Difference between revisions of "Sloppy finger problem"

Revision as of 22:55, 21 November 2021

Gemstone based tool-tips

It turned out that the elasticity of the tool-tips can, by choice of sturdy bulky geometry,
be sufficiently far decreased that thermal vibrations at room temperature
are not too big to make sufficiently reliable piezochemical mechanosynthesis impossible.
Even more so in case active cooling is applied.

Proteins

Floppy fingers enforce fat fingers. Stiff fingers (e.g. red spiroligomers) allow thinner fingers. But such stiffer fingers are still hard to make and spacially arrange (2021).

(1) Side-chains on proteins (dark blue shown, light blue indicated) are floppy.
For side-chains to assume a certain pose (=position and orientation)
due to their unconstrained sloppiness when standing alone,
they must be packed tightly between neighboring side-chains.

Since one side-chain cannot hold its pose on its own it is per our definition not a "finger" on it's own.
Backbones of proteins (black; head on viewed spirals) can be optimized for stiffness by de-novo protein design.
Enough side-chains on a section of stiff backbone can make a true standalone "finger".
That is: Changes in one finger do barely influence other fingers as it needs to be for our definition of a "finger".
But such separable fingers (two red dashed boxes) are way too fat to reach down to one and the same moiety on a molecule.

(2) Locally stiff molecules like spiroligomers (small solid red rectangles) can make
small independent fingers that have better chances to reach down to one and the same moiety on
a molecule while still staying independently adjustable. They are independent "fingers".
But placing these stiffer molecules in a finely adjustable way is likely not easily achievable. In fact this has not been done as of 2021.

A perhaps fruitful approach for a solution:
Integrating stiffer less scalable spiroligomers (2) in less stiff but more scalable proteins (1).
This may combine the best parts of both and solve both problems.