Catalysis construction kit approach - Revision history

Apm: category:Incremental path

2026-03-29T16:23:36Z

← Older revision		Revision as of 18:23, 29 March 2026
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	* [[Positional assembly]]		* [[Positional assembly]]
	* [[Functional block construction kit approach]]		* [[Functional block construction kit approach]]

			[[category:Incremental path]]

Apm: removed {{stub}}

2022-09-18T07:16:39Z

removed {{stub}}

← Older revision		Revision as of 09:16, 18 September 2022
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	~~{{stub}}~~

	[[File:APM-EarlyDevelopmentPaths.jpg\|500px\|thumb\|right\|Possible map for the incremental path.]]		[[File:APM-EarlyDevelopmentPaths.jpg\|500px\|thumb\|right\|Possible map for the incremental path.]]

Apm: /* Related */

2022-09-16T15:18:16Z

← Older revision		Revision as of 17:18, 16 September 2022
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	* [[Positional assembly]]		* [[Positional assembly]]
	* [[Pathways]]		* [[Pathways]]
	---		----
	* [[Incremental path]]		* [[Incremental path]]
	* [[Pathways]]		* [[Pathways]]

Apm: major changes

2022-09-16T13:33:12Z

major changes

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 {{stub}}
-This approach involves getting to a [[positional assembly kinematic loop]] ASAP.
+[[File:APM-EarlyDevelopmentPaths.jpg|500px|thumb|right|Possible map for the incremental path.]]
 It is basically the '''[[functional block construction kit approach]]''' but <br>
@@ Line 9: / Line 47: @@
 Since '''foldamer based artificial catalysis is a very hard problem''' <br>
 a sensing/detecting is possibly a sub-problem to split off and solve first.
 == Related ==
 * [[Incremental path]]
 * [[Positional assembly kinematic loop]]
 * [[Functional block construction kit approach]]

Apm: linebreak

2022-05-16T14:28:54Z

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← Older revision		Revision as of 16:28, 16 May 2022
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	It is basically the '''[[functional block construction kit approach]]''' but <br>		It is basically the '''[[functional block construction kit approach]]''' but <br>
	with [[self assembly\|selfassembled]] actuation elements of some sorts in order to better facilitate chemical reactions.		with [[self assembly\|selfassembled]] actuation elements of some sorts in order to better facilitate chemical reactions.<br>
	Or at least sensing like in a [[molecular universal testing machine]].		Or at least sensing like in a [[molecular universal testing machine]].

Apm: moved stuff over to Functional block construction kit approach

2022-05-16T14:28:22Z

moved stuff over to Functional block construction kit approach

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 This approach involves getting to a [[positional assembly kinematic loop]] ASAP.
-{{wikitodo|extend intro}}
+It is basically the '''[[functional block construction kit approach]]''' but <br>
+with [[self assembly|selfassembled]] actuation elements of some sorts in order to better facilitate chemical reactions.
-== Static version – no actuation – [[block construction kit approach]] ==
+Or at least sensing like in a [[molecular universal testing machine]].
 Since '''foldamer based artificial catalysis is a very hard problem''' <br>
-a sensing/detecting is possibly a sub-problem to split off and solve first
+a sensing/detecting is possibly a sub-problem to split off and solve first.
 == Related ==
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 * [[Incremental path]]
 * [[Positional assembly kinematic loop]]

Apm: basic page

2022-05-16T14:14:32Z

basic page

New page

{{stub}}

This approach involves getting to a [[positional assembly kinematic loop]] ASAP.

{{wikitodo|extend intro}}

== Static version – no actuation – [[block construction kit approach]] ==

The idea is to create chemical reaction facilitating [[positional assembly kinematic loop]]
by using a modular construction kit of reusable structural self assembled components/parts/blocks
such that at least some separation of concerns in their structural behavior remain preserved.
E.g. that the blocks don't remain individually exchangeable and addition and or subtraction of blocks disturbs the rest of the structure only minimally.

Given the limitations it is highly unlikely that a great separation of concerns in the '''function''' can be achieved.
That is there is no way to exchange a block to get a desired change in function.
It's rather a giant game of trial and error in a very big search-space.
This is still far from deliberate positional control.

Since '''foldamer based artificial catalysis is a very hard problem''' <br>
a sensing/detecting is possibly a sub-problem to split off and solve first

== Problems of this approach ==

A main issue is the that early loops suffer from incapability of proper separation of concerns in both
* their makeup and
* their function

'''Makeup:'''<br>
E.g. in proteins sidechains compete for 3 different functions:
* cohesion (outside needs to be hydrophile, inside needs to be hydrophobe, otherwise no protein forms)
* definition of exterior complementary surfaces
* definition of external functions (fubctional group sidechains – tooltips so to say - sometines called fingers – bad misnomer see below)

'''Function:'''<br>
To give an intuitive analogy: Side-chains of proteins behave a bit like wobbly slightly magnetic noodles under permanent shaking. They do not operate individually but holistically. One cannot just slot one out and another one in at a critical tooltip-spot without changing both its spacial configuration and all the configuration of all the sidechains in the local environment too. To make them stick and stay despite the shaking they need to be packed tightly with sidechains that pack for minimal wiggleroom. The possibility space quickly gets hyper-astronomically big.

== Floppy fingers or fat fingers, pick your poison ==

A fingers purpose is to stably point to something '''on its own'''. So naming sidechains fingers seems like a bit of a misnomer.
If anything it's a [[floppy finger]].

What can stably make a shape is a whole bunch of side-chains when they are well and tightly packed.
That is also barely callable a finger because it's not sharp and pointy like a finger. If anything it's a fat finger.
This is perhaps what Richard Smalley was thinking about when putting out his [[fat finger problem]] critique.
(That diamondoid tips do not suffer from [[fat finger problem]] to a crippling degree should be pretty obvious.)

== Fancy stiff fingers ==

Adding in special unnatural side-chains that are stiffer due to them containing more polycyclic elements is a theoretical option. But ...
* there is still no complete decoupling from the local environment, just less so
* even if more decoupled there is still barely any control for orientation ([[pose]])
* this limits one to [[abiotic peptide synthesis]] – (expensive, only short strands, no "randomization for free")
* lack of randomization limits the playability of the giant game of trial and error mentioned in the intro.

'''A question naturally popping up is:'''
* conventionally synthesized long peptides and
* abiotically synthesized short peptides
can these be combined to get the best of both worlds?

== Related ==

* [[Incremental path]]
* [[Positional assembly kinematic loop]]