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Recent advances in the applications of graphene and its derivatives, nanotubes as well as other types of nano-materials in biotechnology areas such as biosensoring, gene and drug delivery systems are extremely promising. Carefully designed patterned nanofilter arrays can have significant contributions to future therapy of various diseases. Furthermore, a systematic investigation of functional biomaterials including silkworm silk, bone collagen, DNA, etc. will provide great insights to future design of bio-inspired materials. In this review we’ll introduce the most recent advances in computational simulations and tools on nanomaterials, their interface with solvent, and computational biology for biomedical applications. The underling physical and mechanical process involves multi-disciplinary knowledge which will make a huge contribution to the computational mechanics and biomechanics community. In particular, the ACES colleagues are devoted in the development of most cutting-edge theoretical platforms to descript the complex systems, and have drawn well-established attention in the area.