No abstract

The dynamics of N(2) molecules blocked in open single-walled carbon nanotubes is investigated using molecular dynamics simulations. It is found that periodic axial and radial oscillations with extremely high frequency exist widely among these molecules. Between the two nanotube ends, N(2) molecules oscillate along or parallel to the nanotube axis, and their frequencies show an inverse length dependence in the range of 22 to 64 GHz. Accompanying the axial oscillation, the molecules oscillate radially with small amplitudes in the lateral potential well. The corresponding frequencies have a magnitude of several hundred gigahertz, and the maximum exceeds 1800 GHz. These periodic oscillations contribute to the molecular blockage in nanotubes.

The capacity of silencing genes makes small interfering RNA (siRNA) appealing for curing fatal diseases. However, the naked siRNA is vulnerable to and degraded by endogenous enzymes and is too large and too negatively charged to cross cellular membranes. An effective siRNA carrier, PMAL (poly(maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine), has been demonstrated to be able to assist siRNA transmembrane by both experiments and molecular simulation. In the present work, the mechanism of siRNA transmembrane assisted by PMAL was studied using steered molecular dynamics simulations based on the martini coarse-grained model. Here two pulling rates, i.e., 10−6 and 10−5 nm·ps−1, were chosen to imitate the passive and active transport of siRNA, respectively. Potential of mean force (PMF) and interactions among siRNA, PMAL, and lipid bilayer membrane were calculated to describe the energy change during siRNA transmembrane processes at various conditions. It is shown that PMAL-assisted siRNA delivery is in the mode of passive transport. The PMAL can help siRNA insert into lipid bilayer membrane by lowering the energy barrier caused by siRNA and lipid bilayer membrane. PMAL prefers to remain in the lipid bilayer membrane and release siRNA. The above simulations establish a molecular insight of the interaction between siRNA and PMAL and are helpful for the design and applications of new carriers for siRNA delivery.