Research Article
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework
Table 3
An approximation between experimentally calculated kinetic parameters and the parameters simulated by our model.
| | Enzyme identification |
Experimental kinetics | Simulation parameters | Approximated kinetics | | | % reactive collision | Time step | (mM) | (s−1) |
| | EC 1.8.1.9—glutathione reductase activity | 0.404 | 0.39 | 25 | 100 | 0.531257304 | | | EC 4.1.1.11—aspartate 1-decarboxylase | 0.219 | 0.65 | 75 | 75 | 0.37565 | | | EC 1.1.1.1—alcohol dehydrogenase | 0.41 | 1 | 95 | 75 | 0.34196 | | | EC 1.1.1.205—IMP dehydrogenase | 1.7 | 1.9 | 25 | 25 | 2.45375 | | | EC 3.4.13.22—D-Ala-D-Ala dipeptidase | 1 | 4.7 | 75 | 25 | 1.13387 | | | EC 4.1.1.1—pyruvate decarboxylase | 1.8 | 1.2 | 25 | 5 | 1.36829 | |
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