Hi, here are some details, on a hypothetical Molecular Scale Computer, focus on Boolean process.
I'm thinking 512 K separate ALU 'channels', running at, I don't know, how about 900 GHz (?).
Diagram starts off fundamentals, for using particle collision dynamics in a practical ALU subsystem.
It does not show the 3D aspects, but you can see: there are two input, moving particles arranged and timed for accurate collision zone. Now, since depth axis is not shown, please assume each in the particle pair will experience a glancing blow, each off of the other.
So you could work out the varieties of result:
In a case where only one (particle-signal) has entered the 'collision zone' that single particle can be captured to exit, and literally represents an XOR outcome. That is, an EXCLUSIVE OR signifying that only one of two 'input' signals is present, a binary 'ONE' bit.
Reader's can note, on the various outputs, the XOR function result can be taken from two duplicate places, that is, can be viewed as each incomplete. To solve this minor dilemma one merely has to combine both partial XOR outputs, using a simple funnel structure, in the crystal 'substrate', or whatever that implementation needs, to 'OR' combine for a conventional XOR result.
Considering the case for the (two) logical AND outputs, it appears that either signal can be chosen, while other signal AND can be discarded, assuming not needed further along (as a signal duplicate).
It appears this scheme experiences difficulty producing logical OR signal; that could be generated using combination of AND (either output), with each of XOR1 with XOR2.
Thus portions of full Boolean operatives can be built, the limits being when each type of output is demanded, all at once. So some work-arounds needed for that, general, case.
Now, of course, processing for doing logical invert (NOT) that is problematic... But so is organizing 512,000 ALU units, together, into a full molecular computer.
Yes, that's called 'forward thinking', I heard Einstein got called that, or worse. (Lol)