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Fabricating fuel cells by using Layer-by-Layer (LBL) technology bypasses the need to use lithographic and sputtering techniques to fabricate a large number of flat microelectrodes. Micropatterened LBL polyelectrolyte graphite electrodes are capable of reducing chemical and mechanical degradation and ensure proper passage of the ions. This allows the fuel cells to be capable of producing open-circuit-potentials similar to a pure metal. A novel proton exchange membrane (PEM) is fabricated by depositing polyelectrolyte LBL films on a porous support. A carbon-based gas diffusion layer (GDL) acts as a current collector and at the same time allows the diffusion of gases. Structural properties of LBL carbon electrodes are different from conventional carbon electrodes due to the polyelectrolytes embedded inside the LBL carbon electrode. By embedding polyelectrolytes inside the LBL carbon electrondes, the fuel cell's performance now depends more on the chemical properties of the polyelectrolytes themselves, and allows one to tune the thickness and permeability, as well as the composition, of these films to match the desired qualities.