Difference between revisions of "Convergent assembly to hierarchical assembly correspondences"

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Revision as of 09:16, 17 September 2022

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First level

First assembly level in a gemstone metamaterial on chip factory,
See: Assembly level 1

First self-assembly level in SDN:

  • from single stranded DNA
  • to SDN blocks (needs a better name)

More precisely input parts are:

  • DNA oglionucleotides (aka staple strands, aka DNA bricks) and optionally mixed in ...
  • longer viral DNA strands (aka scaffold strands)

The process is mostly self-finding type self-assembly. With scaffold strands there is a bit of crossover to self-folding bringing

First self-assembly level in de-novo protein engineering engineering:
self-folding of the chain of amino acids

  • from primary structure
  • to secondary and tertiary structure

Side-note: secondary structure is often quite stable
Artificial de-novo protein will mostly stick to tertiary structure
that does not reduce stability by a lot.
Anything nearing an intrinsically disordered protein is likely of little systematic engineering interest.

Second level

Second assembly level in a gemstone metamaterial on chip factory,
See: Assembly level 2

Second self-assembly level in SDN:

  • from SDN blocks (needs a better name)
  • to SDN multi block assemblies
  • This is done by changing salt concentrations
  • This assembly step is reversible.
  • SDN Blocks are semi rigid
  • SDN Blocks are made to have shape complementary surfaces
  • SDN Blocks typically have a (slightly twisted) cartesian or hexagonal voxel grid

Second self-assembly level in de-novo protein engineering engineering:
self-finding type of self-assembly

  • from fully folded proteins (secondary and tertiary structure)
  • to multi protein assemblies (quaternary structure)

Side-note: secondary structure is often quite stable Artificial de-novo protein will mostly stick to tertiary structure that does not reduce stability by a lot. Anything nearing an intrinsically disordered protein is likely of little systematic engineering interest.

For both DNA-Blocks and folded-proteins:

  • The process is purely self-finding type self-assembly.
  • Bigger block sizes means smaller diffusion speeds.
  • Stiff blocks mean erroneous assemblies can't zip off again (German saying: "was liegt das pickt")

Third level (and above)

Third assembly level in a gemstone metamaterial on chip factory,
See: Assembly level 3

Both

have not reached this level yet (as of 2022)

Related

External links

Wikipedia:

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