MorphogenCellwiseSourceParabolicPde.hpp"
#include "VolumeTrackingModifier.hpp"
#include "MorphogenDependentCellCycleModel.hpp"
#include "CellDataItemWriter.hpp"
#include "OffLatticeSimulation.hpp"
#include "OnLatticeSimulation.hpp"
#include "CellsGenerator.hpp"
#include "RandomCellKiller.hpp"
#include "MeshBasedCellPopulationWithGhostNodes.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "RepulsionForce.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "HoneycombVertexMeshGenerator.hpp"
#include "NagaiHondaForce.hpp"
#include "SimpleTargetAreaModifier.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "PottsMeshGenerator.hpp"
#include "VolumeConstraintPottsUpdateRule.hpp"
#include "AdhesionPottsUpdateRule.hpp"
#include "SurfaceAreaConstraintPottsUpdateRule.hpp"
#include "CaBasedCellPopulation.hpp"
#include "DiffusionCaUpdateRule.hpp"
#include "ShovingCaBasedDivisionRule.hpp"
#include "AdhesionCaSwitchingUpdateRule.hpp"
#include "PetscSetupAndFinalize.hpp"
static const double M_TIME_FOR_SIMULATION = 100; //100
static const double M_NUM_CELLS_ACROSS = 10; // 10
static const double M_UPTAKE_RATE = 0.01; // S in paper
static const double M_DIFFUSION_CONSTANT = 1e-4; // D in paper
static const double M_DUDT_COEFFICIENT = 1.0; // Not used in paper so 1
class TestMorphogenMonolayerLiteratePaper : public AbstractCellBasedWithTimingsTestSuite
{
private:
void GenerateCells(unsigned num_cells, std::vector<CellPtr>& rCells)
{
MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(DefaultCellProliferativeType, p_transit_type);
RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
for (unsigned i=0; i<num_cells; i++)
{
//UniformlyDistributedCellCycleModel* p_cycle_model = new UniformlyDistributedCellCycleModel();
MorphogenDependentCellCycleModel* p_cycle_model = new MorphogenDependentCellCycleModel();
p_cycle_model->SetDimension(2);
p_cycle_model->SetCurrentMass(0.5*(p_gen->ranf()+1.0));
p_cycle_model->SetMorphogenInfluence(10.0);
CellPtr p_cell(new Cell(p_state, p_cycle_model));
p_cell->SetCellProliferativeType(p_transit_type);
// Note the first few recorded ages will be too short as cells start with some mass.
//p_cell->SetBirthTime(0.0);
p_cell->SetBirthTime(-20);
p_cell->InitialiseCellCycleModel();
// Initial Condition for Morphogen PDE
p_cell->GetCellData()->SetItem("morphogen",0.0);
// Set Target Area so dont need to use a growth model in vertex simulations
p_cell->GetCellData()->SetItem("target area", 1.0);
rCells.push_back(p_cell);
}
}
public:
void TestCaBasedMorphogenMonolayer()
{
// Create a simple 2D PottsMesh
unsigned domain_wide = 20*M_NUM_CELLS_ACROSS;
PottsMeshGenerator<2> generator(domain_wide, 0, 0, domain_wide, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
p_mesh->Translate(-(double)domain_wide*0.5 + 0.5,-(double)domain_wide*0.5 + 0.5);
// Specify where cells lie, i.e only within the specified initial radius
std::vector<unsigned> location_indices;
for (AbstractMesh<2, 2>::NodeIterator node_iter = p_mesh->GetNodeIteratorBegin();
node_iter != p_mesh->GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
c_vector<double,2> node_location = node_iter->rGetLocation();
if (norm_2(node_location)<0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
location_indices.push_back(node_index);
}
}
std::vector<CellPtr> cells;
GenerateCells(location_indices.size(),cells);
// Create cell population
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices);
// Set population to output all data to results files
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
// Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Ca");
simulator.SetDt(1/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Add Division Rule
boost::shared_ptr<AbstractCaBasedDivisionRule<2> > p_division_rule(new ShovingCaBasedDivisionRule<2>());
cell_population.SetCaBasedDivisionRule(p_division_rule);
// Add switching Update Rule to smooth out the edge of the monolayer note no Temp as don't want random switches
MAKE_PTR(AdhesionCaSwitchingUpdateRule<2u>, p_switching_update_rule);
p_switching_update_rule->SetCellCellAdhesionEnergyParameter(0.1);
p_switching_update_rule->SetCellBoundaryAdhesionEnergyParameter(0.2);
p_switching_update_rule->SetTemperature(0.0); //
simulator.AddUpdateRule(p_switching_update_rule);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}
void TestPottsBasedMorphogenMonolayer()
{
unsigned cell_width = 4;
unsigned domain_width = M_NUM_CELLS_ACROSS*cell_width*20;
PottsMeshGenerator<2> generator(domain_width, 2*M_NUM_CELLS_ACROSS, cell_width, domain_width, 2*M_NUM_CELLS_ACROSS, cell_width);
PottsMesh<2>* p_mesh = generator.GetMesh();
p_mesh->Translate(-(double)domain_width*0.5+0.5,-(double)domain_width*0.5+0.5);
//p_mesh->Scale(0.25,0.25); // Not scaling
//Remove all elements outside the specified initial radius
for (PottsMesh<2>::PottsElementIterator elem_iter = p_mesh->GetElementIteratorBegin();
elem_iter != p_mesh->GetElementIteratorEnd();
++elem_iter)
{
unsigned elem_index = elem_iter->GetIndex();
c_vector<double,2> element_centre = p_mesh->GetCentroidOfElement(elem_index);
if (norm_2(element_centre)>0.5*M_NUM_CELLS_ACROSS *cell_width + 1e-5)
{
p_mesh->DeleteElement(elem_index);
}
}
p_mesh->RemoveDeletedElements();
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumElements(),cells);
PottsBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.SetTemperature(0.1);
cell_population.SetNumSweepsPerTimestep(1);
// Set population to output all data to results files
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
// Set the Temperature
cell_population.SetTemperature(0.1); //Default is 0.1
OnLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Potts");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Create update rules and pass to the simulation
MAKE_PTR(VolumeConstraintPottsUpdateRule<2>, p_volume_constraint_update_rule);
p_volume_constraint_update_rule->SetMatureCellTargetVolume(16); // i.e 4x4 cells
p_volume_constraint_update_rule->SetDeformationEnergyParameter(0.1);
simulator.AddUpdateRule(p_volume_constraint_update_rule);
MAKE_PTR(SurfaceAreaConstraintPottsUpdateRule<2>, p_surface_constraint_update_rule);
p_surface_constraint_update_rule->SetMatureCellTargetSurfaceArea(16); // i.e 4x4 cells
p_surface_constraint_update_rule->SetDeformationEnergyParameter(0.01);
simulator.AddUpdateRule(p_surface_constraint_update_rule);
MAKE_PTR(AdhesionPottsUpdateRule<2>, p_adhesion_update_rule);
p_adhesion_update_rule->SetCellCellAdhesionEnergyParameter(0.1);
p_adhesion_update_rule->SetCellBoundaryAdhesionEnergyParameter(0.2);
simulator.AddUpdateRule(p_adhesion_update_rule);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,(double)cell_width*(double)cell_width*M_DIFFUSION_CONSTANT,M_UPTAKE_RATE, 8.0));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}
void TestNodeBasedMorphogenMonolayer()
{
HoneycombMeshGenerator generator(2.0*M_NUM_CELLS_ACROSS, 3.0*M_NUM_CELLS_ACROSS,0);
MutableMesh<2,2>* p_generating_mesh = generator.GetMesh();
p_generating_mesh->Translate(-M_NUM_CELLS_ACROSS,-sqrt(3.0)*M_NUM_CELLS_ACROSS);
//Remove all elements outside the specified initial radius
for (AbstractMesh<2, 2>::NodeIterator node_iter = p_generating_mesh->GetNodeIteratorBegin();
node_iter != p_generating_mesh->GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
c_vector<double,2> node_location = node_iter->rGetLocation();
if (norm_2(node_location)>0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
p_generating_mesh->DeleteNodePriorToReMesh(node_index);
}
}
p_generating_mesh->ReMesh();
double cut_off_length = 1.5; //this is the default
NodesOnlyMesh<2>* p_mesh = new NodesOnlyMesh<2>;
p_mesh->ConstructNodesWithoutMesh(*p_generating_mesh, cut_off_length);
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumNodes(),cells);
NodeBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Node");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Create a force law and pass it to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetMeinekeSpringStiffness(50.0);
p_linear_force->SetCutOffLength(cut_off_length);
simulator.AddForce(p_linear_force);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
delete p_mesh; // to stop memory leaks
}
void TestMeshBasedMorphogenMonolayer()
{
HoneycombMeshGenerator generator(2.0*M_NUM_CELLS_ACROSS,3.0*M_NUM_CELLS_ACROSS);
MutableMesh<2,2>* p_mesh = generator.GetMesh();
p_mesh->Translate(-(double)M_NUM_CELLS_ACROSS*0.5,-sqrt(3)*M_NUM_CELLS_ACROSS);
//Remove all elements outside the specified initial radius
for (AbstractMesh<2, 2>::NodeIterator node_iter = p_mesh->GetNodeIteratorBegin();
node_iter != p_mesh->GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
c_vector<double,2> node_location = node_iter->rGetLocation();
if (norm_2(node_location)>0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
p_mesh->DeleteNodePriorToReMesh(node_index);
}
}
p_mesh->ReMesh();
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumNodes(),cells);
MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);
// Set population to output all data to results files
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variabl name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
cell_population.SetWriteVtkAsPoints(true);
cell_population.AddPopulationWriter<VoronoiDataWriter>();
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Mesh");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetMeinekeSpringStiffness(50.0);
p_linear_force->SetCutOffLength(1.5);
simulator.AddForce(p_linear_force);
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}
void TestVertexBasedMorphogenMonolayer()
{
// Create Mesh
HoneycombVertexMeshGenerator generator(2.0*M_NUM_CELLS_ACROSS, 3.0*M_NUM_CELLS_ACROSS);
MutableVertexMesh<2,2>* p_mesh = generator.GetMesh();
p_mesh->SetCellRearrangementThreshold(0.1);
p_mesh->Translate(-M_NUM_CELLS_ACROSS,-sqrt(3.0)*M_NUM_CELLS_ACROSS+ sqrt(3.0)/6.0);
//Remove all elements outside the specified initial radius
for (VertexMesh<2,2>::VertexElementIterator elem_iter = p_mesh->GetElementIteratorBegin();
elem_iter != p_mesh->GetElementIteratorEnd();
++elem_iter)
{
unsigned elem_index = elem_iter->GetIndex();
c_vector<double,2> element_centre = p_mesh->GetCentroidOfElement(elem_index);
if (norm_2(element_centre)>0.5*M_NUM_CELLS_ACROSS + 1e-5)
{
p_mesh->DeleteElementPriorToReMesh(elem_index);
}
}
p_mesh->ReMesh();
// Create Cells
std::vector<CellPtr> cells;
GenerateCells(p_mesh->GetNumElements(),cells);
// Create Population
VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
cell_population.AddCellWriter<CellIdWriter>();
cell_population.AddCellWriter<CellAgesWriter>();
cell_population.AddCellWriter<CellMutationStatesWriter>();
//Make cell data writer so can pass in variable name
boost::shared_ptr<CellDataItemWriter<2,2> > p_cell_data_item_writer(new CellDataItemWriter<2,2>("morphogen"));
cell_population.AddCellWriter(p_cell_data_item_writer);
// Create Simulation
OffLatticeSimulation<2> simulator(cell_population);
simulator.SetOutputDirectory("MorphogenMonolayer/Vertex");
simulator.SetDt(1.0/200.0);
simulator.SetSamplingTimestepMultiple(200);
simulator.SetEndTime(M_TIME_FOR_SIMULATION);
simulator.SetOutputDivisionLocations(true);
// Create Forces and pass to simulation NOTE: these are not the default ones and chosen to give a stable growing monolayer
MAKE_PTR(NagaiHondaForce<2>, p_force);
p_force->SetNagaiHondaDeformationEnergyParameter(50.0);
p_force->SetNagaiHondaMembraneSurfaceEnergyParameter(1.0);
p_force->SetNagaiHondaCellCellAdhesionEnergyParameter(1.0);
p_force->SetNagaiHondaCellBoundaryAdhesionEnergyParameter(10.0);
simulator.AddForce(p_force);
// Create Modifiers and pass to simulation
// Create a pde modifier and pass it to the simulation
// Make the Pde and BCS
MAKE_PTR_ARGS(MorphogenCellwiseSourceParabolicPde<2>, p_pde, (cell_population, M_DUDT_COEFFICIENT,M_DIFFUSION_CONSTANT,M_UPTAKE_RATE));
MAKE_PTR_ARGS(ConstBoundaryCondition<2>, p_bc, (0.0));
// Create a PDE Modifier object using this pde and bcs object
MAKE_PTR_ARGS(ParabolicGrowingDomainPdeModifier<2>, p_pde_modifier, (p_pde, p_bc, true));
p_pde_modifier->SetDependentVariableName("morphogen");
simulator.AddSimulationModifier(p_pde_modifier);
simulator.Solve();
}
};