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... and since the surface area of a capacitor is directly proportional to its energy density, I see no reason why such a "nano-ultracapacitor" couldn't eventually surpass the energy density of the best batteries.
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Real physical things never scale linearly over orders of magnitude.
"Surface area is directly proportional to its energy density" actualy means the error in calculating it in this way is insignificant. But this changes dramaticaly as you start to reach ultra high densities comparable with intramolecular bonds. When that happens linear scaling disappears. People that know something about making ultracapacitors don't see how this limit could be overcome buy simply "scaling up" of current principles.