If you could build mechanisms atom-by-atom, you could make reversible mechanical computers that are orders of magnitude faster than what we have today.
This is because the speed of sound, which limits how fast mechanical signals can propagate, is much lower than the speed of light.
The main advantages of rod logic is that its compact and power efficient. The aforementioned CPU would consume ~100 nW.
Really the reason why Drexler analyzed rod logic in the first place is that it was easy to analyze and something that his proposed assemblers could plausibly construct, better alternatives for fast computing may exist.
You're implying that parallelization can make up for the slower clock speeds, which is true but only for some workloads, and then the system is constrained by bandwidth to get instructions and data to the parallel cores as fast as possible.
Of course electronics aren't standing still, but resistance tends to get harder to deal with as feature sizes decrease.
I've marked your account legit so this will not happen to you again, and I've approved your comments that got throttled, so they're up now. Welcome to HN and congratulations on this exceedingly cool work.
Reversible computing tries not to destroy information, allowing to go under Laundauer's limit [1].
When you discard the previous value held by your flip-flop, you clear the output bit, returning electrons (or a chain displacement) to the power supply. If you can instead repurpose that energy, you'll have to supply a lot less energy since you'll dissipate less. That would be reversible or adiabatic computing [2]. I have to note that processors these days are mostly power-limited, trying not to melt themselves as the energy flux inside a chip approaches that of a nuclear reactor. Just look at modern sockets and count the pins dedicated to power supply![3]
[1]: https://en.wikipedia.org/wiki/Landauer's_principle
[2]: https://en.wikipedia.org/wiki/Reversible_computing#Reversibi...
[3]: https://arstechnica.com/gadgets/2015/11/5d-electronic-blood-...