ATP synthase in action

Chemicals don't need to chemically react. Especially for biology, merely existing is enough. Lots of biological regulation is done by influencing three-dimensional shapes of the huge highly complex structures called proteins. Organic chemistry especially is a science of complex three dimensional structures and its dynamic changes, at least as important as actually altering the chemical structure. Often they are not static but have moving parts, because not all bonds restrict movement of the atoms connected through that bond in relation to the other part. Many have what's call binding sites - other molecules fitting to those sites won't be altered or alter the chemical structure of the protein. They alter the shape . Proteins are machines, pretty much literally. For example, there are channel proteins, and a molecule docking on a binding site of such a protein might open or close that channel for certain molecules. The variety of those molecular machinery (really, literally) is huge. You can influence machines not just by breaking them down, you can just throw a spanner between their gears. Things that matter are not just shape and size, but also polarity of the parts. Polar components of a molecule influence polar components of proteins if they can get close enough, which influence the shape. Binding sites, as only one example: Description: [link] Images: [link] Example - 22 second movie - for a protein-machine whose function it is to move stuff around: [link] Example for ion

It seems like you've misremembered the situation somewhat. Merkle developed several of his families of mechanical logic, including this one, in order to answer some criticisms of Drexler's earliest mechanical nanotechnology proposals. Specifically: 1. Chemists were concerned that rod logic knobs touching each other would form chemical bonds and remain stuck together, rather than disengaging for the next clock cycle. (Macroscopic metal parts usually don't work this way, though "cold welding" is a thing, especially in space.) So this proposal‚ like some earlier ones like Merkle's buckling-spring logic, avoids any contact between unconnected parts of the mechanism, whether sliding or coming into and out of contact. 2. Someone calculated the power density of one of Drexler's early proposals and found that it exceeded the power density of high explosives during detonation, which obviously poses significant challenges for mechanism durability. You could just run them many orders of magnitude slower, but Merkle tackled the issue instead by designing reversible logic families which can dissipate arbitrarily little power per logic operation, only dissipating energy to erase stored bits. So, there's nothing preventing this kind of mechanism from scaling down to single atoms, and we already have working mechanisms like the atomic force microscope which demonstrate that even intermittent single-atom contact can work mechanically in just the way you'd expect it to from your macroscopic in