  The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers
depends on molecular motion over distances of the order of 1-2 nm. From the
concentration dependence of the excimer photoemission curve, it is possible to
derive a value for the lipid self-diffusion coefficient. This technique has
been intensively used in the past twenty years, leading to rather large
numerical values for self-diffusion compared with other approaches based on
fluorescent probes tracking. In most cases, the interpretation of the
experimental data rely on models for diffusion limited 2d reaction rates, or
comparison with 2d lattice random walks. Our approach uses realistic molecular
dynamics trajectories to reinterpret these experiments. Based on a well
established coarse-grained model for lipid MD simulations (Martini), we show
how to relate simulation results to experimental data on excimer formation. Our
procedure is quite general and is applicable to all diffusion-limited kinetic
processes. Key to our approach is the determination of the acceleration factor
of lipid coarse-grained numerical models compared to reality. We find a
significant reduction of the diffusion coefficient values, in particular when
interleaflet association is taken into account. Our work does not point to
deviation from a diffusion-limited mechanism but indicates that the excimer
formation across bilayer leaflets could be hindered.
