An Agent-Based Modeling Approach at Molecular Scale for Biochemical Networks: Simulating from Stochastic Molecular Events

Modeling and simulation of intracellular biochemical networks is essential to further our understanding of biological system behaviors. Most of current modeling approaches used in Computational Systems Biology considers general phenomena of the whole system but ignoring the micro detail and individuality of each molecule. In this study, we present a new computational modeling paradigm, agent-based modeling at molecular scale (ABMMS), which simulates the interactions between internal autonomous agents and external environment. We also verified the accuracy and efficiency of our strategy with several case studies, and the experimental results demonstrated that the strategy matches well with the ODE in the macroscopic behaviors and also allows further analysis of individual agent behaviors at molecule level.