Computer applications in the classroom are increasingly becoming effective tools for model-based teaching in science. A novel instructional computer simulation that incorporates a dynamic analogy to represent Le Chatelier’s Principle was designed for this study. The simulation provides an analogy to a chemical reaction, a scale, and links the analogy’s functionality to a chemical reaction. This connection where the analogy view is mapped to the components of a chemical reaction is hypothesized to be beneficial for visualization of students’ conceptual models of molecular interactions. Two study groups of 12th grade Chemistry students interacted with instructional computer simulation during the study. Both groups did the same simulation acti...