Table 2 List of parameters used in each simulation. CD, confined domain. Please note in this context, kd and kb are implemented as a rate in unit time as described in the “Methodology” section.
Simulation type | Binding rate (kb) (per molecule per unit time) | Dissociation rate (kd) (per unit time) | Diffusivity outside CD (Do) (unit lenght2 per unit time) | Diffusivity inside CD (Di) (unit lenght2 per unit time) | CD occupied area (%) | Number of added inert proteins (molecule) | Number of inert protein packs (dimensionless) | Fold number of CD merging (dimensionless) | GPVI number per platelet (% of 9600) |
|---|---|---|---|---|---|---|---|---|---|
1. Receptors in CD area vs Di | 0 | 0 | 1 | 1,2−1…,2−9,2−10 | 35 | 0 | 0 | 1 | 100 |
2. Dimerisation (with CD) vs Di | 0.05 | 0.01 | 1 | 1,2−1…,2−9,2−10 | 35 | 0 | 0 | 1 | 100 |
3. Dimerisation vs %CD & Di | 0.05 | 0.01 | 1 | 1,2−1…,2−4,2−5 | 0,5…,75,80 | 0 | 0 | 1 | 100 |
4. Dimerisation vs CD merging | 0.05 | 0.01 | 1 | 0.1 | 35 | 0 | 0 | 0.5,1…,7.5,8 | 100 |
5. Added inert proteins | 0.05 | 0.01 | 1 | 1 | 0 | 0,25…,175,200 | 0,25…,175,200 | 1 | 100 |
6. Disintegrated inert proteins | 0.05 | 0.01 | 1 | 1 | 0 | 100 | 1,21…,27,28 | 1 | 100 |
7. Dimerisation (w/o CD) vs D | 0.05 | 0.01 | 2−5,2−4…,24,25 | 1 | 0 | 0 | 0 | 1 | 100 |
8. Receptors in CD area vs %CD | 0, 0.01, 0.005, …, 0.000625 | kb/5 | 1 | 0.1 | 15,16,…,22 | 0 | 0 | 1 | 100 |
9. Dimerisation vs receptor number | 0.05 | 0.01 | 1 | 0.1 | 35 | 0 | 0 | 1 | 25, 50, …, 150, 175, 200 |
10. Dimerisation vs kb & kd | 60, 70, …, 130, 140% of 0.05 | 60, 70, …, 130, 140% of 0.01 | 1 | 0.1 | 35 | 0 | 0 | 1 | 100 |
