Flexible Large-scale Agent Modeling Environment (FLAME) has been very successful in modeling a variety of biological experiments. Working with various biologists and involved in their projects, it has studied systems such as epithelial tissue healing, bacterial concentrations in oxygen-starved environments, ant and pheromone behavior and even sperm behavior in reproductive systems. Successful models of local interactions at different levels of biological organisation, including epithelial tissue and ant colonies, have demonstrated the benefits of such 'agent-based' modeling. Agent-based modeling relies on in silico reproductions of systems through the interactions of its components. And provides a reliable tool in investigations of biological processes, which require spatial considerations and involve complex formation and translocation of regulatory components. Nanoparticle properties such as size, shape and surface chemistry can be controlled to improve their performance in biological systems. This enables modulation of immune system interactions, blood clearance profile and interaction with target cells, thereby aiding effective delivery of cargo within cells or tissues.