We used molecular dynamics simulations to study the diffusive motions of lipids, membrane-spanning nanopores, and integral membrane proteins within lipid membranes. We found that their apparent diffusion coefficients diverge logarithmically as the width of the simulation box is increased, seemingly without bound. This divergence would appear to preclude the calculation of proper size-independent diffusion coefficients that can be compared to experiment. However, in simulations with systems of more than 100 million particles, we show that a hydrodynamic model not only explains the divergence, but can also be used to obtain both proper diffusion coefficients and difficult-to-calculate membrane properties. We also study the assembly of membrane-spanning carbon nanotube pores within the membranes. In our simulations, we follow the spontaneous formation of nanostructured membranes with dense arrays of nanotubes, and characterize the driving forces and kinetics of the assembly process. The observations from this study point to applications in nanotechnology but also serve as a model system for membrane proteins. Overall, we present a possible solution to the problem of calculating membrane diffusion coefficients from simulations that can be compared to experiment, and show how simulations can be used to study complex self-assembly processes within lipid membranes.

Diffusion and self-assembly of nanostructures in lipid membranes

256th National Meeting (2018)

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