Effective concentration

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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.

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

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.


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