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);

Create 8 cells in a 2x2x2 grid setup

auto construct = [&](const Double3& position) {
  Cell* cell = new Cell(position);
  cell->SetDiameter(30);
  cell->SetMass(1.0);
  cell->AddBehavior(new Chemotaxis("Kalium", 0.5));
  return cell;
};
ModelInitializer::Grid3D(2, 100, construct);

The cell responsible for secretion

auto* secreting_cell = new Cell({50, 50, 50});
secreting_cell->AddBehavior(new Secretion("Kalium", 4));
simulation.GetResourceManager()->AddAgent(secreting_cell);

Run simulation for n timesteps

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

Simulation completed successfully!

Let's visualize the output!

VisualizeInNotebook();