Agent-based modeling of complex molecular mechanisms

The diverse molecular mechanisms that orchestrate cellular processes typically involve a complex network of actors and span broad ranges of spatial and temporal scales that no single experimental or computational technique can cover. While several multiscale methods are increasingly capable of connecting across scales, bridging molecular and cellular levels remains a challenge. Agent-based modeling (ABM) is a computational paradigm that models a complex system and its emergent properties from the perspective of its individual components whose behaviors are governed by a set of predefined rules. As long as these rules are biophysically accurate, the flexibility of this framework makes it uniquely positioned to fill the gap between spatially detailed and computationally efficient approaches and emerge as an effective mesoscopic modeling method that could bring valuable mechanistic insight into how complex behaviors arise in cellular environments. In this review, we summarize ABM principles and current capabilities in the realm of molecular biology and discuss potential directions for the development of additional features that would further broaden the scope of the method.