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By Vanderah T.A.(ed)

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Although this model did not have discontinuities it was necessary to tune a large number of free parameters and consequently non-unique solutions were possible. Two models were developed and used by Nagle and co-workers using liquid crystal theory and, more recently, simulations (Klauda et al. 2006; Tristram-Nagle and Nagle 2004; Nagle and Tristram-Nagle 2000) to interpret X-ray di=raction data. In simulations one can directly calculate the electron density. However, direct comparison of this electron density is not possible because the experimental electron density is model dependent.

10. Here, for each phosphorus in the top leaflet one locates the phosphorus in the lower leaflet which is approximately below it. This is achieved by • Tesselating the lower leaflet into voronoi polygons. • Projecting coordinates of phosphorus from the top leaflet on to this tesselated surface. • Identifying the polygon in which the projected coordinates fall. This procedure identifies a trans-bilayer “neighbor” for each lipid in the top leaflet. With such identification we define the distance of phosphorus in the top leaflet with respect to the surface defined by the phosphorus atoms in the lower leaflet as the normal distance between phosphorus atoms from two leaflets that are “vertical neighbors” of each other.

In this Section we now turn to the specific design and execution phases of a molcular dynamics simulation of a lipid bilayer. These include the initial state construction, equilibration of the simulation and the overall length of the simulation. 1 System Construction and Simulation Design An initial salient point to consider in the design of an molcular dynamics simulation of a lipid bilayer is that single component lipid bilayers exhibit a first order phase transition with respect to temperature.

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Chemistry of superconductor materials by Vanderah T.A.(ed)

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