Lipid electropore geometry in molecular models

Abstract

Molecular dynamics (MD) simulations recently proved to be a useful tool for unveiling many aspects of pore formation in lipid membranes under the influence of external electric fields. In particular, the study of the structure and transport properties of electropores must definitely take advantage of a rigorous characterization of pore geometry and its evolution in time. In order to compare sizerelated properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed. In the present chapter three different methodologies to evaluate electropore geometrical behavior will be presented: (i) the first developed method which allows the analysis of the dimensions of the pore through an algorithm that uses a Monte Carlo simulated annealing procedure to find the best route for a sphere with variable radius to squeeze through the pore channel; (ii) a more recent one allowing the three-dimensional modeling of the irregular shape of the pores obtained as the quantification of its volume; and (iii) a new method based on a statistical approach (following essential dynamics principles), able to describe pore geometrical fluctuations in a robust and reproducible way. The three approaches described here are not system specific, i.e., the methods can be generalized for any kind of pore for which appropriate structural information is available.