Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation - Simulation and Modeling Methodologies, Technologies and Application - page 181

(a) Time plot of actin-agents. (b) Time plot of arp-agents.

Fig. 8. The time plots show the result of the branching simulation for 1200 actin-agents, 30
Arp2/3-agents and a time step Δt =1 s

(a) Time plot of actin-agents. (b) Time plot of arp-agents.

Fig. 9. The time plots show the result of the branching simulation, including the disassembly
process, for 1200 actin-agents, 30 Arp2/3-agents and a time step Δt =1 s

After introducing this new variable, the assembly of the actin filament slowed down.
As shown in Figure 9(a), the assembly of 200 molecules and therefore an overall length
of 1 μm is reached after 760 seconds. After one hour, the filament contained 717 fully
bounded actin-agents and is branched out at 14 different positions (see also Figure 9(b)).
This model shows therefore a comparable time progression to the simulation of Cardelli
et al. (2009), especially for Arp2/3, although our filamental growth is somewhat slower.

4 Conclusions and Outlook

Instead of the commonly used rate equations to simulate intracellular molecular pro-
cesses, we introduced an agent-based approach. This allowed us to overcome some
restrictions imposed by differential equation models, more precisely any number and