title: Geometrical Characterization of an Electropore from Water Positional Fluctuations.
abstract: We present here a new method for calculating the radius of a transmembrane pore in a phospholipid bilayer. To compare size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed. Operational metrics can be associated with some observed behavior. For example, pore size can be defined by the largest object that will pass through the length of the pore. The novelty of the present approach resides in the characterization of electropore geometry via a statistical approach, based on essential dynamics rules. We define the pore size geometrically with an algorithm for determining the pore radius. In particular, we extract the radius from the tri-dimensional surface of a defined pore region. The method is applied to a pore formed in a phospholipid bilayer by application of an external electric field. Although the details described here are specific for lipid pores in molecular dynamics simulations, the method can be generalized for any kind of pores for which appropriate structural information is available.
authors.affiliation: Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy. marracino@diet.uniroma1.it.
authors.forename: P
authors.identifier: 0000-0003-4742-8170
authors.initials: P
authors.lastname: Marracino
authors.affiliation: Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, 23508, USA.|Biomedical Engineering Institute, Frank Batten College of Engineering and Technology, Old Dominion University, Norfolk, VA, 23529, USA.
authors.forename: F
authors.initials: F
authors.lastname: Castellani
authors.affiliation: Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, 23508, USA.
authors.forename: P T
authors.initials: PT
authors.lastname: Vernier
authors.affiliation: Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Liberti
authors.affiliation: Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Apollonio
mesh_terms: D000465:Algorithms; D008051:Lipid Bilayers / Q000737:chemistry*; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D010743:Phospholipids / Q000737:chemistry
chemical_list: D008051:Lipid Bilayers; D010743:Phospholipids
keywords: Electroporation; Electropore geometry; Molecular dynamics; Pore radius