- Nanochannels have been widely interested because they have a great potential in widely applications such as drug delivery, nano-sensors, and DNA sequence reader. The usage of the most applications is related to the transportation through nanopore. Unfortunately, previous knowledge in Bulk and microscale could not be directly applied. Since going from micro to nano is not like from Bulk to micro, sometime physics change due to comfinement in nanoscale. We propose to study the transportation of small molecules through nanochannel. In this study, we are using molecular dynamics (MD) simulation which is a very powerful computational technique and has been highly performed to study the molecular behavior in the nanoscale system. Alpha hemolysin (AHL) is a biological channel that can self-assemble to form a non-selective pore on a lipid membrane. Moreover, the pore size of AHL is large (about 2.5 nm in diameter) and it allows water and small molecules to permeate through it across the membrane. This is leading to ion/pressure imbalance between cell and its environment and causing cell dead. One had proposed to use this protein to kill cancer cell or make cancer cell more permeable to special medicines. However, the transportation of molecules through hemolysin is not well understood. The pore is pretty small for doing the experiment and too big for previous computational simulation but not for now. Molecular dynamics simulation had been extremely developed; plus a huge improvement on computer hardware, thus one could model in larger scale and longer time scale. By using MD simulation, we could model in nanoscale system to investigate the molecular behavior of water and small molecules in nanochannel and demonstrate the transport mechanism through nanochannel. Furthermore, we will have more understanding on transportation in nanochannel and hopefully we could found interesting behavior that would be benefit to new nanotechnology.