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Table 2 Comparisons between StochKit and our approach for a chain of N reactions of the shape A i → Ai+1.

From: Modelling non-Markovian dynamics in biochemical reactions

N. Gecode StochKit
1 0.008 0.019
2 0.012 0.034
3 0.012 0.056
4 0.014 0.086
5 0.015 0.126
6 0.017 0.167
7 0.018 0.208
8 0.02 0.26
9 0.021 0.3
10 0.022 0.354
11 0.022 0.424
12 0.027 0.447
13 0.028 0.494
14 0.028 0.545
15 0.03 0.592
16 0.033 0.654
17 0.033 0.714
18 0.037 0.758
19 0.039 0.818
20 0.039 0.87
  1. In each case, the kinetic constants were set to 1.0, the initial amount of each component is 100000 molecules and the simulation time corresponds to 5 time-units.