In recent years, with the development of nano-science and nanotechnology, the application of nano technology in people's life becomes more and more popular, nano materials have extensive applications in the field of biology and chemistry. Carbon nano-materials, with thire unique physical and chemical properties, have many successful applications in many fields, especially in the biomedical and material chemistry fields. For example, fullerenes and graphene derivatives can well inhibit the proliferation of tumor cells. However, the molecular-level mechanisms of the anti-tumor activity are still unknown. Therefore, we studied the interaction mechanism between carbon nano-materials and biological macromolecules using the molecular dynamics simulation. The study has two parts. The first part is the interaction of fullerenes and thire hydroxyl derivatives with tumor necrosis factor (TNF-a) and the further rational drug design based on these calculations. The secondpart is the interaction between graphene oxide and cytochrome c.1 The interaction between TNF-a and fullerene or fullerene derivatives Based on molecular dynamics simulation of the interaction between fullerenes and their derivatives with TNF-a, we found that these materials’ binding sites with TNF-a were similar to small molecule inhibitors SPD304 that was previously reported. All were combined in the middle of the binding site of the TNF-a dimer. By the calculation of binding free energy, we found several kinds of carbon nanomaterials C60, C60 (OH) 12, Gd@C60, C82, C82 (OH)12, Gd@C82, Gd@C82(OH)13 and Gd@C82(OH)21 have better inhibiting ability with the TNF-a than the previously reported small molecules. 2 Graphene or its oxide interacting with cytochrome CThrough studying the interaction mechanism between graphene or graphene oxide with cytochrome c, we found that graphene oxide and cytochrome c have strong interaction. The increase of graphene’s oxidation degree of enhances the interaction between them. Through molecular dynamics simulation with the grapheme oxide fixed, we found that graphene oxidation could change the structure of cytochrome c. Through studying the interaction mechanism between double-layer graphene oxide with cytochrome c, we found that the random coil structure of cytochrome c had a stronger interaction with graphene oxide. The above result suggests that graphene oxide has strong influence on the structure of cytochrome c; and that random coil structure plays a main role in their interaction.