Biological software developped in Serrano's laboratory

Diffusion vs Active Transport

In SmartCell, 2 kinds of events are available to describe the movement of particles inside the cell: the diffusion and the active transport.

The diffusion

The diffusion describes the movement of a particle inside a compartment or between 2 compartments. The diffusion is multi-directional and can then need a lot of steps before migration from inside one compartment to another one.

The active transport

The active transport is always defined from one compartment (Comp1) to another (Comp2). Wherever the species involved in the active transport are located in Comp1, they will move in a voxel of Comp2 (if there is one voxel of Comp2 neighbor of the current voxel) or in the voxel of Comp1 with the shortest distance with any voxel of Comp2.

Example

If we consider a cell divided in 10 voxels, 9 voxels composing the cytosol and 1 voxel composing the nucleus. We distribute randomly 10 particles inside the cytosol. In the diffusin model we define a diffusion inside the cytosol and from the cytosol to the nucleus. In the active transport we define an active transport from the cytosol to the nucleus. We simulate the network during 100s and we compare the number of particles in the nucleus every second.


As we can see, in both case the particles arrive finally in the nucleus but the movement is faster in the case of active transport.