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Our work is motivated by an understanding that form, duration, and location of antigen encounter in vivo all dictate the resulting fate of key immune players (such as B and T lymphocytes) and whether they trend towards anergy, deletion, ignorance, or activation. Our rational molecular design approach is guided by inherent transport and cellular mechanisms, with a particular focus on targeting the mucosal immune system. We consider antigen-specificity on a cellular level and targeted delivery on a tissue level to reach immune cells and tissues of interest. Tuning the physicochemical properties of our molecular platforms allows us to direct 1) antigen or immune cargo delivery, 2) cellular interactions and signaling, and 3) the resulting immune response. The development of molecules capable of targeting the immune system in a specific manner will address a pressing need for safer and more effective disease interventions across multiple disease settings, ranging from autoimmune diseases like multiple sclerosis to infectious diseases like COVID-19. Additional value of this work lies in using the molecules we design as investigative tools to provide mechanistic insight, both to further our understanding of the immune response and to guide future design of immunotherapies and vaccines.