Difference between revisions of "Catalysis construction kit approach"

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[[File:APM-EarlyDevelopmentPaths.jpg|500px|thumb|right|Possible map for the incremental path.]]
  
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This approach involves getting to a [[positional assembly kinematic loop]] ASAP.
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This is about a possible sub-branch of the [[incremental path]]. <br>
  
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{{wikitodo|extend intro}}
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This approach involves getting to a [[positional assembly kinematic loop]] ASAP. <br>
  
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== Static version – no actuation – [[block construction kit approach]] ==
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The idea here is to scale up general purpose [[self-assembly]] capabilities of various [[foldamer]] technologies just enough,
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such that one arrives at basic building block modularity sufficient for creating [[positional assembly kinematic loop]]s.
  
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The idea is to create chemical reaction facilitating [[positional assembly kinematic loop]]  
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Despite building block modularity there is no modularity of functionality within the creatable [[positional assembly kinematic loop]]s yet though. I.e. while blocks are modular, catalysis/sensing/… functionality on the blocks is not modular (highly cross talking).
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by using a modular construction kit of reusable structural self assembled components/parts/blocks
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such that at least some separation of concerns in their structural behavior remain preserved.
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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.
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Given the limitations it is highly unlikely that a great separation of concerns in the '''function''' can be achieved.
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== On the partial lack of separability of engineering concerns ==
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That is there is no way to exchange a block to get a desired change in function.
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It's rather a giant game of trial and error in a very big search-space.
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This is still far from deliberate positional control.
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Since '''foldamer based artificial catalysis is a very hard problem''' <br>
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'''For the sake of getting early to marketable products still absent separation of engineering concerns in block functionality is accepted!''' <br>
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a sensing/detecting is possibly a sub-problem to split off and solve first
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'''Meaning:'''
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----
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* switching out one block can change the functionality of all the other blocks in hard to predict ways. But:
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* switching out blocks is easy and straightforward as their base shape is modular and predictable
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----
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Only building block modularity is present. <br>
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Not modularity of functionality carried by the blocks. <br>
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Related: The infamous [[fat finger problem]]
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----
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There is building block modularity that allows for combinatoric exploration of <br>
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a hyper-giant very-hard-to-seach-through space the non-modular functions crated by combination of blocks.
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----
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Aspects of the design concerning a potentiall present closed [[positional assembly kinematic loop]]
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cannot yet be changed independently.<br>
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----
  
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== Problems of this approach ==
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'''Delineation:''' <br>
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This is unlike in the [[printer approach]].  <br>
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There functionality of products allows for separation of engineering concerns.<br>
  
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A main issue is the that early loops suffer from incapability of proper separation of concerns in both
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== Evaluation scheme ==
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* their makeup and
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* their function
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'''Makeup:'''<br>
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{{wikitodo|eventually add [[functional block combinatoric evaluation scheme]]}}
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E.g. in proteins sidechains compete for 3 different functions:
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* cohesion (outside needs to be hydrophile, inside needs to be hydrophobe, otherwise no protein forms)
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* definition of exterior complementary surfaces
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* definition of external functions (fubctional group sidechains – tooltips so to say - sometines called fingers – bad misnomer see below)
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'''Function:'''<br>
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== More simple sub-problem ==
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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.
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== Floppy fingers or fat fingers, pick your poison ==
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A fingers purpose is to stably point to something '''on its own'''. So naming sidechains fingers seems like a bit of a misnomer.
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It is basically the '''[[functional block construction kit approach]]''' but <br>
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If anything it's a [[floppy finger]].
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with [[self assembly|selfassembled]] actuation elements of some sorts in order to better facilitate chemical reactions.<br>
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Or at least sensing like in a [[molecular universal testing machine]].
  
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What can stably make a shape is a whole bunch of side-chains when they are well and tightly packed.
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Since '''foldamer based artificial catalysis is a very hard problem''' <br>
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That is also barely callable a finger because it's not sharp and pointy like a finger. If anything it's a fat finger.
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a sensing/detecting is possibly a sub-problem to split off and solve first.
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This is perhaps what Richard Smalley was thinking about when putting out his [[fat finger problem]] critique.
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(That diamondoid tips do not suffer from [[fat finger problem]] to a crippling degree should be pretty obvious.)
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== Fancy stiff fingers ==
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As there is nor catalytic manipulation there is no [[positional assembly kinematic loop]] present in this case.
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Adding in special unnatural side-chains that are stiffer due to them containing more polycyclic elements is a theoretical option. But ...
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* there is still no complete decoupling from the local environment, just less so
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* even if more decoupled there is still barely any control for orientation ([[pose]])
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* this limits one to [[abiotic peptide synthesis]] – (expensive, only short strands, no "randomization for free")
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* lack of randomization limits the playability of the giant game of trial and error mentioned in the intro.
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'''A question naturally popping up is:'''
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* conventionally synthesized long peptides and
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* abiotically synthesized short peptides
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can these be combined to get the best of both worlds?
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== Related ==
 
== Related ==
  
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* Turn left much later: [[Robo approach]]
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* Turn left later: [[Printer approach]]
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* Turn left here: [[Catalysis construction kit approach]]
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----
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* [[Incremental path]]
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* [[Positional assembly]]
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* [[Pathways]]
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----
 
* [[Incremental path]]
 
* [[Incremental path]]
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* [[Pathways]]
 
* [[Positional assembly kinematic loop]]
 
* [[Positional assembly kinematic loop]]
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* [[Positional assembly]]
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* [[Functional block construction kit approach]]

Latest revision as of 08:16, 18 September 2022

Possible map for the incremental path.

This is about a possible sub-branch of the incremental path.

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

The idea here is to scale up general purpose self-assembly capabilities of various foldamer technologies just enough, such that one arrives at basic building block modularity sufficient for creating positional assembly kinematic loops.

Despite building block modularity there is no modularity of functionality within the creatable positional assembly kinematic loops yet though. I.e. while blocks are modular, catalysis/sensing/… functionality on the blocks is not modular (highly cross talking).

On the partial lack of separability of engineering concerns

For the sake of getting early to marketable products still absent separation of engineering concerns in block functionality is accepted!
Meaning:

  • switching out one block can change the functionality of all the other blocks in hard to predict ways. But:
  • switching out blocks is easy and straightforward as their base shape is modular and predictable

Only building block modularity is present.
Not modularity of functionality carried by the blocks.
Related: The infamous fat finger problem

There is building block modularity that allows for combinatoric exploration of
a hyper-giant very-hard-to-seach-through space the non-modular functions crated by combination of blocks.

Aspects of the design concerning a potentiall present closed positional assembly kinematic loop cannot yet be changed independently.

Delineation:
This is unlike in the printer approach.
There functionality of products allows for separation of engineering concerns.

Evaluation scheme

(wiki-TODO: eventually add functional block combinatoric evaluation scheme)

More simple sub-problem

It is basically the functional block construction kit approach but
with selfassembled actuation elements of some sorts in order to better facilitate chemical reactions.
Or at least sensing like in a molecular universal testing machine.

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

As there is nor catalytic manipulation there is no positional assembly kinematic loop present in this case.

Related

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