Determining Structural and Mechanical Properties from Molecular Dynamics Simulations of Lipid Vesicles.

ABSTRACT: We have developed an algorithm to determine membrane structure, area per lipid, and bending rigidity from molecular dynamics simulations of lipid vesicles. Current methods to extract structure from vesicle simulations define densities relative to the global center of mass of the vesicle. This approach ignores the long-wavelength fluctuations (undulations) that develop across the sphere and broaden the underlying structure. Our method establishes a local reference frame by defining a radially undulating reference surface (URS) and thereby removes the broadening effect of the undulations. Using an arc-length low-pass filter, we render the URS by defining the bilayer midplane on an equi-angular θ, ϕ-grid (colatitude, longitude). This surface is then expanded onto a truncated series of

SUBMITTER: Braun AR 

PROVIDER: S-EPMC4159217 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature