Expanding the kinematic loop - Revision history

Apm: Category:Incremental path

2026-03-29T19:02:18Z

← Older revision		Revision as of 21:02, 29 March 2026
Line 95:		Line 95:
	* [https://en.wikipedia.org/wiki/Substrate_(chemistry) Substrate_(chemistry)]		* [https://en.wikipedia.org/wiki/Substrate_(chemistry) Substrate_(chemistry)]
	* [https://en.wikipedia.org/wiki/Kinematic_chain Kinematic_chain]		* [https://en.wikipedia.org/wiki/Kinematic_chain Kinematic_chain]

			[[Category:Incremental path]]

Apm: /* Related / added link to page Introduction of total positional control

2025-04-26T14:30:52Z

Related: added link to page * Introduction of total positional control

← Older revision		Revision as of 16:30, 26 April 2025
Line 80:		Line 80:

	* '''[[Positional assembly kinematic loop]]''' & same page: [[Expanding the catalytic loop]])		* '''[[Positional assembly kinematic loop]]''' & same page: [[Expanding the catalytic loop]])
			* [[Introduction of total positional control]]
	----		----
	* [[Separation of concerns]]		* [[Separation of concerns]]

Apm: /* Related */ added a lot of links from the backlinks

2025-04-26T14:26:25Z

Related: added a lot of links from the backlinks

← Older revision		Revision as of 16:26, 26 April 2025
Line 79:		Line 79:
	= Related =		= Related =

	* '''[[Positional assembly kinematic loop]]'''		* '''[[Positional assembly kinematic loop]]''' & same page: [[Expanding the catalytic loop]])
			----
			* [[Separation of concerns]]
			* [[Fat finger problem]]
			* [[Spiroligomer]] & [[Highly polycyclic small molecule]]
			* [[Modular molecular composite nanosystem]], [[Effective concentration]]
			----
			* [[Bootstrapping methods for productive nanosystems]]
			* [[Most relevant R&D construction sites for progress in APM]]

	= External links =		= External links =

Apm: added link to Positional assembly kinematic loop

2025-04-26T14:22:05Z

added link to Positional assembly kinematic loop

← Older revision		Revision as of 16:22, 26 April 2025
Line 76:		Line 76:
	* it assembles pre-assembled foldamer blocks instead of absolute minimal molecule fragments		* it assembles pre-assembled foldamer blocks instead of absolute minimal molecule fragments
	* it only activates sites		* it only activates sites

			= Related =

			* '''[[Positional assembly kinematic loop]]'''

	= External links =		= External links =

Apm: /* Expanding the loop */

2021-03-26T18:41:49Z

Expanding the loop

← Older revision		Revision as of 20:41, 26 March 2021
Line 45:		Line 45:
	while simultaneously retaining and improving on stiffness such that		while simultaneously retaining and improving on stiffness such that
	* positional assembly of pre-assembled foldamer blocks can be introduced		* positional assembly of pre-assembled foldamer blocks can be introduced
	* tips become stiff enough such that eventually early in-solvent mechanosynthesis can be started.		* tips become stiff enough such that eventually early in-solvent mechanosynthesis can be started <br> the kinematic cycle becomes catalytic cycle like in the case of a protein. Just disentangled.

	== [[Upward and outward]] ==		== [[Upward and outward]] ==

Apm: Apm moved page Expanding the catalytic loop to Expanding the kinematic loop without leaving a redirect: "catalytic loop" was not general enough

2021-03-26T18:34:31Z

Apm moved page Expanding the catalytic loop to Expanding the kinematic loop without leaving a redirect: "catalytic loop" was not general enough

← Older revision	Revision as of 20:34, 26 March 2021
(No difference)

Apm: basic version of the page

2021-03-26T18:27:37Z

basic version of the page

New page

{{stub}}
{{wikitodo|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. <br>
This would not work because unmodified proteins feature a unbreakable see-saw between <br>
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 finger problem|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 finger problem|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 <br>
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:
* [https://en.wikipedia.org/wiki/Substrate_(chemistry) Substrate_(chemistry)]
* [https://en.wikipedia.org/wiki/Kinematic_chain Kinematic_chain]