Latest revision as of 12:48, 6 October 2024

(wiki-TODO: Split level pages from step pages. - (solves fence-post problem))

semi biomimetic self assembly

We want to find out what needs to be done to gain basic digital robotic control over atomically precise building blocks (like e.g. DNA bricks).
At the current technology level we have a top-down bottom-up technology-gap which needs to be bridged.
New developments make it seem that it is already about to close.

Alternatively it might be possible to cheat and skip technology levels that is go directly from here to technology level III.

Technology Overview

The here presented list of technologies is not intended to be exhaustive. There is a plethora of analytic methods available for structural clarification. But actually many of them are completely non-contact non-local or give information about inverse space (diffraction patterns) which is not directly useful for actually building stuff. For the sake of brevity and relevance those are thus excluded.

Bottom-up with self assembly:

• DNA bricks from structural DNA nanotechnology^[1] [1] & Co (self assembling structures) [2]
• foldamers designed for predictable folding (e.g. synthetic polypeptides)
  
• polyoxymetalates (POMs)
• other [add if you know relevant ones]

Bottom-up with mechanosynthesis and self assembly:

• patterned layer epitaxy with scanning tunneling microscopes (STM)
• other [add if you know relevant ones]

Top-down side:

• MEMS technology (e.g. grippers, MEMS AFM)
• microelectronics (e.g. for electrostatic actuation)
• AFM arrays (cruder then singe tip AFMs)
• other [add if you know relevant ones]

Capabilities, Limits and Unknowns

[TODO clarify the problems]

Level of control over self assembly processes

Main article: self assembly

Simple self assembly

There are many natural examples like soft lipid bilayers [3] and more sturdy polypeptide structures like microtubuli [4]. Lipid layers are more a thing of synthetic biology heading towards technology path µ though one cannot exclude their use with all certainty. Natural polypeptides are not that useful for the creation of artificial systems. They did not evolve to behave predictably in folding to their three dimensional shape, instead quite the opposite is the case [Todo: add ref]. Also natural polypeptides don't come in a set thats very suitable to build circuit board like structures.

What one desires for the first steps toward APM are building blocks that are more predictable and designable. To archive this one can limit the motives of polypeptides (amino acid subsequences) to ones that fold predictably. There also have been discovered artificial molecular structures similar to polypeptides like peptoids and foldamers which seem helpful. Also there is structural DNA nanotechnology with a quite different characteristic going beyond simple self assembly.

The issue with too simple self assembly methods is that they usually do not know when to stop (ever growing rod or plane) and do not make specific locations addressable that is one can not bind blocks to specific locations of the assembly.

Modular Molecular Composite Nanosystems (MMCS)

An MMCS is a self assembled structure which provide addressable spots so that one can mount various chooseable subunits (e.g. the ones described in the simple self assembly section or just simple molecules) to them. The result is something like a two or possibly three dimensional circuit board like structure.

If they're also made to know when to stop they may be usable as prebuild robotic parts.

Currently (2013) structural DNA nanotechnology is the best contender for this purpose.

Two dimensional structural DNA grids with perfect short range order have been created [Todo:add link] but for basic mainipulators longer range order seems necessary. Those grids could form a basis for 2D MMCSs and later manipulator mechanisms. [Todo: check wether a two or three layeres structure can increase long range order]

Links:

• Introduction of MMCS
• Ned Seeman's Laboratory Home Page
• http://www.isnsce.org/

The step towards the next technology level

• See: Introduction of positional control

Related

• Technology levels

Medicine

The focused interest in medical devices of T.Level 0 motivated by near term benefits is a good part of what drove and drives development now.
Advances in medicine are undoubtably very valuable and may lead to technology path µ but APM aims in a very different direction. With rising technology levels we want to get further away from biological nanosystems. If the situation prevails that too little dedicated non medical research is done we might be stuck for a longer time than necessary.

External links

• Molecular building blocks and development strategies for molecular nanotechnology - Ralph C. Merkle
• Wikipedia: DNA machines

• Image of holiday junction in DNA: [5]

Partial machine phase nanomotors:

• DNA screw - by Komaba-Team at The University of Tokyo
• Integrating DNA nanotechnology and RNA to transport nanoparticles along nanotubes
• Spiders at the Nanoscale: Molecules that Behave Like Robots

References

1. ↑ "Cryo-EM structure of a 3D DNA-origami object" Xiao-chen Bai, Thomas G. Martin, Sjors H. W. Scheres, Hendrik Dietz