Engineering >> Computer Science & EngineeringApproximating Average Surface Area of Fluctuating Lipid Leaflets Using Weighted Grid Tessellationby Ahnaf Siddiqui
Submitted : Fall 2015 The surface area per lipid is an important quantity useful in characterizing lipid bilayer structure and dynamics. However, simply dividing the flat surface area covered by the number of lipids does not give a sufficient characterization of surface dynamics in cases where parts of the lipid leaflets have curvaceous trajectories in three dimensions and therefore a significant perpendicular component of surface area. This is usually the case due to membrane undulations as well as external forces acting on the lipids. To take the perpendicular component of lipid leaflet surface dynamics into account, this paper proposes an algorithm that calculates surface area per lipid from a molecular dynamics simulation by loading a 3D weighted grid with trajectory data and then tessellating the grid. The surface area obtained from the 3D triangular tessellation takes into account the vertical fluctuations of the lipids in addition to the horizontal area covered. Applying this method on a lipid bilayer system simulated over a charged nano-porous substrate demonstrates that this algorithm can reveal differences in dynamics between leaflets under different conditions that are otherwise invisible with a flat surface study. Related Links:
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