Interactive computer simulations with complex representations and sophisticated graphics are a relatively new addition to the classroom, and research in this area is limited. We have conducted over 275 individual student interviews during which the students described what they were thinking as they interacted with simulations. These interviews were conducted as part of the research and design of simulations for the Physics Education Technology (PhET) project. PhET is an ongoing project that has developed over 75 simulations for use in teaching physics, chemistry, and physical science. These interviews are a rich source of information about how students interact with computer simulations and what makes an educationally effective simulation. We have observed that simulations can be highly engaging and educationally effective, but only if the student's interaction with the simulation is directed by the student's own questioning. Here we describe our design process, what features are effective for engaging students in educationally productive interactions and the underlying principles which support our empirically developed guidelines. In a companion article we describe in detail the design features used to create an intuitive simulation for students to use.