Title: Pore formation in Polymer Electrolytes Abstract: Much of our quality of life in the 21st century will depend upon how efficiently we use our energy resources. The efficient conversion of energy from one form to another, particularly solar, chemical or thermal to electric, requires detailed nano-structured morphology. The polymer electrolytes in Polymer Electrolyte Membrane (PEM) fuel cells conduct protons while forming a barrier for electrons and molecular gases. We provide experimental evidence that they dynamically form a complex nanostructured pore network when exposed to liquid water, and provide a novel mathematical model for the solvent-polymer interaction which incorporates the functionalization of the polymer sidechains. We show that our model resides within a mathematical class of energies, which we call functionalized Lagrangians, which have a rich structure, preserving the critical points of the old Lagrangian, while generating new critical points (here the pore network) in a controllable, if hysteric, manner.