Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation - Simulation and Modeling Methodologies, Technologies and Application - page 178

Fig. 3. In addition to the actin-agent (Figure 2), the simulation was extended with a second type of
agent for Arp2/3. This agent can bind to an bottom-bound actin-agent. Then another actin-agent
can bind to the top-binding side of the Arp2/3-agent, the next actin-agent to the middle binding
side and the Arp2/3-agent becomes fully bound.
Fig. 4. The physical size of Arp2/3 determines the size of the agents in the simulation [24]
To compare our results with the simulation of Cardelli et al. (2009), we used the
same number of 1200 free actin agents and 30 Arp2/3 agents. Cardelli uses this number
of agents to simulate a concentration of 1200 μ M. For concentration values in a spatial
simulations, it is necessary to calculate the volume of the environment:
n Actin =N A × V × c [1 /mol × l × mol/l ]
V = 1200 / (N A · 1200 × 10 − 6 )
V =1 . 66 × 10 − 18 l =1 . 66 × 10 − 21 m 3 ,
where n Actin is the number of molecules, N A is again Avogadro's constant, c is the
concentration of molecules and V is the volume. Assuming the environment as a cube,
the length of a side is approximately 1184.0 A.