The study of lipid structure and phase behavior at the nanoscale is of utmost importance due to implications in understanding the role of the lipids in biochemical membrane processes. Supported lipid bilayers play a key role in understanding real biological systems, but they are vastly underrepresented in computational studies. In this paper, we discuss molecular dynamics simulations of supported lipid bilayers using a coarse-grained model. We first focus on the technical implications of modeling solid supports for biomembrane simulations. We then describe noticeable influences of the support on the systems. We are able to demonstrate that the bilayer system behavior changes when supported by a hydrophilic surface. We find that the thickness of the water layer between the support and the bilayer (the inner-water region in the latter part of this paper) adapts through water permeation on the microsecond time scale. Additionally, we discuss how different surface topologies affect the bilayer. Finally, we point out the differences between the two leaflets induced by the support.

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The study of lipid membrane structure and phase behavior at the nano-scale is of utmost importance due to implications in understanding the interplay of lipids and membrane proteins in biochemical membrane processes. Supported lipid bilayers play a key role in providing the means to understand real biological systems. Yet, with regard to membrane protein activation and their functions, the limitations of supported membranes and the possible artifacts they may induce are weakly understood. Here, we study DPPC (dipalmitoylphosphatidylcholine) bilayers on a weakly hydrophilic substrate using coarse grained simulations and show that the lateral pressure profile of a supported bilayer is distinctly different from the corresponding pressure profile for a free-standing DPPC bilayer. The results indicate that due to the substrate, the lateral pressure profile becomes asymmetric, expressing major peaks at the proximal leaflet of the membrane, implying the membrane to be under strong tension. The results provide a new mechanism to explain malfunctions of transmembrane proteins used in supported bilayers.

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In this contribution, we discuss several important technical aspects which are relevant for the molecular modeling of biomembranes in aqueous environments. We study the effect of coarsegrained water models on free and supported systems and show that the choice of water model has dramatic repercussions on the phase behavior. We characterize the phase behavior of a widely used water model and discuss the technical implications of modeling solid supports for biomembrane simulations. Finally, we compare the effect of anisotropic pressure coupling with surface tension coupling in atomistic bilayer simulations including alcohols.