Abstract: Nanoparticles have been widely utilized in many health-related fields, such as drug delivery, cancer therapy, biolabeling, and biosensors. Studies on the molecular details of the interaction between nanoparticles and biological nanosystems are crucial for obtaining information on the mechanisms of the possible outcomes of these nanomaterials, such as cytotoxicity, biological accumulation, and long-term effects. In this talk, we will introduce a recent model that we are developing to help understand and predict the interaction between carbonaceous nanoparticles and biological membrane based on the molecular structural information. The model presents in detail how molecular properties of nanoparticles such as size, shape and chemical properties affect the organization of the nanoparticles in the membrane, as well how different components in the membrane affect the selectivity on nanoparticles. This critical information is helpful for designing engineered nanoparticles that are biocompatible, bioavailable for different environmental and biological applications.