This thesis uses a number of Open Source Physics simulations to explore issues related to students' common difficulties in learning upper-level undergraduate quantum mechanics and how these difficulties can be reduced by research-based learning tutorials and peer instruction tools. The thesis investigated students' difficulties in learning quantum mechanics by administering written tests and surveys to many classes and conducting individual interviews with a subset of students. Based on these investigations, the thesis developed Quantum Interactive Learning Tutorials (QuILTs) and peer instruction tools to help students build a hierarchical knowledge structure of quantum mechanics through a guided approach. Preliminary assessments indicate that students' understanding of quantum mechanics is improved after using the research-based learning tools in the junior-senior level quantum mechanics courses. The thesis author also includes a standardized conceptual survey that can help instructors better probe students' understanding of quantum mechanics concepts in one spatial dimension. The validity and reliability of this quantum mechanics survey is discussed.