  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.
