An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface

We propose an algorithm for the general description of rugged molecular scale interfacial surfaces. This algorithm was implemented in the description of a phospholipid membrane/water interface with the rugged surface defined by the phospholipid phosphorous atoms. The method allowed us to clearly discern four layered regions of water based upon the water local density as a function of the distance from the membrane surface. Furthermore, the water in each of the layered regions was found to have distinct orientational properties. The classification we make based on density due to our new algorithm is in agreement with that delineated in previous studies based on water orientation. The contribution of the different water regions to the total electrostatic potential reveals the particular way in which each layer’s water polarization contributes to the total dipole potential of the hydrated membrane.