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Urban BEZELJAK
Rab5 spatial stochastic model
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ed51f56a
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ed51f56a
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Apr 02, 2020
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Urban BEZELJAK
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@@ -27,7 +27,7 @@ By far the best resource is the Smoldyn User Manual and Examples, which are incl
## Model
The basic model includes the following reactions:
The basic model
simulates a 4x4x0.2 um box and
includes the following reactions:
```
reaction rxn_1_1 Rab5GDP:GDI(fsoln) <-> Rab5GDP(fsoln) + GDI(fsoln) k_1 k_2
...
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@@ -57,5 +57,11 @@ Smoldyn uses parameters in micrometer and second units, which have to be recalcu
| k_rr_off | / | 1 s-1 |
### Model configuration files
*
Default model with 5x5 grid:
[
200325_Rab5config.txt
](
200325_Rab5config.txt
)
*
4x4 grid:
[
200325_Rab5config_4x4.txt
](
200325_Rab5config_4x4.txt
)
*
3x3 grid:
[
200325_Rab5config_3x3.txt
](
200325_Rab5config_3x3.txt
)
*
2x2 grid:
[
200325_Rab5config_2x2.txt
](
200325_Rab5config_2x2.txt
)
*
1x1 grid (4x4 um membrane with rigid walls):
[
200325_Rab5config_1x1.txt
](
200325_Rab5config_4x4.txt
)
*
continous membrane (periodic walls):
[
200330_Rab5config.txt
](
200330_Rab5config.txt
)
### Python script for parameter scans
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