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This book outlines key issues for addressing the grand challenges posed to educators, developers, and researchers interested in the intersection of simulations and inquiry-based science education (IBSE). To achieve this, the authors explore the use of computer simulations as instructional scaffolds that provide strategies and support when students are faced with the need to acquire new skills or knowledge. A goal of the monograph is to provide insight into what research has reported on navigating the complex process of IBSE and whether computer simulations as instructional scaffolds support specific aims of IBSE for students.