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The safe and successful application of nanotechnology in the biological realm remains a challenge due to the inherent multiscale nature of biology. Engineering nanoBIO devices requires the knowledge of how nanotechnology-based devices interact with biological systems at the protein, cell, tissue, and organ levels. The Engineered nanoBIO node at Indiana University (IU) will develop a powerful set of integrated computational nanotechnology tools (apps) that address this complex, multiscale problem in both education and research and facilitate the discovery of customized, efficient, and safe nanoscale devices for biological applications. These computational tools will be tested and validated experimentally and they will be integrated with nanoHUB exploiting IU’s cyberinfrastructure strengths in high-performance computing and scalable data-analysis platforms to be able to run effectively on both clusters (education) and leading edge supercomputers.