12.6. Direct Transport with Compartments Model

12.6.1. Description

Similarly as in the Direct Transport Model, here we exemplified the usage of reactions with absolute orientation but this time also using compartments. The use of compartments is needed to bring space-independent models written in BioNetGen to MCell 4 (i.e. spatial models). Volume molecules V in the interior of a cube react with surface molecules S, producing volume molecules V in the exterior of the cube, inside the World (reaction v@Cube + s@Membrane -> s@Membrane + V@World). World is define as a parent compartment from the Cube, and Membrane is define as the surface of the object Cube. The surface areas of the cube and the World (another cube) are made reflective to emulate a bigger surrounding environment, and keep the number of molecules constant in the interior of the World.

12.6.2. Demonstrated features

  • Reactions with absolute orientation.

  • A surface classes is used to make objects reflective.

  • Usage of BioNetGen compartments.