Package bio.singa.simulation.model.modules.concentration.imlementations.transport

Class MembraneDiffusion

  • All Implemented Interfaces:
    UpdateModule, Runnable
    public class MembraneDiffusion
extends ConcentrationBasedModule<UpdatableDeltaFunction>
    The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo. The cargo molecules are crossing a membrane from one side to the other side. The flux of concentration is determined by terms of 
      JM = Pd * A * (c1 - c2)
    where Pd is the MembranePermeability, A is the area of the membrane, and c1 and c2 are the concentrations on both sides of the membrane; as in: 
      Stein, Wilfred. Transport and diffusion across cell membranes. Elsevier, 2012.
    This concentration based module applies SemiDependentUpdates and is UpdatableSpecific. 
      // define the feature to parametrize the diffusion
  MembranePermeability membranePermeability = new MembranePermeability(Quantities.getValue(3.5E-03, CENTIMETRE_PER_SECOND),
         Evidence.MANUALLY_ANNOTATED);
  // assign it to the chemical entity
  SmallMolecule water = new SmallMolecule.Builder("water")
         .assignFeature(membranePermeability)
         .build();
  // create the module
  MembraneDiffusion.inSimulation(simulation)
         .cargo(water)
         .build();
    Author:
    cl