This study investigates pervaporation performances for the separation of ethanol-water mixtures using composite polydimethylsiloxane (PDMS). The probability of cluster formation into PDMS matrix was analyzed by molecular dynamics simulation (MD) technique. Cluster formations within water-water and ethanol-ethanol molecules into PDMS were not observed, but ethanol-water dimerization was evidenced by MD simulation. When molecules aggregate, their average sizes increase; hence, diffusion coefficients of components decrease. Based on these assumptions, a new semi-empirical model for diffusion coefficients of penetrants in membrane was proposed. Then using this theory, the solution-diffusion model was modified and the process was simulated. Diffusion coefficient parameters were obtained by minimization error between simulation and experimental results at different concentrations. The behaviour of pervaporation experimental results as a function of concentration has confirmed the proposed model. Influences of feed temperature, feed flow rate, membrane thickness and permeate-side pressure on the membrane separation performance were predicted by the model. Simulation results showed excellent agreement with the experimental data. (C) 2010 Elsevier B.V. All rights reserved.