Effective concentration - Revision history

Apm at 16:12, 29 March 2026

2026-03-29T16:12:34Z

← Older revision		Revision as of 18:12, 29 March 2026
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	* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]		* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]

			[[category:Incremental path]]

Apm: /* Related / added Piezochemical mechanosynthesis

2021-07-05T12:39:17Z

Related: added * Piezochemical mechanosynthesis

← Older revision		Revision as of 14:39, 5 July 2021
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	* [[Machine phase]]		* [[Machine phase]]
	* '''[[Lattice scaled stiffness]]''' – can locally concentrate effective concentration and deplete it around – factor in avoiding atom placement errors		* '''[[Lattice scaled stiffness]]''' – can locally concentrate effective concentration and deplete it around – factor in avoiding atom placement errors
			* [[Piezochemical mechanosynthesis]]

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

	* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]		* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]

Apm: /* Related */

2021-07-05T12:38:18Z

← Older revision		Revision as of 14:38, 5 July 2021
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	* [[Activity]]		* [[Activity]]
	* [[Machine phase]]		* [[Machine phase]]
	* '''[[Lattice scaled stiffness]]''' – factor in avoiding atom placement errors		* '''[[Lattice scaled stiffness]]''' – can locally concentrate effective concentration and deplete it around – factor in avoiding atom placement errors

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

	* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]		* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]

Apm: /* External links */

2021-07-05T12:35:16Z

External links

← Older revision		Revision as of 14:35, 5 July 2021
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	== External links ==		== External links ==

	* [[https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]]		* [https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]

Apm: /* Related / added '''Lattice scaled stiffness'''

2021-07-05T12:35:04Z

Related: added * '''Lattice scaled stiffness'''

← Older revision		Revision as of 14:35, 5 July 2021
Line 63:		Line 63:
	* [[Activity]]		* [[Activity]]
	* [[Machine phase]]		* [[Machine phase]]
			* '''[[Lattice scaled stiffness]]''' – factor in avoiding atom placement errors

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

	* [[https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]]		* [[https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]]

Apm: /* Effective concentration in piezosynthesis */

2021-07-05T11:29:46Z

Effective concentration in piezosynthesis

← Older revision		Revision as of 13:29, 5 July 2021
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	Once motion is fully constraint (down to acceptable levels of thermal vibration amplitudes), <br>		Once motion is fully constraint (down to acceptable levels of thermal vibration amplitudes), <br>
	high forces, torques, and bending moments ([[like present in [[piezosynthesis]]) can further increase reaction rates.		high forces, torques, and bending moments (like present in [[piezosynthesis]]) can further increase reaction rates.

	While the math for effective-concentration makes less intuitive sense it cans till be applied.		While the math for effective-concentration makes less intuitive sense it cans till be applied.

Apm: basic page

2021-07-05T11:29:24Z

basic page

New page

{{stub}}

Effective concentration (activity):

Spatially constraining the motion of two chemical reaction partners increases their mutual encounter rate induced by thermal [[diffusion transport]]. 
"Encounter rate" means how often the potential reaction partners bump into each other per unit of time. 
Given a certain chance of reaction per bump, one can get an average time for a reaction to occur. 

An increase of encounter rate (to boost a desired reaction) can be achieved via various ways:
* Restriction to [[diffusion transport]] on 2D-surfaces rather than in fully open 3D space
* Restriction of [[diffusion transport]] to a finite sub-volume of fully open 3D space - (aka compartmentalization)
* Restriction of [[diffusion transport]] by limiting the range-of-motion via a semi-stiff-background-framework (like the folded up backbone of an [[enzyme]]).
* Restriction to [[diffusion transport]] by tying reactants onto the tip of tethers that are anchored nearby to each other

== Effective concentration in piezosynthesis ==

Once motion is fully constraint (down to acceptable levels of thermal vibration amplitudes), 
high forces, torques, and bending moments ([[like present in [[piezosynthesis]]) can further increase reaction rates.

While the math for effective-concentration makes less intuitive sense it cans till be applied.

Some reactions that need many many bumps per reaction to occur 
can be made to occur on pretty much every single encounter. 
One instead gets error rates as a result of the math. 
[[Piezochemical mechanosynthesis]] should allow for placement error rates as low as 10-15 
Source: [[Nanosystems]] (from memory - to check if correct)

== Activity vs specificity & how to break preservation of misery ... ==

In [[thermally driven self assembly]] there is always a fight/compromise between activity an specificity.

What one desires is an "orthogonal set of interfaces". 
That is some set of interfaces where
* some combinations clearly bind to each other and
* some other combinations clearly do not bind to each other.

This design goal can be hard to achieve in say (intentionally brick-like) [[de-novo protein]] design. 
An intended change in activity can easily cause an unintended change in specficity (and vice versa). 
With the additional complication that too much change of the (side chains for the) interfaces can 
mess up the rigid backbone given "base structure" of the intentionally brick-like de-novo proteins.

Sidenote: 
Sometimes one actually wants to make binding strength intentionally weak in order to avoid some kinds of [[kinetic traps]]. 
That is in order to let falsely assembled combinations disassemble again.

=== How to get to ultra high specivicity and ultra high activity at the same time ===

The strategy needed is basically an iterative improvement of [[separation of concerns]] by aiming at
* [[stiffness]] and
* [[controllaby terminating self assembly]].

Given the positional constraint in [[mechanosynthesis]] unintended reactions to sites that the guidance prevents form being encountered can be excluded. 
Effect of application of forces? ...

Of course there's a bit of a chicken and egg problem here. 
See:
* [[Expanding the catalytic loop]]
* ([[Bootstrapping]], [[Bridging the gaps]])

== Related ==

* [[Specifity]]
* [[Activity]]
* [[Machine phase]]

== External links ==

* [[https://en.wikipedia.org/wiki/Thermodynamic_activity Thermodynamic activity]]