[extropy-chat] Nanotech educations

[Eugen Leitl]

On Mon, Jun 28, 2004 at 08:16:12AM -0700, Adrian Tymes wrote:

> Technically, 3d structure editors are a form of
> Computer Aided Design.  I see what you mean, but you

Yes. But they're specialized to deal with full atomic detail, including
realtime display, editing, and dynamics (VMD-NAMD) good enough to handle
biomolecules. And they're programmable.
Also, they're open source. And they scale to mesoscale. 

Any vanilla CAD is designed to deal with solids. It is the wrong-headed approach. 
You can't hack it top-down to include atomic scale. You have to start with
a system including atomic scale, and hack bottom-up. It's trivial that way.

> might want to phrase it differently.
> 
> > I find VMD has no trouble manipulating systems the 
> > size of an SV40 virus. Given that we can't do more
> > than to break and form a
> > few bonds in toto currently, the capabilities of
> > manipulating and rendering
> > molecules and molecular systems in machina.
> 
> "...the capabilities...in machina" what?  Did you
> mean, "exist only in machina"?

Of course we're stuck with numerical models right now. Making and breaking
bonds in reality with sufficient degree of control is reserved to some 
very well equipped labs and teams.

The capabilities in machina currently far outstrip anything we can do in the
lab, and will be quite for some time. In fact, the disparity is likely to
grow further, due to Moore's law. Until, hopefully, the in vitro capabilities
will make a giant leap forward. But by that time the tools will be ready.
 
> If I understand "machine-phase people" correctly, this
> is largely because there are no existing tools for
> doing that sort of manipulation.  People who work on

It's all about building the tools. So we have the computational chemistry
people working on an unified format, and machine-phase people are
conspicuously absent. This is not good. This makes me think about cryonics
people who do crap science (with some very notable exceptions) as far as 
cryobiology is concerned.

No wonder cryobiology people are shunning them, like country cousins with
poor personal hygiene.

> the tools that exist tend to focus on the tools that
> exist.  (Which is not to say that other people can't
> work on the problem, just that this specific group is
> focussed on its immediate needs.)

If people are building standards, it costs you very, very little to make your
voice heard. And it reflects quite some of the glory of the finished product.
 
> And we need tools to perform those validations.

I mentioned these tools. Why hasn't any nanotechnology enthusiast picked up a
package like Gamess? I'm just picking an example, there are other, better
suitable tools. But Gamess is free, good, and could use some hacking.

> Creating the tools seems to be a bigger problem than
> using them to create the library once they exist.
> (Not to mention, the details of the tools will tend to
> shed light on the proper format of the library.)

The details of the tools only matter if your physics is wrong. A molecule
colliding with another molecule is your hard validation criterium, and your
package has got to get details of their interaction right.

This is the hard part, and next to no one in the hobbyist machine-phase 
camp is working on that. Don't bother building the home STM machine.
Understand the interactions at the tip first.
 
> One could possibly build MNT systems around a very
> very limited library of mechanosynthesis reactions.

Indeed, but we don't even have that very limited mechanosynthesis reaction.
It's all 95% vapor at this point.

> Maybe just one or two eactions (bombardment with high
> energy photons or electrons, and exposure to high
> electrical current when bonded to a conductive
> manipulator), with variations for different power
> levels and different atoms.

You're not describing just "two reactions". Activating moieties with current
is actually a good idea, but you have to include what you're zapping, how the
orientation is controlled, and how much current you use.

How many degrees of freedom do you see here?
 
> > I will people here would talk Jaguar, Gaussiand and
> > Gamess (and that package
> > Zyvex is using) instead of AutoCAD.
> 
> Once they're no longer talking about purely
> theoretical stuff?  Sure.  In the mean time, I've got

I wish the machine-phase people would get cracking at least at the
theoretical stuff. It's easy enough to validate interesting candidates in the
lab, once you know what exactly you're trying to do.

> my current project, for which the first three tools
> are not suited.  (Then again, one could maybe write
> extensions to AutoCAD that emulate the functions of
> the other tools, no?)

You could generate huge structures with some trivial Python macros in VMD
directly (or MMTK). You can dump these as voxel data sets, and vizualize them
in realtime with OpenQVis or similiar. 
 
> > Anyone now go read
> > http://discuss.foresight.org/~pcm/nanocad/index.html
> 
> Umm...the archive ends in September 2001.  Might its
> contents be a bit dated by now?

The very opposite. We haven't had any progress since. The entire discussion
has gone nowhere.

The degree of detail and sophistication (which, really, was a sad joke in
comparison to what is required) dealt with there hasn't recurred. 

In fact, we have regressed since. There are people out there hacking open
source stuff, but no nanotechnology people. Granted, some of them have been
too busy writing papers and grant proposals, which is probably the right
course of action to take.

Still, I see no movement at all on open source nanotechnology. The open
source hackers don't understand the science and the challenge, the people who
do are too few, and they apparently don't have the skills, or the time.

Do you now see why I'm frustrated?

-- 
Eugen* Leitl <a href="http://leitl.org">leitl</a>
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