While carbon nanotubes have been put into massive practical industrial, environmental and biomedicine applications, the cytotoxicity effects or the effect to the ionic channels they bring into the living cells need to be thoroughly investigated. In this work, molecular dynamic simulations have been carried out to investigate the ionic diffusion through the single wall armchair carbon nanotube embedded right inside the cell membrane. By modeling a two-membrane system, we build a virtual cytoplasm environment including a cell chamber and an extracellular space, in which a certain amount of solute is dissolved. The system is first brought to its equilibrium by deployment of minimization and then simulated. The results suggested that carbon nanotubes (CNTs) with size less than (12, 12) shall be less cytotoxic since it does not bring any ionic diffusion through the CNT channel, so as to maintain active cytoplasm environment. Another phenomenon we observed is a notable shifting angle of the carbon nanotube which was normal to the surface of cell membrane initially. In general, the inclination angle of the carbon nanotube increases with its radius.
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