As part of the methodology to control gas permeability of functional materials, mathematical approach is considered that takes into account a diffusion process through a plate with the boundary conditions of the 1st and 2nd types. The methodology under discussion provides methods for estimating parameters of the diffusion by using methods of exceptional points, functional scale and statistical moments. Computer software package HPRON has been developed to provide mathematical modeling, planning, processing and data interpretation of different variants of gas permeability method. The results are used to optimize the performance of the membrane electrode assembly (MEA) for the automotive fuel cell and electrolyzer applications with a perfluorinated proton-conducting membrane such as nafion. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.