Molecular machines, such as bio-molecular motors and ion pumps are fascinating subjects for study because they transform energy between different forms in an efficient manner. The functional mechanism of molecules machines is often complex and involves numerous physical and chemical processes that occur at multiple spatial & temporal scales. Therefore, it is increasingly clear that the most productive strategy would be to integrate experiment, molecular simulation and theory. In reality, however, such integration is rarely done and the three disciplines remain largely segregated. In this workshop, we bring together active investigators in these three disciplines to identify and discuss burning mechanistic questions concerning molecular machines that will best benefit from an effective integration of experiment, simulation and theory. In addition to discussions of recent technical developments, specific mechanistic findings and novel ideas/hypotheses, we hope the workshop can help reduce communication barriers between different disciplines and foster new collaborations.