Abstract : This thesis concerns the theoretical study of the interaction mechanisms of carbon-based nanostructures with cell membranes, being the essential compound of living cells. This very complex study of the multidisciplinary nature was essentially done using numerical simulations. We have voluntarily spitted this work in two distinct parts. First, we studied the membrane ion channels using molecular dynamics and ab initio approaches. These channel proteins being essential for cell function are also common therapeutic targets for new drugs design. Second, we studied the behavior of pristine and functionalized carbon species such as fullerenes (C60) and nanotubes (CNT) in the presence of the cell membrane. The results focus mainly on passive uptake phenomenon of these potential drugs vectors by biological membranes. The molecular dynamics studies on a very long time scale (sub-1 microseconds) and on very large systems were also the challenge of the IT perspective. To solve the given problematic in the limited time of a single PhD the development of high performance parallel computing CPU/GPU had to be put in place. The obtained results tempt to highlight the toxic role of nanostructures versus previously studied membrane proteins. This thesis naturally opens the way for the study of biocompatible nanocarriers for drug delivery.