Ab initio molecular dynamics (MD) simulations are done to elucidate the electronic structure properties of a short-side-chain perfluorosulfonic acid (SSC PFSA) membrane at low humidity conditions. The artificial neural network (ANN) approach along with statistical methods is then employed to model and analyze these properties. The ANN method substantially speeds up the ab initio electronic structure calculations and has superior accuracy in mimicking the results of such calculations. The aim of this study is to understand the effects of hydration level, temperature, side chain flexibility of the SSC PFSA membranes, and backbone flexibility of the SSC PFSA membranes on the proton transfer in these membranes. Statistical analysis of results using analysis of means (ANOM) and analysis of variance (ANOVA) methods shows that no proton transfer from the SSC PFSA to the neighboring water molecules occurs at considerably low hydration levels. However, an increase in the probability of proton transfer is observed when the SSC PFSA membrane is sufficiently saturated. This process is more favorable at low temperatures. Moreover, the flexibility of either the side chains or the backbone of the SSC PFSA membrane has a great influence on the proton transfer phenomenon in such a way that allowing them to move freely causes an increase in the affinity of the SSC PFSA membrane to share its protons with water molecules. Further investigation is performed concerning the combined effect of the independent parameters (i.e., hydration level, temperature, side chain flexibility of the SSC PFSA membrane, and backbone flexibility of the SSC PFSA membrane) on the proton transfer process and the results are reported in detail. (C) 2010 Elsevier B.V. All rights reserved.