Termination control - Revision history

Apm: /* Related */

2026-03-29T16:08:27Z

← Older revision		Revision as of 18:08, 29 March 2026
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	{{todo\|look into formally quantifying the quantity of termination control}}		{{todo\|look into formally quantifying the quantity of termination control}}

			[[category:Incremental path]]

Apm: /* Related / added link to Hierarchical selfassembly

2024-07-11T13:32:16Z

Related: added link to * Hierarchical selfassembly

← Older revision		Revision as of 15:32, 11 July 2024
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	* [[Algorithmic selfassembly]]		* [[Algorithmic selfassembly]]
	* [[Fully addressable lattice selfassembly]]		* [[Fully addressable lattice selfassembly]]
			* [[Hierarchical selfassembly]]

	{{todo\|look into formally quantifying the quantity of termination control}}		{{todo\|look into formally quantifying the quantity of termination control}}

Apm: improved on the intro

2022-09-16T09:19:42Z

improved on the intro

@@ Line 2: / Line 2: @@
 '''Examples of termination control:''' <br>
 – rotationally symmetric assembly with specifiable number of segments left out <br>
-– in self-assemlbly terminating grid of voxels (carterian, hexagonal, or whatever) where <bR>subsets of those voxels (ideally each one individually) can be set or unset (addressed) individually.<br>
+– in self-assemlbly terminating A grid of voxels (carterian, hexagonal, or whatever) that when self-assembled deterministically terminates this self assembly at some point.
 Using the terminology of "addressing voxels" may be confusing:<br>
 There are no changes after assembly. Static structural structures are assumed here.<br>
 '''Delineation from superficially impressive firatures like size and symmetry:'''<br>

Apm: /* Related */ bold

2022-09-16T08:41:30Z

Related: bold

← Older revision		Revision as of 10:41, 16 September 2022
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	== Related ==		== Related ==

	* [[Incremental path]]		* '''[[Incremental path]]'''
	* [[Self assembly]]		* [[Self assembly]]
	* [[Algorithmic selfassembly]]		* [[Algorithmic selfassembly]]

Apm: /* Related */ added backlink to Incremental path

2022-08-05T09:09:45Z

Related: added backlink to Incremental path

← Older revision		Revision as of 11:09, 5 August 2022
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	== Related ==		== Related ==

			* [[Incremental path]]
	* [[Self assembly]]		* [[Self assembly]]
	* [[Algorithmic selfassembly]]		* [[Algorithmic selfassembly]]

Apm: /* de-novo proteins */ capitalization

2022-08-05T08:56:03Z

de-novo proteins: capitalization

← Older revision		Revision as of 10:56, 5 August 2022
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	= Limiting factors in termination control and countermeasures =		= Limiting factors in termination control and countermeasures =

	== de-novo proteins ==		== De-novo proteins ==

	* ~~artificial~~ de-novo proteins can only provide a small set of orthogonal interfaces. <br>And it is hard to get high specificity and activity at the same time		* Artificial de-novo proteins can only provide a small set of orthogonal interfaces. <br>And it is hard to get high specificity and activity at the same time
	* ~~their~~ otherwise desired [[stiffness]] gets in the way. <br>There is no DNA like step by step unzipping process possible. <br>All bond breaking energy needs to be supplied in one fell swoop. <br>That is: [[Kinetic trap]]s can become a bigger problem.		* Their otherwise desired [[stiffness]] gets in the way. <br>There is no DNA like step by step unzipping process possible. <br>All bond breaking energy needs to be supplied in one fell swoop. <br>That is: [[Kinetic trap]]s can become a bigger problem.
	* Internal cohesion, external intefaces and eventual other external functionality are <br>three mutually competing factors on the choice of side-chain sequences. <br>Such a situation is not present in [[structural DNA nanotechnology]].		* Internal cohesion, external intefaces and eventual other external functionality are <br>three mutually competing factors on the choice of side-chain sequences. <br>Such a situation is not present in [[structural DNA nanotechnology]].
	'''Countermeasures:'''		'''Countermeasures:'''
	* [[Squigglesembly]]		* [[Squigglesembly]]
	* [[Circumsembly]]		* [[Circumsembly]]
	* ~~integrate~~ into more termination-control-scalable background framework <br>like e.g. [[structural DNA nanotechnology]]		* Integrate them into more termination-control-scalable background framework <br>like e.g. [[structural DNA nanotechnology]]

	== Structural DNA nanotechnology ==		== Structural DNA nanotechnology ==

Apm: /* Spiroligomers */ capitalization

2022-08-05T08:55:15Z

Spiroligomers: capitalization

← Older revision		Revision as of 10:55, 5 August 2022
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	* Their otherwise desires [[stiffness]] gets in the way of self assembly and termination control. <br> Due to them being less conforming they are less and tolerant to variations in complementary surface shapes. Also they are small-ish limiting the amount of encodable shape.		* Their otherwise desires [[stiffness]] gets in the way of self assembly and termination control. <br> Due to them being less conforming they are less and tolerant to variations in complementary surface shapes. Also they are small-ish limiting the amount of encodable shape.
	* ~~they~~ are still quite small molecules which limits their reachion-site-choosing-specificity. Similar to the [[site specificity limitation problem]] in conventional chemistry.		* They are still quite small molecules which limits their reachion-site-choosing-specificity. Similar to the [[site specificity limitation problem]] in conventional chemistry.
	'''Countermeasures:'''		'''Countermeasures:'''
	* ~~integrate~~ into more termination-control-scalable background framework like e.g. as artificial side-chains in [[de-novo proteins]].		* Integrate into more termination-control-scalable background framework like e.g. as artificial side-chains in [[de-novo proteins]].

	== Related ==		== Related ==

Apm: /* spiroligomers */ big cleanup

2022-08-05T08:54:49Z

spiroligomers: big cleanup

← Older revision		Revision as of 10:54, 5 August 2022
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	* Maybe tether-based / hinged-based assembly approaches?		* Maybe tether-based / hinged-based assembly approaches?

	== ~~spiroligomers~~ ==		== Spiroligomers ==

	* ~~their~~ otherwise desires [[stiffness]] gets in the way. <br> ~~They~~ are less ~~conforming~~ and ~~less tolearant~~ to in ~~variation to~~ complementary shapes		* Their otherwise desires [[stiffness]] gets in the way of self assembly and termination control. <br> Due to them being less conforming they are less and tolerant to variations in complementary surface shapes. Also they are small-ish limiting the amount of encodable shape.
	* they still quite small molecules ~~limiting~~ their ~~rreachion~~ site choosing specificity ~~similar~~ to conventional chemistry		* they are still quite small molecules which limits their reachion-site-choosing-specificity. Similar to the [[site specificity limitation problem]] in conventional chemistry.
	'''Countermeasures:'''		'''Countermeasures:'''
	* integrate into more termination-control-scalable background framework like e.g. [[de-novo proteins]].		* integrate into more termination-control-scalable background framework like e.g. as artificial side-chains in [[de-novo proteins]].

	== Related ==		== Related ==

Apm: /* Structural DNA nanotechnology */ improvements

2022-08-05T08:48:18Z

Structural DNA nanotechnology: improvements

← Older revision		Revision as of 10:48, 5 August 2022
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	== Structural DNA nanotechnology ==		== Structural DNA nanotechnology ==

	* Diffusuion time. Especially for larger 3D structures exclusively made from short strands yields drop far ~~down~~.		* Diffusuion time.<br> Especially for larger 3D structures exclusively made from short strands (oglionucleotide staple strands) the achievable yields drop down far.
	'''Countermeasures:'''		'''Countermeasures:'''
	* ~~Using~~ longer backbone strands ~~shortening the finding process~~ can ~~help, but~~ <br>~~these come~~ with tradeoffs. {{wikitodo\|refresh on that one}}		* Inclusion of longer strands (backbone scaffold strands) can increase [[effective concentration]] and<br> thereby speed up selfassembly considerably. This comes with tradeoffs though. {{wikitodo\|refresh on that one}}
	* Hierarchical self-assembly aka [[convergent self-assembly]]		* Hierarchical self-assembly aka [[convergent self-assembly]]
	* Maybe tether-based / hinged-based assembly approaches		* Maybe tether-based / hinged-based assembly approaches?

	== spiroligomers ==		== spiroligomers ==

Apm: /* de-novo proteins */ sie => side

2022-08-05T08:40:23Z

de-novo proteins: sie => side

← Older revision		Revision as of 10:40, 5 August 2022
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	* artificial de-novo proteins can only provide a small set of orthogonal interfaces. <br>And it is hard to get high specificity and activity at the same time		* artificial de-novo proteins can only provide a small set of orthogonal interfaces. <br>And it is hard to get high specificity and activity at the same time
	* their otherwise desired [[stiffness]] gets in the way. <br>There is no DNA like step by step unzipping process possible. <br>All bond breaking energy needs to be supplied in one fell swoop. <br>That is: [[Kinetic trap]]s can become a bigger problem.		* their otherwise desired [[stiffness]] gets in the way. <br>There is no DNA like step by step unzipping process possible. <br>All bond breaking energy needs to be supplied in one fell swoop. <br>That is: [[Kinetic trap]]s can become a bigger problem.
	* Internal cohesion, external intefaces and eventual other external functionality are <br>three mutually competing factors on the choice of ~~sie~~-chain sequences. <br>Such a situation is not present in [[structural DNA nanotechnology]].		* Internal cohesion, external intefaces and eventual other external functionality are <br>three mutually competing factors on the choice of side-chain sequences. <br>Such a situation is not present in [[structural DNA nanotechnology]].
	'''Countermeasures:'''		'''Countermeasures:'''
	* [[Squigglesembly]]		* [[Squigglesembly]]