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Fig. 5. The interaction boundary (dashed circle) defines the reaction volume around an agent. If
a second agent enters this area, the reaction takes place
Fig. 6. The time plot shows the result of the simulation for a simple actin polymerisation with
1200 agents and a time step Δt =1 s . Inset: Linear slope of the binding process in the beginning
For a simulation including the dissolving of actin from a filament, we used the rate
constant of 5.4 s 1 for ADP-actin at the barbed end from the literature [7]. Only agents
with a free top-bound (in case of Arp2/3 also middle bound) can be released from the
filament. To avoid an instant re-coupling, the molecule will be moved to outside the
interaction boundary.
Our present agent-based simulation takes place in a 2D environment, so that we have
to introduce a factoring constant of 100 for the radius, the dissolving rate constant and
the size of the environment, following the paper of Cardelli et al. (2009).
3R su s
3.1
Actin-Actin Interactions
Figure 6 shows the time plot of the growth of one filament. The curve shows in the
beginning a linear increase (see inset of Figure 6), but later becomes logarithmic. After
390 seconds 50 agents were integrated in the filament, which corresponds to a filament
of length 0 . 25 μm . A length of 1 μm is reached after 1882 seconds and at the end of
one hour, 240 agents form a filament with a length of 1 . 2 μm . In agreement with pub-
lished measurements [7], the increase in length of actin is linear in the beginning of the
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