Molecular Simulation Of Transportation Of Biological Molecules And Ions In Nanofluidic Channels

Nanofluidic channels show the great potential value in single molecule detection, molecular sieve filtration, DNA separation, microfluidic connection and many other areas. At present, moving and manipulating properties of biological molecules and ions have become a hot topic in the international area, have been to realize satisfied base for nanofluidic technology.Molecular dynamics can study biological molecules and ions moving at the molecular level and get information that the experiment can not. In present paper, molecular dynamics simulations were performed to study the biological molecules and ions moving in nanofluidic with GROMACS software.Firstly, the systematic investigation on the molecular dynamics method and the GROMACS software has been carried out, and simulation model of biological molecules and ions moving in a3.1nm high parallel channel has been constructed. Simulation method based on molecular dynamics simulation was build. Price ion、molecular distribution and flow characteristics were analyzed.Then, and effects of some conditions that include different sizes nano-channels, different concentration and different electric field strength on the biological molecules and ions moving process were studied, which analyzed the distribution of ions and water molecules, the RMSD value of protein molecules and the role of the potential energy throughout the simulation process under the several factors.Finally, simulation results indicate that the density of Water molecules and ions near the wall appears layered, the layers increases with increasing ions density. Attraction between the wall and the solution greater impacts on the density distribution of fluid and the protein also affects. Channel size being close to the electric double layer, the movement of charged ions and protein molecules greatly affected, movement speeds increase; the solution concentration increased results in lower speed of water molecules, but protein movement speed increases; when the solution concentration decreases, the nano-channel wall has weakened the force for ions. Electric field strength greatly impacts on the migration of protein and ions.