Abstract
Modeling and optimization of metabolic networks has been one of the hottest topics in computational systems biology within recent years. However, the complexity and uncertainty of these networks in addition to the lack of necessary data has resulted in more efforts to design and usage of more capable models which fit to realistic conditions. In this paper, instead of optimizing networks in equilibrium condition, the optimization of dynamic networks in non-equilibrium states including low number of molecules has been studied using a 2-D lattice simulation. A prototyped network has been simulated with such approach, and has been optimized using Swarm Particle Algorithm the results of which are presented in addition to the relevant plots.
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