While simulations have widely been used to facilitate conceptual change in learning science, results indicate that significant disparity or gap between students' prior conceptions and scientific conceptions still exists. To bridge the gap, we argue that the applications of computer simulation in science education should be broadened to enable students to model their thoughts and to improve and advance their theories progressively. While computer simulations are often used to offer opportunities for students to explore scientific models, they do not give them the space to explore their own conceptions, and thus cannot effectively address the challenge of changing students' alternative conceptions. Findings from our recent empirical study reveal that, firstly, dynamic modelling using the environment WorldMaker 2000 in conjunction with the use of a cognitive perturbation strategy by the teacher was effective in helping students to migrate from their alternative conceptions towards a more scientifically inclined one; secondly, the pathways of conceptual change across groups were idiosyncratic and diverse. Respecting students' ideas seriously and providing cognitive perturbation at appropriate junctures of the inquiry process are found to be conducive to fostering conceptual change. In this paper, we will report on the details of the pedagogical approach adopted by the teacher and portray how students' conceptions change during the entire process of model building.