We investigate the effects of interactive computer-based simulations which are presented prior to inquiry-based laboratory experiments on students' conceptual understanding of mechanics, waves/optics, and thermal physics. In principle, the simulations should serve as a cognitive framework for enhancing the subsequent more open-ended inquiry learning in the subject matter domain of the experiments. To test this prediction, the simulations and experiments were integrated into a one semester class for prospective physics teachers who served as students in the study. Semi-structured interviews were used to assess their ability to make correct predictions about the phenomenon in the experiments before using the latter and give correct explanations of the discrepancies between their predictions and their following observations. Conceptual tests were presented to assess conceptual understandings of each topic. Our results indicate that the use of the simulations improved the students' ability to make acceptable predictions and explanations of the phenomena in the experiments. The use of simulations also fostered a significant conceptual change in the physics content areas that were studied.