Modeling Instruction is an active learning strategy for introductory physics built on the premise that science proceeds through the iterative process of model construction, development, deployment and revision. We describe the role that participating in modeling has in learning and then explore how students engage in this process in the classroom. We begin with a background on models and modeling and describe how these theoretical elements are enacted in the introductory university physics classroom. Recent work has been a neuroimaging study of students pre and post instruction. We describe the development of this project, the varied analyses of neuroimaging data in an educational context, and the findings. Among the findings are neurobiological changes pre to post instruction, differences in activation patterns during physics reasoning tasks, and identification of a three-part brain network that correlates with science anxiety during resting state. We conclude with a discussion of future work.