| Â | k2/k
D
|
f
vol.
|
f
diff
|
f
acc.
|
f
eff
|
|
|
|
|---|
Detailed model | 0.01 | 1.44 | 1.00 | 0.97 | 1.39 | 1845 ± 37 | 1853 ± 40 | 1.00 |
cell | 0.1 | 1.44 | 0.97 | 0.97 | 1.35 | 1879 ± 38 | 1839 ± 40 | 0.98 |
|  | 0.3 | 1.44 | 0.91 | 0.97 | 1.27 | 2058 ± 40 | 1996 ± 40 | 0.97 |
Homogenized/ | 0.01 | 1.44 | 1.00 | 1.00 | 1.43 | 1783 ± 36 | 1757 ± 40 | 0.99 |
averaged cell | 0.1 | 1.44 | 0.97 | 1.00 | 1.39 | 1815 ± 37 | 1802 ± 40 | 0.99 |
|  | 0.3 | 1.44 | 0.91 | 1.00 | 1.32 | 1989 ± 39 | 2003 ± 40 | 1.01 |
- Results of the effective reaction rate in the virtual cell. The free volume fraction for the test spheres with a radius of 2.5 nm is Ï• = 0.695 in the detailed model cell used for the simulations, leading to f volume = 1.44. Alternatively the crowding effect is included by homogenizing the obstacles in the whole cell. The cell size is reduced by a factor of 0.695 in order to yield the same reduced volume and the diffusion is artificially and homogeneously reduced accordingly to the values of the detailed cell. Since no obstacles are present, f access = 1. Additional file 1, Section 1 shows the corresponding temporal development of N
S
in the 'in vitro' and 'in vivo' simulation, including the evaluation of the performance of the simulation.
