Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework

Figure 5

The number of agents of different species interacting in the environment during 15000 simulation steps. From top to bottom, and from left to right, the above plots represent the number of agents of benzyl alcohol, NAD⁺, benzaldehyde, NADH, aryl-alcohol dehydrogenase holoenzyme, and benzaldehyde dehydrogenase holoenzyme. At the bottom, there is the number of occurring reactions and the number of molecules of benzoate excreted the extracellular medium.

(a)

(b)

(c)

(d)

(e)

(f)

(g)

(h)