Revision as of 15:56, 17 December 2013

Overview

At the current technology level we have a top-down bottom-up technology-gap which is about to close.

Bottom-up with self assembly:

• structural 3D 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]

[TODO clarify the problems]

Level of self assembly control

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 level 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.

Structural DNA nanotechnology

[...]

When one watches the simulation of the self assembly process of DNA bricks [TODO add link] one is led to doubt the stiffness of the product. The DNA double helix can create siff polymeres if the used doublehelix segments are kept in the length range from one to three turns. Mentioned here [5] under the section "DNA as Construction Material" and referenced here ^[2] (unchecked). Is there quantitative information about the stiffness of whole DNA bricks (to investigate)?

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 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.

Links:

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

Capabilities, Limits and Unknowns

Mechanical and micro-mechanical systems such as AFMs and MEMS are generally very slow to slow. [TODO add quantitative numbers]
beside the problem of yet unstable tooltips and insufficient vacuum It seems certain that they are to slow to do direct mechanosynthesis.
To investigate: Will they be fast enough to do e.g. assembly of DNA-bricks or MMCS parts?

Electric fields generated by microelectronics acting on a DNA brick structure or an other type of structure in machine phase provide less degrees of freedom than a mechanical gripper. More problematically the blocks need to be made dielectric or charged to be effected by the field.
To investigate: Can blocks/block structures be made dielectric or charged sufficiently?

The size of the smallest possible MEMS grippers and DNA-bricks aren't overlapping yet [TODO add size comparison], that is the tip radius of the grippers tend to be greater than the DNA-brick sizes. So they need to be aggregated to even bigger sizes to be grippable.
To investigate:

• Can 3DDNA-blocks be hierarchically self assembled, that is can the blocks surfaces be glued together by adding strands in a second step?
• Alternatively do complementary surfaces stick by VdW interaction even though there are no open strands (or the strands doesn't match)?
  

To be usable for somewhat functional robotic applications the blocks need to fulfill some criteria:
To investigate:

• Can an axle bearing system be built that runs non self destructively wit sub block-size precision?
• Can the blocks bind strong enough together to avoid falling apart when actuated?
• Are the surfaces of 3DDNA blocks made with half strands, that is are there surfaces smooth ore more like a hairy ball) [TODO dig out the known answer]
• Can two blocks be connected with a edge to edge hinge? (similar to the hierarchical assembly question)

To use electric fields as input the block structures need to provide at least one internal 1D degree of freedom which can be compressed to 0D (machine phase)
To investigate: How to create minimal sized block structures for mechanical or electrostatical actuation that are productive and capable of self replication?

Proposals for the step from T.Level 0 to 1

[TODO to myself: add the one I've archived] technology level I

Some raw notes about ideas to block based Nanosystems:

• (enclosed) Serving plates
• exoergic chain & alternatives?
• "look" and pick
• tooltip size adapter - spanning up down gap
• block reloading

• electrostatic actuation & signal collector bundles & broadcasting
• bulldozing
• pros of dry operation

• parallel robots -> less complex mechanics
• linkages
• temporary pinning
• rotation vs reciprocation

• replicative: build volume limit -> 2D mobility
• parallel: accuracy issue - effort in parallelization of tips leaves them too un-precise ...

Investigation Results

Space for investigation results and further investigation-directions:

[yet empty]

Medicine

The focused interest in medical devices of T.Level 0 motivated by near term benefits drives development now.
With rising technology levels we want to get further and further away from biological nanosystems though.
If the situation prevails that too little dedicated non medical research is done we might be stuck for a longer time than necessary.

References

1. ↑ "Cryo-EM structure of a 3D DNA-origami object" Xiao-chen Bai, Thomas G. Martin, Sjors H. W. Scheres, Hendrik Dietz
2. ↑ Hagerman, P.J. (1988), Flexibility of DNA, Ann. Rev. Biophys. & Biophys. Chem. 17, 265-286.

DNA screw