Diffusion

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This model creates 8 cells at each corner of a cube, and one in the middle. The cell in the middle secretes a substance. The cells are modeled to move according to the extracellular gradient; in this case to the middle.

%jsroot on
gROOT->LoadMacro("${BDMSYS}/etc/rootlogon.C");

INFO: Created simulation object 'simulation' with UniqueName='simulation'.

#include "biodynamo.h"

List the extracellular substances

enum Substances { kKalium };

Initialize biodynamo

Simulation simulation("diffusion");

Define the substances that cells may secrete

ModelInitializer::DefineSubstance(kKalium, "Kalium", 0.4, 0, 25);
auto* rm = simulation.GetResourceManager();
auto* dgrid = rm->GetDiffusionGrid(kKalium);

auto construct = [&](const Double3& position) {
  Cell* cell = new Cell(position);
  cell->SetDiameter(30);
  cell->SetMass(1.0);
  Double3 secretion_position = {{50, 50, 50}};
  if (position == secretion_position) {
    cell->AddBiologyModule(new Secretion(dgrid, 4));
  } else {
    cell->AddBiologyModule(new Chemotaxis(dgrid, 0.5));
  }
  return cell;
};
std::vector<Double3> positions;
positions.push_back({0, 0, 0});
positions.push_back({100, 0, 0});
positions.push_back({0, 100, 0});
positions.push_back({0, 0, 100});
positions.push_back({0, 100, 100});
positions.push_back({100, 0, 100});
positions.push_back({100, 100, 0});
positions.push_back({100, 100, 100});

The cell responsible for secretion

positions.push_back({50, 50, 50});
ModelInitializer::CreateCells(positions, construct);

Run simulation for n timesteps

simulation.GetScheduler()->Simulate(300);
std::cout << "Simulation completed successfully!\n";

Simulation completed successfully!

Let's visualize the output!

VisualizeInNotebook();