Exponential drop in yield - Revision history

Apm: /* Related / added links to Structural DNA nanotechnology & * De-novo protein engineering

2024-11-19T11:04:41Z

Related: added links to * Structural DNA nanotechnology & * De-novo protein engineering

← Older revision		Revision as of 13:04, 19 November 2024
Line 39:		Line 39:
	* [[Foldamer]]s, [[Spiroligomer]]s, peptidomimentics		* [[Foldamer]]s, [[Spiroligomer]]s, peptidomimentics
	* [[Iterated one pot binding site finding]]		* [[Iterated one pot binding site finding]]
			----
			* [[Structural DNA nanotechnology]]
			* [[De-novo protein engineering]]

Apm: /* Related */ fixed links

2021-07-06T10:13:22Z

Related: fixed links

← Older revision		Revision as of 12:13, 6 July 2021
Line 37:		Line 37:

	* [[Chemical synthesis]]		* [[Chemical synthesis]]
	* [[~~Foldamers~~]], [[~~Spiroligomers~~]], peptidomimentics		* [[Foldamer]]s, [[Spiroligomer]]s, peptidomimentics
	* [[Iterated one pot binding site finding]]		* [[Iterated one pot binding site finding]]

Apm: /* Related */ synthetic chemistry => chemical synthesis (latter does not seem to exclude using biologically preproduced compunds as "ingredients")

2021-07-06T06:58:59Z

Related: synthetic chemistry => chemical synthesis (latter does not seem to exclude using biologically preproduced compunds as "ingredients")

← Older revision		Revision as of 08:58, 6 July 2021
Line 36:		Line 36:
	= Related =		= Related =

	* [[~~Synthetic chemistry~~]]		* [[Chemical synthesis]]
	* [[Foldamers]], [[Spiroligomers]], peptidomimentics		* [[Foldamers]], [[Spiroligomers]], peptidomimentics
	* [[Iterated one pot binding site finding]]		* [[Iterated one pot binding site finding]]

Apm at 19:19, 5 July 2021

2021-07-05T19:19:52Z

← Older revision		Revision as of 21:19, 5 July 2021
Line 3:		Line 3:
	Given that the success ratios at each steps on average and in general not exceedingly high, <br>		Given that the success ratios at each steps on average and in general not exceedingly high, <br>
	the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br>		the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br>
	For a large number of identical chains molecules synthesized together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed.		For a large number of identical chains molecules synthesized simultaneously together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed.

	= Ways to avert this yield-drop in the synthesis of chain molecules (polymers, [[foldamers]]) =		= Ways to avert this yield-drop in the synthesis of chain molecules (polymers, [[foldamers]]) =

Apm at 19:18, 5 July 2021

2021-07-05T19:18:30Z

← Older revision		Revision as of 21:18, 5 July 2021
Line 1:		Line 1:

	Synthesizing linear chain molecules iteratively in vivo the failure likelihood (success rate smaller than factor one) at each addition reaction multiplies. <br>		Synthesizing linear chain molecules (polymers, oldamers) iteratively in vivo the failure likelihood (success rate smaller than factor one) at each addition reaction multiplies. <br>
	Given that the success ratios at each steps on average and in general not exceedingly high, <br>		Given that the success ratios at each steps on average and in general not exceedingly high, <br>
	the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br>		the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br>

Apm at 19:17, 5 July 2021

2021-07-05T19:17:57Z

← Older revision		Revision as of 21:17, 5 July 2021
Line 1:		Line 1:

	Synthesizing ~~liner~~ chain molecules iteratively in vivo the failure likelihood (success rate smaller than factor one) at each addition reaction multiplies. <br>		Synthesizing linear chain molecules iteratively in vivo the failure likelihood (success rate smaller than factor one) at each addition reaction multiplies. <br>
	Given that the success ratios at each steps on average and in general not exceedingly high, <br>		Given that the success ratios at each steps on average and in general not exceedingly high, <br>
	the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br>		the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br>

Apm at 19:17, 5 July 2021

2021-07-05T19:17:39Z

← Older revision		Revision as of 21:17, 5 July 2021
Line 5:		Line 5:
	For a large number of identical chains molecules synthesized together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed.		For a large number of identical chains molecules synthesized together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed.

	= Ways to avert this in the synthesis of chain molecules (polymers, [[foldamers]]) =		= Ways to avert this yield-drop in the synthesis of chain molecules (polymers, [[foldamers]]) =

	== Near term ==		== Near term ==
Line 21:		Line 21:
	[[Piezochemical machanosynthesis]] has low enough error rates for this to not be a problem and even error corrention can be implemented.		[[Piezochemical machanosynthesis]] has low enough error rates for this to not be a problem and even error corrention can be implemented.

	= Ways to avert this in thermally driven selfassembly of blocks =		= Ways to avert this yield-drop in thermally driven selfassembly of blocks =

	Self assembly via [[iterative binding site finding]] suffers from the exact same problem as iterative syntesis of polymers in [[synthetic chemistry]].		Self assembly via [[iterative binding site finding]] suffers from the exact same problem as iterative syntesis of polymers in [[synthetic chemistry]].
Line 37:		Line 37:

	* [[Synthetic chemistry]]		* [[Synthetic chemistry]]
	* [[~~foldamers~~]], [[Spiroligomers]], peptidomimentics		* [[Foldamers]], [[Spiroligomers]], peptidomimentics
	* [[~~iterated~~ one pot binding site finding]]		* [[Iterated one pot binding site finding]]

Apm: basic version of page

2021-07-05T19:16:13Z

basic version of page

New page

Synthesizing liner chain molecules iteratively in vivo the failure likelihood (success rate smaller than factor one) at each addition reaction multiplies. 
Given that the success ratios at each steps on average and in general not exceedingly high, 
the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. 
For a large number of identical chains molecules synthesized together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed.

= Ways to avert this in the synthesis of chain molecules (polymers, [[foldamers]]) =

== Near term ==

=== Employing natural synthesis mechanisms ===

* Hijacking the cells machinery (ribosomes & more) for making proteins according to artificial plan
* There are even chaperone proteins that helping along in post synthesis correct folding
Still expensive experimental stuff:
* Artificial amino acid tweaks (?)
* Artificial codon tweaks

== Far term ==

[[Piezochemical machanosynthesis]] has low enough error rates for this to not be a problem and even error corrention can be implemented.

= Ways to avert this in thermally driven selfassembly of blocks =

Self assembly via [[iterative binding site finding]] suffers from the exact same problem as iterative syntesis of polymers in [[synthetic chemistry]].
The same exponential drop in yield with chain length is prestent.

Self assembly via [[one pot binding site finding]] of 2D or even 3D structures 
hugely averts the problem in that assembly can just move around sites of faulty assembly. 
For a complete breakdown of all further assembly all paths need to be blocked simultaneously which can get exceedingly unlikely.
[[One pot binding site finding]] comes with other downsides though. Including steric kinetic traps. 

Best may be an intermediate approach: [[iterated one pot binding site finding]] 
{{todo|Work out the math for the assembly of a stiff rod that is a bundle of several rods where selfassembly can move redundantly arrond faulty assembly sites}}

= Related =

* [[Synthetic chemistry]]
* [[foldamers]], [[Spiroligomers]], peptidomimentics
* [[iterated one pot binding site finding]]

Exponential drop in yield - Revision history

Apm: /* Related */ added links to * Structural DNA nanotechnology & * De-novo protein engineering

Apm: /* Related */ fixed links

Apm: /* Related */ synthetic chemistry => chemical synthesis (latter does not seem to exclude using biologically preproduced compunds as "ingredients")

Apm at 19:19, 5 July 2021

Apm at 19:18, 5 July 2021

Apm at 19:17, 5 July 2021

Apm at 19:17, 5 July 2021

Apm: basic version of page

Apm: /* Related / added links to Structural DNA nanotechnology & * De-novo protein engineering