Building a nanoblock

From: Jack (jack_removethis__at_mail.com)
Date: 06/12/04 

Date: 12 Jun 2004 15:44:57 GMT

I am a long time reader of this forum (since early 90s) but rarely posted
anything here. I was wondering for a long time, like many of you I suppose,
why there is no assembler built yet. Recently, I was asking myself if I can
give a shot at it, just for the sake of an exercise. I am not a chemist or
nanotechnologist so my musings on the problem are very very rough indeed.
But I tought I may just do this exercise maybe to try to understand how
difficult the problem is.

I was inspired by reading the Chris Phoenix's paper "Design of a Primitive
Nanofactory" (http://www.jetpress.org/volume13/Nanofactory.htm) . The paper
leaves out the design of the nanoassembler that would build, among other
things, the basic nanoblock. That's where I tried to fill in the blank.
Well, of course, I could not do much since my knowledge of the chemistry is
so poor. But the apparent thing that came to my mind was that the easiest
way for me to do any model would be to use selfassembly and also to assume
building out of nanobricks (a molecule size, say around 10 nanometers)
rather than atoms. I tought this may limit the problem mostly to general
mechanics.

Now, I was wondering what you think about such an attempt or is that
complete waste of time :-) If this is a reasonable approach why don't we
have the working model of the assembler so far? Do you think it would be
very difficult to build such a nanoblock in reality? If you are a chemist,
can you tell if nanobricks I am using in my model could be built?
Especially, the "power brick". Could you suggest improved or better models?
I am using MDL Chime to model the bricks as atoms(!), just because I had no
knowledge of any other 3D CAD tool. Are there any better CAD programs? Are
they free as well?

Below there are some description about this model. Bare in mind that this is
more like a work-in-progress. You can find the data file (a400.xyz) on the
following web page: http://republika.pl/nanotech/
You need to download it (or better yet its zipped version since its much
smaller) and view it with MDL Chime program (that you can download for free,
after you register, from www.mdl.com).

Best to all,

Jack Kucharewicz
nano@poczta.onet.pl

----------------
Some description:

I have not worked out the whole model, just part of it and I still had some
problems with it. However, the short experience of this exercise shown that
there are many solution to a single problem. So my intuition tells me that
one should be able to find the right design.

This model works similar to a ribosome, but with few differences. Mainly,
there are no translation process: the bricks are just assembled into a
structure (nano-block). The "DNA" is already a "protein": the information is
the building material. Also, I need the power brick to move the process on
(to provide the energy to the process). The definition is provided further
down.

The whole process starts with a chain of bricks (a DNA) carrying the
information about the structure. Initially, other components are also
provided: the platform for the whole assembly, small molecules such as power
bricks and other small helper molecules allowing the power bricks to attach
themselves to the bigger structures and to apply the push. All those
components are floating in some medium.

The chain of bricks, at some point in time, randomly finds the starting
point on the platform. That's when the whole process really begins and that'
s where the animation starts.

The power bricks grab hold of both the chain and the platform and they push
the chain around to form the new structure. The most common push is a push
of the chain onto the platform, but from time to time (as coded into the
chain) some chain brick can be broken from its preceding neighbor and pushed
perpendicular to the whole chain. This way the chain can be folded into
three-dimensional structure. See the animation for details. You can see
there that I have stopped detailed animation after few dozen steps for
simplicity of the presentation.

The structure construction ends when the whole chain is being used up. That'
s where the animation ends too. However, there is a next step involved.
Some of the bricks (and possibly the platform and helping molecules) have to
be irradiated (loosen) and then "washed out" to leave holes or caves in the
structure where desired. I think I saw similar idea in somebody's post on
the sci.nanotech group. I think that the final nanoblock has to be fairly
flat to wash out desired material in most cases or the block should have
some kind of "weep holes" to wash out the material. But at this point I am
not concerned with this problem.

When I created this model, I had the following assumptions in my mind:

   1. The whole process is powered by a "power brick", shown in brown. It
doubles in size to push the two halves of itself apart. In doing so it
pushes any other bricks that are attached to it. Originally, I had in mind a
simple model of two caps pushed inside another: one smaller and one slightly
bigger bottom up, with a spring inside connecting the two. The spring inside
could push away the caps when triggered by some event on the outside surface
of the caps (i.e. attaching to some other molecule). But now I think the
molecule implementation may be more like scissors or something else to
simplify the design. BTW, I think the size of such brick will dictate the
size of the chain brick and therefore the whole nano-block. I wonder if
there are currently such molecules that can be used or would one need to
design.
   2. The whole process is based on self-assembly; therefore, the medium,
the structures are in, must be able to float material (molecules) randomly
to most of the places in it. The molecules should be able to attach to other
molecules. Some molecules should attach for (randomly) short period of time,
others till they perform a given task (e.g. power brick) or till they are
affected by other bricks. Yet some others should attach permanently or until
they are washed away.
   3. The attachment type of molecules is governed by type of the bricks
being in contact and the side of each brick in contact. In other words, the
bricks are not isotropic but have preferable sides for the attachment.
   4. Not all the helper and power bricks are shown for clarity of the whole
process. But I hope that if I had any more of those bricks floating around,
the whole process will be as shown in animation.