Molecular dynamics (MD) simulations have proved to be a useful tool for unveiling many aspects of pore formation in lipid membranes under the influence of external electric fields. In order to compare the size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed for characterizing pore geometry and its evolution over time. In the present paper three different methodologies for evaluating electropore geometrical behavior will be compared: (i) the first allows 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 procedure extracts pore volume from an integration of a three-dimensional model of the irregular shape of the pore; (III) a new method based on a statistical approach (following essential dynamics principles) describes pore geometrical fluctuations in a robust and reproducible way. For the same pore height of 2 nm the three methods give rise to mean electropore radii up to 3-fold different. 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.

A statistical analytical model for hydrophilic electropore characterization. A comparison study / Marracino, Paolo; Liberti, Micaela; Vernier, P. T.; Apollonio, Francesca. - In: RSC ADVANCES. - ISSN 2046-2069. - ELETTRONICO. - 7:51(2017), pp. 31997-32007. [10.1039/c7ra03812g]

A statistical analytical model for hydrophilic electropore characterization. A comparison study

MARRACINO, PAOLO;LIBERTI, Micaela;APOLLONIO, Francesca
2017

Abstract

Molecular dynamics (MD) simulations have proved to be a useful tool for unveiling many aspects of pore formation in lipid membranes under the influence of external electric fields. In order to compare the size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed for characterizing pore geometry and its evolution over time. In the present paper three different methodologies for evaluating electropore geometrical behavior will be compared: (i) the first allows 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 procedure extracts pore volume from an integration of a three-dimensional model of the irregular shape of the pore; (III) a new method based on a statistical approach (following essential dynamics principles) describes pore geometrical fluctuations in a robust and reproducible way. For the same pore height of 2 nm the three methods give rise to mean electropore radii up to 3-fold different. 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.
2017
Electric fields; geometry; molecular dynamics; Monte Carlo methods; simulated annealing
01 Pubblicazione su rivista::01a Articolo in rivista
A statistical analytical model for hydrophilic electropore characterization. A comparison study / Marracino, Paolo; Liberti, Micaela; Vernier, P. T.; Apollonio, Francesca. - In: RSC ADVANCES. - ISSN 2046-2069. - ELETTRONICO. - 7:51(2017), pp. 31997-32007. [10.1039/c7ra03812g]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/996975
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