A silicon-based proton exchange membrane for a membrane electrode assembly comprises a silicon wafer including a back side, a front side, and a membrane region therebetween, where the membrane region includes a plurality of channels extending from openings in the front side of the silicon wafer through the membrane region to openings in the back side of the silicon wafer. Walls of the channels include active sites to which a molecular species may be attached. Each of the front side and the back side of the silicon wafer includes a porous capping layer thereon. The capping layer comprises a plurality of through-thickness apertures contiguous with at least a portion of the channels of the membrane region.
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