2018 - I should have more time to post

Great,
IMO one of the most advanced and interesting things that are currently going on
are the SW projects of Christian Schafmeister.
Here's a presentation:

Then there also is:
http://cadnano.org/
Which I haven't yet looked into.

As for "Nanoengineer-1", AFAIK it has been abandoned by the original developers.
Eric Drexler somewhere did mention a few details about the exact reasons (can't find it right away).
I think the development ran into a dead end probably due to a combination of
* unready SW technology (especially GUI side) and
* technical debt

We really need functional reactive programming (FRP).
As far as I can see this is the only way to cleanly separate logic from interface
and have GUI programs composable instead of wheel-reinvent throwaway.
(That would change orders of magnitude in productivity.)

NE-1 was picked up by Bruce Allen ***
http://moleculardynamicsstudio.blogspot.com/

But:
* I think this might now go in a bit different direction. Straying away from APM.
It seems the focus went more to highly accurate predictions for research than for
robust feature rich development & exploratory engineering.
* NE1 is a conglomerate of deeply imperative base libraries => I'd wish for pure FRP wrappers. -- But that is not a goal.

----

Nov. 2016 I had some mail traffic with Tom Moore ( http://machine-phase.blogspot.co.at/ )
about APM related SW in general, installing NE-1 on Ubuntu, and what I would concretely wish for in particular.
Here's a crop-out of what I wrote:

"In the long run I want to see detail mipmapping, seamless zoom-out to bulk limit approximation,
black box subsystems with physical geometry and logistic IO parameters (lazy deferrable!).
And maybe polar logarithmic multi-scale view: ..."

I think system level focus this is not really where *** is going.

I also noted the major point that auto-equilibration is not scalable in NE-1 (major weak point)
and pondered about the internal implementation and ways to improve this.
Gotta look into the equilibration source-code sometime.

----

"A couple of months in the laboratory can frequently save a couple of hours in the library."
What a funny reverse formulation.
It's about avoiding the tedious rediscovering of unknown knowns.

But that sometimes works in reverse just as well.
"A couple of months in the library can frequently save a couple of hours in the laboratory."
Then it's about avoiding the tedious reconfirming of known unknowns.

----

Other things coming to mind regarding molecular modelling software: nanohive, boinc, ...
& the preparation for colour 3D printing of models I have done but with which's process I'm not very happy with yet.

Jim Logajan – How are you doing?

I'm helping with a direct path startup ATM (Machine Phase Systems).

Recently more people are talking about APM again. Both direct- and incremental-path.

But that all happened on Twitter (now X-platform, Elons "global town square").

I was quite surprised about the progress with CO molecule wielding qPlus sensor based nc-AFM

on nanographene structures like graphene nanoribbons (GNRs).

And especially surprised that (under certain conditions)
high (higher than the picked up CO molecule) 3D structures
could be subatomically imaged despite high inertia of macroscale drive and only vertical force detection.
This amazing paper changes everything:

2018 – Assigning the absolute configuration of single aliphatic molecules by visual inspection

OA https://www.nature.com/articles/s41467-018-04843-z

This is just scanning though where the forces are very weak. Weak enough to not even
drag a vdW bonded four-cage-nanodiamond (tetramantane) on top of smooth unreactive gold to the side.

Challenge is getting the benefits of this adapter molecule method working for much higher forces in manipulations.
And extend it to indirect pickups. Pick up atoms (H capped) with a formerly picked up tool molecule.
Pick-up and drop-down. Thermodynamic cascade or something less energetically downhill for
more path dependent control (error repairs).

A path towards prototyping of early primitive mechanosynthesis.
May become useful for inclusion in incremental path bootstrapping phase systems too perhaps.

"… found a startup by that name founded by Mark Friedenbach and Aru Hill. I presume that is who you mean?"
Yes, this one.

"Looks like the use of the CO tip was worked out and published back in 2009."
This paper is I think the first (and still only one) where they went seriously high up in 3D and still achieved subatomic resolution.
It is what convinced me that there might be a fighting chance now to get some early primitive mechanosyntehsis prototyping working.
That beside an explosion of papers on subatomically resolved
atomically (semi)precise graphene nanoribbons (after the CO technique emerged).
These miraculous things:
– Wikipedia: https://en.wikipedia.org/wiki/Graphene_nanoribbon
– DDG image seach: https://duckduckgo.com/?q=nc-A…ages&iax=images&ia=images
– google image search

Also there was some relevant progress on the incremental path side. Highlights being …
– de-novo protein foldamer tech catching up to 3D structural DNA nanotech and
– 3D structural nanotech having what I call general "termination control" semonstated on the second hirarchical selfassembly level.
Two papers on that I gotta post here later. TODO

X-platform is IMO on a downhill ensittification spiral. As is the fate of all closed platforms eventually.

But still there's quiet a bit of action recently by young next generation APM pursuing people going on there.
Younger next gen:

– https://x.com/jacobrintamaki

– https://x.com/philipturnerar
– https://x.com/DavidListerYT
So If you wanna engage with the young folks then you may wanna consider an account.
Older gen:
– https://x.com/MarkFriedenbach
– https://x.com/machinesynth (wants to remain pseudonym)

– https://twitter.com/somewhereville (Damian Allis)
– https://x.com/mooreth42 (Tom Moore)
– https://x.com/perrymetzger

– https://x.com/AdamMarblestone

And of course (almost forgot) me:
– https://x.com/mechadense (Lukas M. Süss)

I've recently made a Bluesky account (an open network rather than a closed platform)
– https://bsky.app/profile/mechadense.bsky.social
… in order to build a new place before the old one burns down.
Mostly computer science and future of coding community over there as of yet.
And obviously redecentralization community.
But I started making an APM feed:
– https://bsky.app/profile/did:p…wtsxax/feed/aaagguows5omi

Also Mark Friedenbach works on a software for APM (direct path focused) called AtomCAD.
Posted an invite link to associated discord in an another channel here.
I suggested this place here sci-nanotech.com for general discussions that
is: involving foldamer tech too, but …

There is this generation rift where people wanna use discord instead of old style forums.
I personally rather dislike discord as it is closed and not indexed by public search engines,
(and 💩s on linux users), but one needs to go where the people are 🤷

Jim Logajan – you may perhaps know Perry Metzger
he sad he might want to set up a (general focus) APM discord.
– https://x.com/perrymetzger
·

Also there's some new criticism that needs some better understanding/rebuttal eventually:

– https://muireall.space/pdf/con…#cite.0@mason_phonon_1960