Agent-based Modeling of Molecular Self-assembly Mechanisms

Agent-based modeling and simulation (ABMS) is a powerful tool for studying molecular-level phenomena, due to its ability to combine discrete and continuous-time behaviors and to model heterogeneous systems as well as spatial and temporal events. Previously we applied ABMS to study heterogeneous collections of molecules. Here we use ABMS to study molecular self-assembly in DNA. Our eventual goal is to extend previous work on 2D structural modeling for epithelial cells to 3D structures, with applications to DNA computing and to the growth of carbon nanotubes.