The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate that middle and high schools students can acquire robust mental models of the states of matter through guided explorations of computational models of matter based on molecular dynamics. Using this approach, students accurately recall arrangements of the different states of matter, and can reason about atomic interactions. These results are independent of gender and they hold for a number of different classroom contexts. Follow-up interviews indicate that students are able to transfer their understanding of phases of matter to new contexts.