Figure 4.

Voxelisation of the System Volume. The system volume is shown divided into 5 × 5 × 5 voxels. During the bi-molecular reaction step the list of voxels that contain reacting molecular species is shuffled and each voxel checked sequentially. The reacting molecular species in the voxel and the reacting molecular species in the 26 neighbouring voxels are checked for the occurrence of bi-molecular reactions, based on the binding radius. After the reactions, the centre voxels is removed from further inspection until the iteration cycle starts anew, and the next voxel and its neighbours are inspected. The side length of a voxel must be larger than the largest binding radius in the simulations. Possible binding radii are estimated at program initialisation. The centre voxel is shown in purple. For the sake of clarity only 6 (out of a total of 26) neighbour voxels are highlighted in light green.

Tolle and Le Novère BMC Systems Biology 2010 4:24   doi:10.1186/1752-0509-4-24
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