http://blogs.sciencemag.org/pipeline/archives/2017/09/25/building-our-own-molecular-machines

Standard solution-phase reactions based on reactivities of different sites in molecules, and don't offer control of relative positioning, other than by statistical mechanics.

Stereotactic chemical reactions use molecular/supramolecular components to guide the relative positioning of reactive components.

It has been demonstrated using tip-based methods to juxtapose reactive molecules, or to remove hydrogen from hydrogen-passivated silicon (111) surfaces.

Ribosomes are natural examples.

Method by Turberfield et al uses molecular motors to guide reactive monomers to make polymers with controlled sequence. Very slow for bulk production, but maybe good for research..

Nano 3D printer scheme for APM.

Talk at Martin School on Jan 2016

Other talk by John Randall

Talk by Merkle. Mechanosynthesis, etc.

Structural DNA nanotechnology for APM:

Mechanical design of DNA nanostructures "As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. "

Direct Design of an Energy Landscape with Bistable DNA Origami Mechanisms "Recently we have demonstrated the possibility of implementing macroscopic engineering design approaches to construct DNA origami mechanisms (DOM) with programmable motion and tunable flexibility. "

Artificial molecular machines. Large collection of molecular machines, from the fruitful field of supramolecular chemistry, mainly. See book "molecular machines" by Ross Kelly.

Artificial molecular machines (2000) Artificial molecular-level machines.

Light powered molecular machines.

Computational Design of a Family of Light-Driven Rotary Molecular Motors with Improved Quantum Efficiency.

http://nextbigfuture.com/2011/03/philip-moriarty-discusses.html

http://www.softmachines.org/wordpress/?p=205

http://www.nottingham.ac.uk/~ppzstm/research.php

http://www.molecularassembler.com/Nanofactory/

http://cofes.com/ADMIN-STUFF/Video/Video-Player/VideoId/489/Mark-Sims-Industry-Update-On-Design-Tools-For-The-Nano-Scale.aspx

More molecular machines

More animated simulations from NanoEngineer here

Source

Atomistic Design and Simulations of Nanoscale Machines and Assembly

http://www.wag.caltech.edu/gallery/gallery_nanotec.html

https://www.cgl.ucsf.edu/chimera/data/smart-team-jan2009/smart.html

http://www.imm.org/research/parts/

Chimera molecular modelling software system. Nice

See Computational chemistry

https://www.cgl.ucsf.edu/chimera/data/smart-team-jan2009/smart.html

Diamond mechanosynthesis: http://www.molecularassembler.com/

Some examples from Nature

Books:

"Nanosystems" by Eric Drexler (1992)

"molecular machines" by Ross Kelly (2005)

"Nanoelectronics and Nanosystems" Karl Goser et al. (2004)