A modeling system is provided which comprises a physical atomic modeling system structured for use in conjunction with a computer-implemented application which can execute a vision detection and analysis algorithm. When used to form molecular representations or models, the modeling system can be used to make molecular bonding visible, tangible, and more readily understandable to a student or other user. Various embodiments of the invention leverage the effectiveness of tangible, tactile systems to create a learning experience which increases understanding of atomic bonding at the valence electron interaction level.