Present-forward development - Revision history

Apm: /* Related / Present-forward Future-backward overlap

2023-07-21T16:41:44Z

← Older revision		Revision as of 18:41, 21 July 2023
Line 255:		Line 255:
	* R&D in constructive/additive use of [[Scanning probe microscopy]]		* R&D in constructive/additive use of [[Scanning probe microscopy]]
	* [[Funding contexts and their degree of viability]]		* [[Funding contexts and their degree of viability]]
			* [[Present-forward Future-backward overlap]]

Apm: crude addition - needs improvement - or split-off to own page

2021-03-15T23:25:54Z

crude addition - needs improvement - or split-off to own page

@@ Line 174: / Line 174: @@
 {{wikitodo|add details here}}
 = Related =
@@ Line 180: / Line 254: @@
 * [[Foldamer R&D]]
 * R&D in constructive/additive use of [[Scanning probe microscopy]]

Apm: changed headline hierarchy - prep for adding more top level topics

2021-03-15T09:43:47Z

changed headline hierarchy - prep for adding more top level topics

← Older revision		Revision as of 11:43, 15 March 2021
Line 13:		Line 13:
	* Integrating the learned mechanosynthetic capabilities into the learned foldamer capabilities (likely in solvent first)		* Integrating the learned mechanosynthetic capabilities into the learned foldamer capabilities (likely in solvent first)

			= Areas =

	= Foldamer Technology =		== Foldamer Technology ==

	'''Needed is:'''		'''Needed is:'''
Line 42:		Line 43:
	Or one of the stiffer technologies unexpectedly starts scaling better.		Or one of the stiffer technologies unexpectedly starts scaling better.

	== Low stiffness foldamer technologies ==		=== Low stiffness foldamer technologies ===

	Of main interest here may be the Structural DNA nanotechnologies (SDN). <br>		Of main interest here may be the Structural DNA nanotechnologies (SDN). <br>
Line 82:		Line 83:
	{{wikitodo\|add a sketch of that idea here}} <br>		{{wikitodo\|add a sketch of that idea here}} <br>

	== Mid stiffness foldamer technologies ==		=== Mid stiffness foldamer technologies ===

	'''Of main interest here may be de-novo protein engineering.''' <br>		'''Of main interest here may be de-novo protein engineering.''' <br>
Line 90:		Line 91:
	* their higher folding predictability		* their higher folding predictability

	== High stiffness foldamer technologies ==		=== High stiffness foldamer technologies ===

	'''One promising candidate here may be Spiroligomers.''' <br>		'''One promising candidate here may be Spiroligomers.''' <br>
Line 115:		Line 116:
	(Note that this is somewhat speculative. The author has never worked with Spiroligomers.)		(Note that this is somewhat speculative. The author has never worked with Spiroligomers.)

	= Fat fingers =		== Fat fingers ==

	Here's a motivational/economic problem:		Here's a motivational/economic problem:
Line 127:		Line 128:
	* … is a problem for near term applications - elaboration follows		* … is a problem for near term applications - elaboration follows

	== spacing caused by pushing for modularization ==		=== spacing caused by pushing for modularization ===

	Take a typical proteins(enzymes) active site (the pocket where molecules get bound and manipulated).		Take a typical proteins(enzymes) active site (the pocket where molecules get bound and manipulated).
Line 146:		Line 147:
	* …		* …

	== Effects of very big spacing through foldamer in foldamer insets (pushing for stiffness) ==		=== Effects of very big spacing through foldamer in foldamer insets (pushing for stiffness) ===

	Really far apart spacing like in the case of the proposed foldamer in foldamer insert also comes with another effect.		Really far apart spacing like in the case of the proposed foldamer in foldamer insert also comes with another effect.
Line 158:		Line 159:
	See [[Mechanochemistry]]		See [[Mechanochemistry]]

	== Loss of combinatorial power while gains are not yet harvest-able ==		=== Loss of combinatorial power while gains are not yet harvest-able ===

	The capability of easily trying a huge number of random mutations is a powerful tool for many of today's medical applications.		The capability of easily trying a huge number of random mutations is a powerful tool for many of today's medical applications.
Line 168:		Line 169:
	The fingers that are now spaced apart much more become unable to collaborate in huge number on the same local section of a small molecule. So the power for near term application in this regard is lost.		The fingers that are now spaced apart much more become unable to collaborate in huge number on the same local section of a small molecule. So the power for near term application in this regard is lost.

	= Experimentally accessible very early forms of force applying mechanosynthesis =		== Experimentally accessible very early forms of force applying mechanosynthesis ==

	This has been done on silicon.		This has been done on silicon.
	{{wikitodo\|add details here}}		{{wikitodo\|add details here}}



	= Related =		= Related =

Apm: removed the papers section again since moved to page Foldamer R&D

2021-03-13T11:35:49Z

removed the papers section again since moved to page Foldamer R&D

@@ Line 172: / Line 172: @@
 This has been done on silicon.
 {{wikitodo|add details here}}
 = Related =

Apm: added related section

2021-03-13T11:29:12Z

added related section

← Older revision		Revision as of 13:29, 13 March 2021
Line 209:		Line 209:
	* Weblink (walled access): http://science.sciencemag.org/content/348/6241/1365.figures-only		* Weblink (walled access): http://science.sciencemag.org/content/348/6241/1365.figures-only
	* Open: https://cryoem.ucla.edu/uploads/image/pdfs/2015_gonen.pdf		* Open: https://cryoem.ucla.edu/uploads/image/pdfs/2015_gonen.pdf

			= Related =

			* [[Foldamer R&D]]
			* R&D in constructive/additive use of [[Scanning probe microscopy]]

Apm: added list of relevant seeming papers

2021-03-13T11:26:28Z

added list of relevant seeming papers

@@ Line 167: / Line 167: @@
 This in turn requires spreading out the fingers.
 The fingers that are now spaced apart much more become unable to collaborate in huge number on the same local section of a small molecule. So the power for near term application in this regard is lost.
 = Experimentally accessible very early forms of force applying mechanosynthesis =
@@ Line 173: / Line 172: @@
 This has been done on silicon.
 {{wikitodo|add details here}}

Apm: added link to: page Structural DNA nanotechnology

2021-03-12T16:59:33Z

added link to: page Structural DNA nanotechnology

← Older revision		Revision as of 18:59, 12 March 2021
Line 2:		Line 2:
	Complementary: [[Future-backward development]]		Complementary: [[Future-backward development]]

	Here counting to "~~present~~-forward development" will be everything that is already investigatable by		Here counting to "future-forward development" will be everything that is already investigatable by
	experimental means that are accessible today (more or less widely/costly).		experimental means that are accessible today (more or less widely/costly).

Line 46:		Line 46:
	Of main interest here may be the Structural DNA nanotechnologies (SDN). <br>		Of main interest here may be the Structural DNA nanotechnologies (SDN). <br>
	Especially the DNA-brick kind of SDN. That is: Cuboid blocks from many short DNA oligimer staples.<br>		Especially the DNA-brick kind of SDN. That is: Cuboid blocks from many short DNA oligimer staples.<br>
			Main page: [[Structural DNA nanotechnology]]


	'''Main limitations are:'''		'''Main limitations are:'''

Apm: fixed error: future-forward ==> present-forward

2021-03-12T16:44:24Z

fixed error: future-forward ==> present-forward

← Older revision		Revision as of 18:44, 12 March 2021
Line 2:		Line 2:
	Complementary: [[Future-backward development]]		Complementary: [[Future-backward development]]

	Here counting to "~~future~~-forward development" will be everything that is already investigatable by		Here counting to "present-forward development" will be everything that is already investigatable by
	experimental means that are accessible today (more or less widely/costly).		experimental means that are accessible today (more or less widely/costly).

Apm: added linkt to: Future-backward development

2021-03-12T15:49:42Z

added linkt to: Future-backward development

← Older revision		Revision as of 17:49, 12 March 2021
Line 1:		Line 1:
	~~{{stub}}~~		Up: [[Bridging the gaps]] <br>
			Complementary: [[Future-backward development]]
	[[Bridging the gaps]]

	Here counting to "future-forward development" will be everything that is already investigatable by		Here counting to "future-forward development" will be everything that is already investigatable by

Apm: first version

2021-03-12T15:47:37Z

first version

New page

{{stub}}

[[Bridging the gaps]]

Here counting to "future-forward development" will be everything that is already investigatable by
experimental means that are accessible today (more or less widely/costly).

'''There are basically two fields that need pushing:'''
* Improving on various foldamer technologies (self-assembling and self-folding)
* Prototyping of very early forms of force applying [[mechanosynthesis]]

'''And looking maybe a bit into the future:'''
* Manipulating (and assembling!) self-assembled foldamers bricks with scanning probe tips
* Integrating the learned mechanosynthetic capabilities into the learned foldamer capabilities (likely in solvent first)

= Foldamer Technology =

'''Needed is:'''
* Development of new and
* improvement on existing foldamers technologies

'''With a particular focus on:'''
* [[stiffness]]
* modular reusability
* separation of concerns
* eventual integration of mechanosynthetic aspects (more or less direct)

'''To give concrete targets:''' 

(1) Getting to prismatic or otherwise larger scale highly geometric construction bricks that can be
be connected in a programmable fashion by self assembly.
Or later eventually by guided self assembly or even .... process.

(2) Eventual integration of mechanosynthetic tips for the other development path.

'''There are foldamer technologies with different degrees of stiffness.'''
* Low stiffness (most scaleable it seems)
* mid stiffness
* high stiffness (least scaleable is seems)
It may be possible to combine these (insetting the stiffer in the less stiff ones)
and the fastest progress combining the best of all worlds.
Or one of the stiffer technologies unexpectedly starts scaling better.

== Low stiffness foldamer technologies ==

Of main interest here may be the Structural DNA nanotechnologies (SDN). 
Especially the DNA-brick kind of SDN. That is: Cuboid blocks from many short DNA oligimer staples. 

'''Main limitations are:'''
* not stiff enough for atomically precise placement of anything (with an asterisk).
* programmable attachment points are spaced apart quite far.
* there are pretty big error rates (there is no cell machinery that is helping selfassembly along)
* rapidly dropping yields when going to bigger structure sizes.

'''Main strengths:''' It is the foldamer tech …
* … with the largest number of shape-addressable individual sites in an assembly
* … with the most control beyond infinite translatory or rotatory symmetries

'''The asterisk:'''

Atomically precise placement via SDN actually '''has''' been demonstrated.
But only in a time averaged way. Isn't that completely useless?
Actually not. As known from statistics one can switch out a temporal average for an spacial average.
But how can that be done in an engineering setting?

By integration of a smaller piece of stiffer foldamers (like de-novo proteins) foldamers
into a larger piece of the SDN structure (less stiff foldamers) one can average out spacially over all
interface attachment points.

That is easier said than done tough. In fact this is probably extremely difficult and necessitates great advances
on both involved foldamer technologies. The surrounding and the inserted one.
To have sufficient spacial averaging over thermal vibrations the interface surface needs to be large and stiff enough.

Why not just use the stiffer foldamer technology (e.g. de-novo proteins) to begin with?
Because it may be (and looks like so) that the stiffer foldamer technologies are more difficult to scale to a necessary size, that it is to couple it so a less stiff but more scalable different foldamer technology.

So in summary: 
SDN may be usable as low stiffness very large scale backbone structure for higher stiffness large insets that then do the actual small scale atomically precise holding.

{{wikitodo|add a sketch of that idea here}} 

== Mid stiffness foldamer technologies ==

'''Of main interest here may be de-novo protein engineering.''' 
In particular packed alpha helix bundles and beta sheets are of special interest because of:
* their higher stiffness
* their higher geometry
* their higher folding predictability

== High stiffness foldamer technologies ==

'''One promising candidate here may be Spiroligomers.''' 

These have their individual monomers (base building blocks)
linked together by '''not just one but by two inter-atomic bonds'''.
This prevents free rotation around single sigma-bonds. Thus:

* the structures are likely notably stiffer than proteins.
* there is no folding foldamer folding involved (actually these are not exactly foldamers anymore)
The shape is pretty much uniquely given by sequence of monomers that where linked together.

Limits to increased stiffness:
* intentional bi-stable snap flips or such may be possible to include on purpose.
* long chains might bend a lot to the point of self-entanglement
* side-stacking issues

Side-stacking: Since there is no folding present to archive volumetric structures
it is necessary to stack these spiroligomers sidewards/sideways by some different post processing method.
Final structure stiffness may largely depend on how tight one can stack them sideways.
The higher stiffness along the chain might even be counterproductive here.
That is reduce the sidewards stiffness.

(Note that this is somewhat speculative. The author has never worked with Spiroligomers.)

= Fat fingers =

Here's a motivational/economic problem:

There are two factors that space out the [[thermal motion overpowering holding sites]] stongly:
* separation of concerns by geometric brick modularization
* the afore described approach of stiffer-foldamer in less-stiff foldamer insets

This spacing …
* … is not exactly a problem for far term applications. See [[fat finger problem]]. 
* … is a problem for near term applications - elaboration follows

== spacing caused by pushing for modularization ==

Take a typical proteins(enzymes) active site (the pocket where molecules get bound and manipulated).
When one switches out just one single side-chain "finger" with an other one that has a slightly different shape, then everything else may change with it. Change the shape of one finger slightly and this shape-change propagates to many other (more or less adjacent) ones in highly unpredictable ways.

Through tight packing of the side-chains all the (alone floppy) fingers provide all the other ones mutual support against too big thermal vibrations and against fatal displacements through free rotations.

Changing the structure of "fingers" enough 
(e.g. by switching them out through stiff artificial interlinked side-chains packs or spiroligomer packs), 
such that they can keep their position sufficiently precisely without the need for "mutual support sideward packing" makes them so big/fat that only very few fingers can reach in on specific point on a target molecule.
Certainly not enough to pick out a molecule based on shape.

This is a problem for near term applications. 
This would be a-ok for advanced mechanosynthesis where …
* … molecules to synthesize start out and stay in machine-phase - nothing big and complex needs to be catched from solvent
* … chain polymers can eventually be syntesized by holding them in a "two point stretched out" fashion
* … there is a focus on just a few base simple materials for metamaterials -- and moreover these are crystalline
* …

== Effects of very big spacing through foldamer in foldamer insets (pushing for stiffness) ==

Really far apart spacing like in the case of the proposed foldamer in foldamer insert also comes with another effect.
Whatever these stiff-fingers/tips do they do it slower because there are fewer of them around per fixed volume.

This eventually can be compensated through added active motion and applied mechanical forces like:
* higher reaction success rate nearing one -- instead of like e.g. 1 in 1000 reacts on any given attempt
* increased reaction speeds during the reaction -- if this is was a limiting factor
* increased reloading speed -- this may be limited as long as operations are conducted in a solvent rather than a vacuum

See [[Mechanochemistry]]

== Loss of combinatorial power while gains are not yet harvest-able ==

The capability of easily trying a huge number of random mutations is a powerful tool for many of today's medical applications.
Like e.g. detection of small molecules.

Fighting against conflation of concerns and for modularization for the sake of getting to more advanced forms of APM ASAP
requires stiffening the sidechains/fingers/tips.
This in turn requires spreading out the fingers.
The fingers that are now spaced apart much more become unable to collaborate in huge number on the same local section of a small molecule. So the power for near term application in this regard is lost.

= Experimentally accessible very early forms of force applying mechanosynthesis =

This has been done on silicon.
{{wikitodo|add details here}}