Revision as of 15:09, 9 March 2024

Up: General concept: Convergent assembly

Hierarchical selfassembly (also convergent selfassembly) is the case when
structures get self-assembled from parts that themselves where previously self-assembled.
This implies that hierarchical selfassembly is a subform of iterative self-assembly.
(Iterative self-assembly also covers repeated additions of parts of the same size.)

Note that hierarchical selfassembly is not exclusive to thermally driven self-assembly.
Hierarchical selfassembly is also applicable to:

• non thermally driven self assembly
• positional assembly (See: hierarchical positional assembly).

Experimental demonstrations

As of time of last review (2024-03) hierarchical selfassembly has been …

• … impressively demonstrated with 3D structural DNA nanotechnology.
• … demonstrated with de-novo proteins
  with the large caveat that of missing termination control.

Note that terminating structures like rings or balls is not a form of termination control as defined in this wiki.
Rotation symmetry is an infinite symmetry (just like translation symmetry in a crystal) just that it covers over itself.

Hierarchical selfassembly of 3D structural DNA nanotechnology (3D-SDN)

DNA structures are very soft and mobile thus there is only topological atomic precision present.
But (while merely topological) this already is already real honest to goodness atomically precise LEGO.

At low cryo-temperatures motions may freeze making it more positional atomically precise
Though. 3D-SDN is likely not very compatible with dry conditions in gas or vacuum
likely leading to massive deformations or even fall-apart.

Even individual cryo-frozen water molecules have been imaged by now with stiff cantilever AFM)
3D SDN structures are (just as DNA) not subatomically resolvable with scanning probe microscopy.

Termination control at the second assembly level

(wiki-TODO: Add reference to paper demosntrating that.)

Voxels at the second self-assembly level

Images from paper: "Finite Assembly of Three‐Dimensional DNA Hierarchical Nanoarchitectures through Orthogonal and Directional Bonding" (click image for sources)

First level of self-assembly is self folding of the staples strands (short DNA oligomers) to the hexagonal building blocks. Not shown.
Second level of self-assembly is self finding of the hexagonal building blocks. Shown.
Here this goes one step further in attempting to make a sandard set of blocks for the second assembly level such that arbitrary larger structures can be built quickly and easily. Custom blocks may be more versatile but are one off solutions for specific desireed geometeries. You get individually controllable voxels at the second self-assembly-level too.

Hierarchical selfassembly with de-novo proteins

Second assembly level without termination control

First level of self-assembly is self folding of the polypeptide chain.
That might happen right after protein expression.

The big caveat and still present obstacle to overcome here with proteins is absence of termination control.
(wiki-TODO: Add the paper(s) about non-terminating de-novo protein walls.)
Done't be fooled by the beauty of scale and symmetry of de-novo protein structures that already can't be made.
The difficult part is breaking the symmetry in near arbitrary ways. Like individually controllable voxels.

Related

• Selfassembly level in self assembly
• complementary is: hierarchical positional assembly here
  covered by page convergent assembly & assembly level in positional assembly

• iterative self-assembly

• termination control
• (topological atomic precision)