On Sat, 18 Aug 2001, Robert J. Bradbury wrote:
> > Sterical hindrance or sterical constraint are much harped upon items of
> > every chemical undergrad, and are also mentioned in highschool chemistry.
>
> Are you saying that they aren't thinking it through at a deep enough
> level? Sounds like they need to read Nanomedicine Section 3.5 on
Whom, the chemists? They're very aware of it, because it is one of the
factors which can dominate yield, and push a reaction quantitively towards
and undesired alternative.
> Molecular Receptor Engineering, esp. 3.5.5 regarding the limits
> of atomic positional accuracy.
I've just skimmed it. It's not about diamondoid receptor design, it's
mostly about the bulk around the cavity, and the supporting structure
inferring sufficient rigidity.
> > Yes, but you're not trying to make deep cages, and you're not trying to
> > stick stuff to a surface.
>
> You can assemble deep cages from the inside out and sticking a methyl
> group onto a molecule *is* sticking it on the surface. I *will*
Curved surface, as a shallow cage is all surface. Nature doesn't do highly
crosslinked polymers the enzyme way, because the enzyme can't bind to the
surface of the reactive moiety without interfering with the structure it
is depositing upon, plus each deposition changes the surface and thus
makes complementary binding by a single enzyme impossible.
Plus, of course, once deposited, crosslinked structures are a bitch to
remove, especially in a defined way, so you can consider them to drop down
like bricks outside of the homeostatic equilibrium, once made.
> admit there are going to be some very difficult, perhaps even impossible
> assembly problems without a programmable nanoassembler. But the
> phase space of what you can assemble by tacking things onto each
> other or assembling things as nested hierarchies would seem to
> be some reasonable subset of what you can assemble atom by atom.
There's a large space of possibilities nature hasn't sampled and which we
can, sure. Despite proximal probe nanorobotics making great headway
recently, engineering biology to bootstrap nanotechnology still remains a
very hot topic.
> > Chemists do random polymer libraries now, too.
>
> I was unaware of that. Must make a pretty gooey mess.
And how. They're even doing sugars now.
> > They're molecules, not machines, though. Very different from biochemistry.
>
> Machines are subset of all the possible sets molecules. Nature
> has produced "machines". Polymerases, ion channels and the
> proteosome are some that immediately come to mind. I think
> you are splitting hairs if you consider enzymes to not be machines.
No, you got me wrong. Molecular biology is all about machines. It's just
polymer chemists (by virtue of one of my hats I'm supposed to be one)
don't consider polymers as machines, because they can't make them, and,
worse, unaware that molecules and assemblies thereof can be machines..
> > Not your typical computer scientist. They understand bits, but not atoms.
>
> I was thinking the A-life people.
Oh, these do understand bits allright. But even your typical ALifer
doesn't understand that atoms are much messier and much more difficult to
manipulate objects than bits.
> I think that is because there is so much money in it due to the
> pharmaceutical industry. As soon as you develop some skill set in the
> area you get sucked off into a commercial effort.
I've noticed some of that effect.
> I think Goddard is on the right track with this. And if Nano@Home
> picks up some steam and feeds into what Goddard et al are doing with
> the simulations then I think your vision may be realized. One thing
> is for sure -- with a multi-teraflop machine coming online nanomachine
> simulations will be doable. If the simulations say they should work
> thats going to up the pressure on the synthesists to actually build
> them to confirm what the simulations predict.
Crossing all available digits here, and not only binary.
-- Eugen* Leitl <a href="http://www.lrz.de/~ui22204/">leitl</a>
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