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

Class SingleFileChannelMembraneTransport

  • All Implemented Interfaces:
    UpdateModule, Runnable
    public class SingleFileChannelMembraneTransport
extends ConcentrationBasedModule<UpdatableDeltaFunction>
    The single file channel transport describes the movement of cargo molecules through Transporter proteins, so called membrane channels. In the channels the cargo proteins move in a single file configuration. The kinetics of the transport is guided by the osmotic pressure of solute molecules as well as the OsmoticPermeability of the transporter. The net flux of the cargo through the membrane is: 
      JC = pf * nt * (s1 - s2)
    where pf is the OsmoticPermeability, nt is the number of transporters in the membrane and s1 and s2 are the concentrations of the solute on both sides of the membrane, as in: 
      Finkelstein, Alan. "Water movement through membrane channels."
  Current Topics in Membranes and Transport. Vol. 21. Academic Press, 1984. 295-308.
    This concentration based module applies IndependentUpdates and is UpdatableSpecific. 
      // get water from chebi
  SmallMolecule water = ChEBIParserService.parse("CHEBI:15377", "water");

  // define solutes as a single species
  SmallMolecule solute = new SmallMolecule.Builder("solutes")
         .name("solutes")
         .build();

  // aquaporin 2 as a transporter
  Transporter aquaporin2 = UniProtParserService.parse("P41181", "aqp2").asTransporter();
  aquaporin2.setFeature(new OsmoticPermeability(5.31e-14, BINESH2015));

  // create module
  SingleFileChannelMembraneTransport.inSimulation(simulation)
         .transporter(aquaporin2)
         .cargo(water)
         .forSolute(solute)
         .build();
    Author:
    cl