What type of instruction and representational formats are most effective for different learners when using computer-based simulations? This was examined in an experiment with high-school chemistry students (N = 67) randomly assigned to receive a simulation that varied by instructional format (guided exploration vs. worked examples). Learners' prior chemistry knowledge and executive functions were also examined. Pretest and Posttest data were compared to assess student learning at multiple levels of learning (i.e., Recall, Comprehension & Transfer). Executive functions were found to interacted significantly with instructional format to affect both recall and transfer. Implications of the results are discussed in relation to effective use of animations and simulations for education.