Revision as of 13:43, 29 December 2013

products: side products of technology level 0
sideways: technology level µ
next: technology level I

We want to find out what needs to be done to gain basic digital robotic control over atomically precise building blocks.
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.

Technology Overview

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]

Structural DNA nanotechnology

DNA frameworks

DNA bricks

[...]

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 [3] 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)?

Level of self assembly control

Simple self assembly

There are many natural examples like soft lipid bilayers [4] and more sturdy polypeptide structures like microtubuli [5]. 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.

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/

Proposals for the step from T.Level 0 to 1

Most robotic base parts consist out of structural non functional material with defined inner structure and outer limits. Thus the capability to self assemble some building material with addressable binary voxels (set or unset) suffice for the creation of robotic components or at least parts of them if the structures cannot be made big enough.

DNA-bricks are the first example providing this programmability but they are limited in size. If the limit of addressable size space can't be overcome (changing the blocks aspect ratio may help a bit) then what's needed is some form of post non binary assembly of these or other upcoming binary voxelated bricks to larger structures. The stiffness of the whole structure must thereby be preserved.

Small scale binary voxelated bricks (of any sort) could be further assembled to rigid parts via:

• further self assembly in a second hierarchical step (reduced brownian mobility of the bigger molecules will be a problem here).
• direct robotics (taking a shortcut). For this the parts need to get into machine phase first (more about that below).
• a combination: partial self assembly followed by robotic assembly.

Using self assembly to create sturdy structures with (interlocking) hinges is not yet demonstrated and may be too hard of a problem such that after creation of the complete rigid parts robotic assembly of them seems to be a good approach.

Assuming basic rigid body robotic parts e.g. rods with eyelets for linkages (or even assembled linkages) are buildable via self assembly then to assemble them robotically e.g. via exponential assembly one needs to know their exact locations. They need to be in the machine phase.

Beside their non robotic usefulness as "molecular breadboards" MMCS might be useful to lay out those pre-self assembled functional components in an ordered fashion so that exponential assembly could be done.

Otherwise if one operates with the parts scattered randomly on a surface one somehow must pick the parts up check which type they are sort and store them - a rather complicated procedure. For this approach a more self replicating approach than exponential assembly might be suited better. Simple blocks could be "bulldozed" together for sorting. Bigger parts could be identified by AFM like scanning (which ruins parallelity).

Note: The more basic the structures are which can be handled robotically by the system the more productive this level I nanosystem gets (in the sense that it can produce products that can be fairly different from the system itself). If robotic control isn't voxel-brick based but rigid component based it may be more practical to introduce that capability later on.

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

Useful rigid sub micro components

Size adapters

If AP building blocks can be post self assembled or directly made big enough. It might make sense to create a size adapter that can be gripped by MEMS manipulators on one side and can pick and place single AP blocks with the other side. Thus spanning the top-down bottom-up gap.

Serving plates

To make recognition of the block types easier a set of types could be self assembled to a bigger mounting plate. Designing those serving plates as boxes could provide protection from unwanted self assembly steps like when the building bock supply is depleted and the system is reloaded in liquid phase.

Building plates

Flat structures where products can be built on.

Mixed notes:

exoergic chain

From the blocks creation to their final destination they have to first get bound into machine phase then ave to be picked up and finally be placed down. To archive this either the binding strengths has to strictly monotonically increase from step to step (an exoergic chain) or sterical means have to be employed. ...

When robotically assembling self assembled robotic parts it may be neccesary to temporarily pin down levers to prevent them from spinning on their axles.

choice of kind of mechanisms

With basic AP blocks only very simple mechanisms will be buildable. Parallel robots can provide mechanical simplicity at the cost of control complexity (inverse kinematics)

Since the surfaces of self-assembled AP blocks are far less smooth than the ones of future DMEs sliding rails for reciprocative movement should probably avoided to avoid risks of destructive clogging and low resolution. Linkages could make use of edge to edge seam hinges for rotative movement instead

mechanism actuation

Todays most advanced nanotechnology is electronics. Driving mechanisms with electrostatic forces is thus an obvious route.

Self assembled AP blocks may be (and probably are) electrically isolating. Still with strong electric fields local polarizations may be induced and kind of an "stand up hair effect" could be used as driving method.

To keep the complexity of the mechanical mechanisms low the number of input channels must be kept as high as possible. Since the electric contacts still are rather big compared to AP building blocks one could create mechanical signal collector bundles crossing the electrodes and broadcasting reciprocative movement to a number of mechanisms.

replicative vs parallel

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

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 bigger parts?

Electric fields generated by microelectronics acting on a AP 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? Can the "fly away hair effect" be used instead?

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 DNA-bricks 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 with sub block-size precision?
• Can the blocks bind strong enough together to avoid falling apart when actuated?
• Are the surfaces of DNA-bricks 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?

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 is a good part of what drove and drives drives development now.
Advances in medicine are undoubtably very valuable and may lead to technology level 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
• DNA screw - by Komaba-Team at The University of Tokyo

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.