Kinetic trap - Revision history

Apm at 16:09, 29 March 2026

2026-03-29T16:09:12Z

← Older revision		Revision as of 18:09, 29 March 2026
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	It's a trade-off/balance where even the optimum may be insufficient for some too ambitious ideas. <br>		It's a trade-off/balance where even the optimum may be insufficient for some too ambitious ideas. <br>
	(Was ist about multi-input comuting hitting the limits of this?? Needs a re-read.)		(Was ist about multi-input comuting hitting the limits of this?? Needs a re-read.)

			[[category:Incremental path]]

Apm: /* Related / added link to yet unwritten page Steric trap

2024-07-17T17:41:46Z

Related: added link to yet unwritten page * Steric trap

← Older revision		Revision as of 19:41, 17 July 2024
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	== Related ==		== Related ==

			* [[Steric trap]]
	* [[Thermally driven self assembly]]		* [[Thermally driven self assembly]]
	----		----

Apm: Apm moved page Kinetic traps to Kinetic trap: plural => singular

2023-12-13T10:57:31Z

Apm moved page Kinetic traps to Kinetic trap: plural => singular

← Older revision	Revision as of 12:57, 13 December 2023
(No difference)

Apm: added link to steric traps

2022-08-05T10:33:25Z

added link to steric traps

← Older revision		Revision as of 12:33, 5 August 2022
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			Not to confuse with [[steric traps]].

	== Misassembly trap ==		== Misassembly trap ==

Apm: /* Related */ added a lot of yet links to yet unwritten pages

2021-07-05T18:43:15Z

Related: added a lot of yet links to yet unwritten pages

← Older revision		Revision as of 20:43, 5 July 2021
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	== Related ==		== Related ==

			* [[Thermally driven self assembly]]
			----
			* [[One pot binding site finding]] - this can sometimes allow for steric kinetic traps
			* [[Iterative binding site finding]] <br>- this allows to avert steric kinetic traps by determining the assembly order <br>- this also vcan lead to an [[exponential drop in yield]] though.
	* [[Exponential drop in yield]] - in the synthesis of chain molecules via conventional [[thermodynamic means]].		* [[Exponential drop in yield]] - in the synthesis of chain molecules via conventional [[thermodynamic means]].
	* [[~~Iterative selfassembly~~]] - ~~allowing to avert steric kinetic traps by determining~~ the ~~assembly order.~~		* [[Iterated one pot binding site finding]] - a combination of the former two - the best of both worlds?

	== External links ==		== External links ==

Apm: /* Related */

2021-07-05T18:31:24Z

← Older revision		Revision as of 20:31, 5 July 2021
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	== Related ==		== Related ==

	* [[Exponential drop in yield]] in the synthesis of chain ~~moles~~ via conventional [[thermodynamic means]]		* [[Exponential drop in yield]] - in the synthesis of chain molecules via conventional [[thermodynamic means]].
	* [[Iterative selfassembly]] - allowing to avert steric kinetic traps by determining the assembly order.		* [[Iterative selfassembly]] - allowing to avert steric kinetic traps by determining the assembly order.

Apm: added related section

2021-07-05T18:30:58Z

added related section

← Older revision		Revision as of 20:30, 5 July 2021
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	Actually maybe these shoulkd be calles "[[steric traps]]".		Actually maybe these shoulkd be calles "[[steric traps]]".

			== Related ==

			* [[Exponential drop in yield]] in the synthesis of chain moles via conventional [[thermodynamic means]]
			* [[Iterative selfassembly]] - allowing to avert steric kinetic traps by determining the assembly order.

	== External links ==		== External links ==

Apm: added external links section and link to that awesome selfassembly group wiki

2021-07-05T18:24:32Z

added external links section and link to that awesome selfassembly group wiki

← Older revision		Revision as of 20:24, 5 July 2021
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	The degree to which this happens may be hard to tell since the imaging technology [[cryo-TEM-tomography]] <br>		The degree to which this happens may be hard to tell since the imaging technology [[cryo-TEM-tomography]] <br>
	for the highest resolution images needs to use averages over a large number of images of assemblies to get the fimal pictures (lots of fourier math involved).		for the highest resolution images needs to use averages over a large number of images of assemblies to get the fimal pictures (lots of fourier math involved).

			Actually maybe these shoulkd be calles "[[steric traps]]".

			== External links ==

			'''[http://self-assembly.net/wiki/index.php?title=Main_Page self-assembly group wiki]'''<br>
			The technology presented there makes heavy use of intentionally weak bonds to avert kinetic traps. <br>
			It's a trade-off/balance where even the optimum may be insufficient for some too ambitious ideas. <br>
			(Was ist about multi-input comuting hitting the limits of this?? Needs a re-read.)

Apm: /* Assembly path cutoff trap */

2021-07-05T18:09:50Z

Assembly path cutoff trap

← Older revision		Revision as of 20:09, 5 July 2021
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	'''Example:''' <br>		'''Example:''' <br>
	DNA bricks in [[structural DNA ~~nanotachnology~~]] may assemble such that some voxels that should be filled with an DNA oglionucleotide strands <br>		DNA bricks in [[structural DNA nanotechnology]] may assemble such that some voxels that should be filled with an DNA oglionucleotide strands <br>
	just remain unfilled since the structure around was built up before they got a chance to be filled.		just remain unfilled since the structure around was built up before they got a chance to be filled.

	The degree to which this happens may be hard to tell since the imaging technology [[cryo-TEM-tomography]] <br>		The degree to which this happens may be hard to tell since the imaging technology [[cryo-TEM-tomography]] <br>
	for the highest resolution images needs to use averages over a large number of images of assemblies to get the fimal pictures (lots of fourier math involved).		for the highest resolution images needs to use averages over a large number of images of assemblies to get the fimal pictures (lots of fourier math involved).

Apm: basic version for the page

2021-07-05T18:08:53Z

basic version for the page

New page

== Misassembly trap ==

In [[thermally driven self assembly]] if
* [[specificity]] is low but
* bonding strength is high
things may self assembly in a wrong way and stay there for good.

If the bonding strength is deliberately kept low then even after the fact of a faulty self-assembly-bonding-event 
by thermal vibrations the formed bond can be jostled apart again 
and the part gets a another chance for assembling into one of the intended binding spots. 

In first approximation that typically works the better the slower the cooling profile during selfassembly ([[thermal annealing]]).

== Assembly path cutoff trap ==

Even without any faulty self-assembly-bonding-events a kinetic trap can emerge. 
If the order of assembly is by chance such that access to yet unfinished parts gets and irreversibly stays blocked, that part can never be finished.

'''Example:''' 
DNA bricks in [[structural DNA nanotachnology]] may assemble such that some voxels that should be filled with an DNA oglionucleotide strands 
just remain unfilled since the structure around was built up before they got a chance to be filled.

The degree to which this happens may be hard to tell since the imaging technology [[cryo-TEM-tomography]] 
for the highest resolution images needs to use averages over a large number of images of assemblies to get the fimal pictures (lots of fourier math involved).