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Whole-cell simulation of cell clusters
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Nanoscale integrin cluster dynamics controls cellular mechanosensing via FAKY397 phosphorylation

Procedure

We assumed that integrin cluster formation rate is proportional to the integrin cluster number during the integrin formation phase in the spatial Monte Carlo model. The basic formation rate (kon = cMa ∝ 1/texp) was calculated according to experiments. Again, using the Gillespie algorithm, an integrin cluster is formed in the cell edge (a random angle) and then disappears based on its size and substrate stiffness. Note that all the formed clusters obey the power distribution according to the spatial Monte Carlo model. On the basis of the previous model, the integrin cluster will move toward the cell center as$V(t)=V0(e−c0t+c1)$(12)where V0 = 3, c0 = 2, and c1 = 0.1. These steps are repeated until a steady state is reached. It has been shown that small clusters containing only one or two molecules are not experimentally detectable. So, we defined a minimum integrin cluster size of 10 molecules. We only included these detectable integrin clusters in our simulation. In the whole-cell simulation, the model did not actually simulate the dynamics of the entire FA directly; instead, it only simulated individual clusters that formed in a whole cell. The model did not simulate how these clusters aggregated to form FA.

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