Difference between revisions of "Technology level 0"

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Next: [[technology level I]]
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{{Site specific definition}}
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{| class="wikitable" style="float:right; margin-left: 10px; text-align: center"
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! colspan = "2"|Defining traits of technology level 0
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|-
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| building method
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| mainly self assembly
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|-
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| building material
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| appropriate molecules
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|-
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| building environment
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| liquid (gas or UHV for analysis)
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|-
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! colspan = "2"|Navigation
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|-
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| '''next step'''
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| '''[[introduction of positional control]]'''
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|-
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| next level
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| [[technology level I]]
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|-
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| products of this level
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| [[side products of technology level 0]]
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|-
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| sideways to
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| [[brownian technology path]] <br> [[non mechanical technology path]]
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|-
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| cheat <br> shortcut to primary goal
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| [[skipping technology levels]]
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|}
  
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We want to find out what needs to be done to gain basic digital robotic control over atomically precise building blocks.
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'''[Todo: split level pages from step pages- (solves fence-post problem)]'''
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At the current technology level we have a '''top-down bottom-up technology-gap''' which needs to be bridged.
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'''semi biomimetic self assembly'''
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We want to find out what needs to be done to gain basic digital robotic control over atomically precise building blocks (like e.g. [[structural DNA nanotechnology|DNA bricks]]). <br>
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At the current technology level we have a '''top-down bottom-up technology-gap''' which needs to be bridged. <br>
 
New developments make it seem that it is already about to close.
 
New developments make it seem that it is already about to close.
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Alternatively it might be possible to cheat and [[skipping technology levels|skip technology levels]] that is go directly from here to [[technology level III]].
  
 
= Technology Overview =
 
= Technology Overview =
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The here presented list of technologies is not intended to be exhaustive. There is a plethora of analytic methods available for structural clarification.
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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:
 
Bottom-up with self assembly:
  
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*structural 3D DNA nanotechnology<ref>"Cryo-EM structure of a 3D DNA-origami object" Xiao-chen Bai, Thomas G. Martin, Sjors H. W. Scheres, Hendrik Dietz</ref> [http://www.pnas.org/content/109/49/20012.full] & Co (self assembling structures) [https://en.wikipedia.org/wiki/DNA_origami]
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* DNA bricks from [[structural DNA nanotechnology]]<ref>"Cryo-EM structure of a 3D DNA-origami object" Xiao-chen Bai, Thomas G. Martin, Sjors H. W. Scheres, Hendrik Dietz</ref> [http://www.pnas.org/content/109/49/20012.full] & Co (self assembling structures) [https://en.wikipedia.org/wiki/DNA_origami]
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*foldamers designed for predictable folding (e.g. synthetic polypeptides)<br>
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* foldamers designed for predictable folding (e.g. synthetic polypeptides)<br>
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*polyoxymetalates (POMs)
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* polyoxymetalates (POMs)
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*other [add if you know relevant ones]
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* other [add if you know relevant ones]
  
 
Bottom-up with mechanosynthesis and self assembly:
 
Bottom-up with mechanosynthesis and self assembly:
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== Capabilities, Limits and Unknowns  ==
 
[TODO clarify the problems]
 
[TODO clarify the problems]
  
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== Structural DNA nanotechnology ==
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= Level of control over self assembly processes =
  
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=== DNA frameworks ===
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Main article: [[brownian assembly|self assembly]]
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=== DNA bricks ===
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[...]
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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.
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The DNA double helix can create siff polymeres if the used doublehelix segments are kept in the length range from one to three turns.
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Mentioned here [http://www.foresight.org/Conferences/MNT05/Papers/Seeman/index.html] under the section "DNA as Construction Material" and referenced here <ref>Hagerman, P.J. (1988), Flexibility of DNA, Ann. Rev. Biophys. & Biophys. Chem. 17, 265-286.</ref> (unchecked).
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Is there quantitative information about the stiffness of whole DNA bricks ('''to investigate''')?
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= Level of self assembly control =
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== Simple self assembly ==
 
== Simple self assembly ==
  
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There are many natural examples like soft lipid bilayers [https://en.wikipedia.org/wiki/Lipid_bilayer] and more sturdy polypeptide structures like microtubuli [https://en.wikipedia.org/wiki/Microtubule].
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There are many natural examples like '''soft lipid bilayers''' [https://en.wikipedia.org/wiki/Lipid_bilayer] and '''more sturdy polypeptide structures''' like microtubuli [https://en.wikipedia.org/wiki/Microtubule].
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Lipid layers are more a thing of synthetic biology heading towards [[technology level µ]] though one cannot exclude their use with all certainty.
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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.
 
Natural polypeptides are not that useful for the creation of artificial systems.
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They did not evolve to behave predictably in folding to their three dimensional shape, instead quite the opposite is the case [Todo: add ref].
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They did not [[evolution|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.
 
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.
 
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.
 
To archive this one can limit the motives of polypeptides (amino acid subsequences) to ones that fold predictably.
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There also have been discovered artificial molecular structures similar to polypeptides like peptoids and foldamers which seem helpful.
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There also have been discovered '''artificial molecular structures similar to polypeptides''' like '''peptoids and foldamers''' which seem helpful.
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Also there is structural DNA nanotechnology with a quite different characteristic going beyond simple self assembly.
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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.
 
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.
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An MMCS is a self assembled structure which provide addressable spots so that one can  
 
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.
 
mount various chooseable subunits (e.g. the ones described in the ''simple self assembly'' section or just simple molecules) to them.
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The result is something like a possibly three dimensional circuit board like structure.
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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
 
If they're also made to know when to stop
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Currently (2013) structural DNA nanotechnology is the best contender for this purpose.
 
Currently (2013) structural DNA nanotechnology is the best contender for this purpose.
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Two dimensional structural DNA grids with perfect short range order have been created ['''Todo:'''add link]
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but for basic mainipulators longer range order seems necessary.
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Those grids could form a basis for 2D MMCSs and later manipulator mechanisms.
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['''Todo:''' check wether a two or three layeres structure can increase long range order]
  
 
Links:
 
Links:
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* http://www.isnsce.org/
 
* http://www.isnsce.org/
  
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== Proposals for the step from T.Level 0 to 1  ==
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= The step towards the next technology level =
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Most robotic base parts consist out of structural non functional material.
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Thus binary voxels (set or unset) suffice for components.
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DNA-bricks are the first example providing this programmability but they are limited in size.
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If the limit of adressable 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.
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Small scale binary voxelated bricks could be further assembled to rigid parts (with no hinges) via:
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* further self assembly in a second hirachical step (reduced brownian mobility of the bigger molecules will be a problem here).
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* direct robotics (taking a shortcut). For this the parts need to get into [[machine phase]] first (more about that below).
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* a combination: partial self assembly followed by robotic assembly.
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Assuming basic rigid body robotic parts e.g. rods with eyelets for linkages (or even assembled linkages) are buildable via self assembly then
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to assemble them robotically e.g. via exponential assembly one needs to know their exact locations.
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They need to be in the [[machine pase]].
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Beside their non robotic usefulness as "molecular breadboards" MMCS might be useful to lay out those pre-self assembled functional components in an
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ordered fashion so that [[self replication|exponential assembly]] could be done.
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Otherwise if one operates with the parts scattered randomly n 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 replication|self replicating]] approach than exponential assembly might be suited better.
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Simple blocks could be "bulldozed" together for sorting bigger parts could be identified by AFM like scanning (which ruins parallenity).
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Note: The more basic the structures are which can be handeled robotically by the system the more productive this [[technology level I|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 lateron.
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[TODO to myself: add the one I've archived] [[technology level I]]
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Some raw notes about ideas to block based Nanosystems:
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* (enclosed) Serving plates
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* exoergic chain & alternatives?
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* tooltip size adapter - spanning up down gap
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* block reloading
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* electrostatic actuation & signal collector bundles & broadcasting
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* bulldozing
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* pros of dry operation
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* parallel robots -> less complex mechanics
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* linkages
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* temporary pinning
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* rotation vs reciprocation
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* replicative: build volume limit -> 2D mobility
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* parallel: accuracy issue - effort in parallelization of tips leaves them too un-precise ...
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== Capabilities, Limits and Unknowns  ==
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Mechanical and micro-mechanical systems such as AFMs and MEMS are generally very slow to slow. ['''TODO''' add quantitative numbers]<br>beside the problem of yet unstable tooltips and insufficient vacuum It seems certain that they are to slow to do direct [[mechanosynthesis]].<br>'''To investigate:''' Will they be fast enough to do e.g. assembly of DNA-bricks or bigger parts?
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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.<br>'''To investigate:''' Can blocks/block structures be made dielectric or charged sufficiently? Can the "fly away hair effect" be used instead?
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* See: [[Introduction of positional control]]
  
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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.<br>'''To investigate:'''<br>
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= Related =
  
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*Can DNA-bricks be hierarchically self assembled, that is can the blocks surfaces be glued together by adding strands in a second step?
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* [[Technology levels]]
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*Alternatively do complementary surfaces stick by VdW interaction even though there are no open strands (or the strands doesn't match)?<br>
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To be usable for somewhat functional robotic applications the blocks need to fulfill some criteria:<br>
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== Medicine ==
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'''To investigate:'''
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*Can an axle bearing system be built that runs non self destructively with sub block-size precision?
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*Can the blocks bind strong enough together to avoid falling apart when actuated?
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*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]
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*Can two blocks be connected with a edge to edge hinge? (similar to the hierarchical assembly question)
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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)<br>
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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.<br>
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'''To investigate:''' How to create minimal sized block structures for mechanical or electrostatical actuation that are productive and capable of [[self replication|self replication]]?
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Advances in medicine are undoubtably very valuable and may lead to [[technology path µ]] but APM aims in a very different direction.
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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.
  
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== Investigation Results  ==
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= External links =
  
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Space for investigation results and further investigation-directions:  
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* [http://www.zyvex.com/nanotech/mbb/mbb.html  Molecular building blocks and development strategies for molecular nanotechnology - Ralph C. Merkle]
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* Wikipedia: [//en.wikipedia.org/wiki/DNA_machine DNA machines]
  
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[yet empty]  
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* Image of holiday junction in DNA: [https://en.wikipedia.org/wiki/File:DNA_tensegrity_triangle.jpg]
  
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= Medicine =
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Partial [[machine phase]] nanomotors:
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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.<br>
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* [http://openwetware.org/wiki/Biomod/2013/Komaba DNA screw - by Komaba-Team at The University of Tokyo]
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Advances in medicine are undoubtably very valuable but APM aims in a very different direction.
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* [http://www.foresight.org/nanodot/?p=5999 Integrating DNA nanotechnology and RNA to transport nanoparticles along nanotubes]
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With rising technology levels we want to get further and further away from biological nanosystems though.<br>
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* [http://www.caltech.edu/article/13345 Spiders at the Nanoscale: Molecules that Behave Like Robots]
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If the situation prevails that too little dedicated non medical research is done we might be stuck for a longer time than necessary.
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= References  =
 
= References  =
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<references />
 
<references />
  
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[http://openwetware.org/wiki/Biomod/2013/Komaba DNA screw]
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[[Category:Technology level 0]]
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[[Category:Site specific definitions]]

Latest revision as of 18:18, 14 April 2021

This article defines a novel term (that is hopefully sensibly chosen). The term is introduced to make a concept more concrete and understand its interrelationship with other topics related to atomically precise manufacturing. For details go to the page: Neologism.
Defining traits of technology level 0
building method mainly self assembly
building material appropriate molecules
building environment liquid (gas or UHV for analysis)
Navigation
next step introduction of positional control
next level technology level I
products of this level side products of technology level 0
sideways to brownian technology path
non mechanical technology path
cheat
shortcut to primary goal 		skipping technology levels

[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:

The step towards the next technology level

Related

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

  • Image of holiday junction in DNA: [5]

Partial machine phase nanomotors:

References

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