Brownian dynamics simulation of a lipid chain in a membrane bilayer

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Abstract
A Brownian dynamics simulation of a lipid chain is used to model the motional properties of a dipalmitoyl phosphatidylcholine bilayer. The effects of the bilayer environment on the chain are represented by a mean field derived from an extension of the Marcelja model. The simulation was run 44 million steps, the equivalent of approximately 0.66 μs for a viscosity of 2.2 cp. The results are compared with those of a 30 million step simulation of the chain in the absence of the mean field. Deuterium order parameters for the methylene groups along the chain and the average chain length calculated from the mean field trajectory are shown to converge to the experimentally determined values for DPPC with an appropriate choice of parameters. An analysis of the torsional dynamics of the chain, including transition rates and kink probabilities, is carried out. It is demonstrated that kink formation is sometimes, though not always, concerted. A comparison of the membrane and free chain simulations implies that the internal dynamics of a hydrocarbon chain in a bilayer is very similar to that of a neat alkane. Thus, the significant limits on the orientational freedom of the chain, as expected by the nonzero order parameters, are induced by a potential that has only a small effect on the local motions.