Helping students understand the general nature of scientific models is increasingly regarded as an important goal of the middle and high school science curriculum (e.g., J. K. Gilbert & C. Boutler, 1998. "International Handbook of Science Education"; Kluwer, London; A. G. Harrison & D. F. Treagust, 2000. "Science Education," 352-381). In addition, beginning in middle school, students are introduced to one of the most central models in modern science--the particulate model of matter. Thus, teaching students about this model is an ideal opportunity to help students develop an understanding of the nature of models in the context of learning a central scientific concept--the discontinuity of matter. In this article, we present a software tool that was designed for this purpose. The software engages students with investigating and evaluating competing models of matter in order to help them see the particulate model as a plausible model that can explain a wide range of facts about diverse phenomena. The first and second parts of the paper describe the scientific content of the particulate model and the main ideas about scientific models that we would like to teach, as well as the educational challenges of teaching these ideas to middle school students. The third part describes the structure of the software and the three phenomena we chose to have students explore. These are all phenomena that should be puzzling to students if they assume that matter is continuous, but that can be easily explained if they assume that matter consists of discrete particles. The paper concludes with a description of two studies evaluating the effectiveness of the software in promoting students' understanding of models in general and the particulate model of matter in particular. We found that middle schoolers can engage with fundamental ideas about the nature of models, and that engaging them with these ideas helps them internalize the assumptions of the particulate model of matter. This happened especially for students who had developed relevant macroscopic conceptions of matter based upon quantified and interrelated conceptions of volume, weight, and density. (Contains 6 figures, 3 tables and 7 footnotes.)