Revision as of 19:27, 26 March 2021

(wiki-TODO: add a sketch here)

This relates to using soft nanomachinery to get to stiff nanomachinery ASAP.

The idea here is not to use proteins as they are to do mechanosynthesis.
This would not work because unmodified proteins feature a unbreakable see-saw between
the fat finger problem and the floppy finger problem.

Enzymes and 3D printers - small similarities - huge differences

Enzymes:

• need to catch and hold the molecule(s) they operate on (their substrates)
• need to operate on the molecules they captured
• need to hold both of these together

3D Priners:

• need a print-bed holding a part
• need a nozzle manipulating the part
• need the frame of the printer holding the two parts together

The very big difference is that in Enzymes there is no good "separation of concerns". Instead different functionalities like holding and manipulating (catalyzing) are complexly entangled. Changing a bit here changes everything over there too. Even if not desired. This makes designing enzymes more an case-by-case art rather than a straightforward engineering technique.

Floppy side-chains rely on mutual support from tight stacking to be constrained to the spot they are supposed to. Proteins have fat fingers. So if one wanted to detangle functionalities by moving things apart one only achieves a loss of mutual side chain support leading to a total loss of functionality. One gets floppy fingers.

To be able to separate things apart spatially without loosing absolutely all control there is a need for the integration of stiffer "fingers". This constitute early progress towards Technology level II in-solution mechanosynthesis.

Integration of stiffer molecules is not a prerequisite for more crude positional assembly of big pre-folded foldamer blocks.

Expanding the loop

By combining various foldamer and polymer technologies of different stiffness and scalability together ...

• stiff core (maybe spiroligomers) -- scaling Upward and outward
• medium stiff adapter (maybe stiff de-novo proteins) -- developing Inter foldamer interface design
• and big less stiff but highly scaleable backbone framework -- improving Downward and inward

... it may be possible to expand the kinematic loop in size
while simultaneously retaining and improving on stiffness such that

• positional assembly of pre-assembled foldamer blocks can be introduced
• tips become stiff enough such that eventually early in-solvent mechanosynthesis can be started.

Upward and outward

• One Prime candidate: Structural DNA nanotechnology
• Harder to scale but stiffer de-novo proteins especially predictably folding helices and sheets

Inter foldamer interface design

• SDN to de-novo proteins and
• de-novo proteins to stiffer stuff

Downward and inward

• Eventual candidate: spiroligomers
• artificial side chains on de-novo proteins with lots of poly-aromatic structure that cross link

Site activation foldamer printer

This concept idea was presented by Eric K. Drexler in a more recent talk.

Applying the site activation strategy one can avoid the necessity to seek out and pick up pre-assembled foldamer parts. Instead sites are activated and parts are washed in.

This may constitute an eventual intermediate target towards the far term target that marks a major milestone on technology level I.

This is not a molecular assembler in that

• it assembles pre-assembled foldamer blocks instead of absolute minimal molecule fragments
• it only activates sites

External links

Wikipedia:

• Substrate_(chemistry)
• Kinematic_chain