Molecular Manufacturing

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Molecular Manufacturing is the construction of atomically-precise macroscale products. It does not require the manufacturing process to be computer-controlled at every step or to handle atoms individually, nor does it require the chemical processes to be limited to mechanosynthesis; only the finished product must be machine-phase.

A tabletop nanofactory based on exponential assembly.

Molecular Manufacturing is often used a synonym of Molecular Nanotechnology, the vision of nanotechnology started by Eric Drexler and further explored by Ralph Merkle, Robert Freitas and Zyvex. While Molecular Nanotechnology is centered around a variety of (Diamond-based) molecular machines, from the Drexler Arm (A setting in which one of these builds a copy of itself is pictured below) to the Respirocyte to the Neon Pump, manufacturing is a more global process, that concerns itself with such machines and with more global objectives, such as cheap, distributed manufacturing technologies, which is why 'molecular manufacturing' is the preferred name for this article.

Scales of the Universe
Prefix Value Name
exa- 1018m 1,000,000,000,000,000,000 quintillion
peta- 1015m 1,000,000,000,000,000 quadrillion
tera- 1012m 1,000,000,000,000 trillion
giga- 109m 1,000,000,000 billion
mega- 106m 1,000,000 million
kilo- 103m 1,000 thousand
milli- 10-3m 1/1,000 thousandth
micro- 10-8m 1/1,000,000 millionth
nano- 10-9m 1/1,000,000,000 billionth
pico- 10-12m 1/1,000,000,000,000 trillionth
femto- 10-15m 1/1,000,000,000,000,000 quadrillionth
atto- 10-18m 1/1,000,000,000,000,000,000 quintillionth

Nanotechnology, in general, is the art of building practical, complex machinery with sizes varying from 100 to 1 nanometers. Nanoscience and nanotechnology are new names for the gradually, naturally extended discipline of chemistry; and so nanoscience should not be confused with the much more specific field of Molecular Nanotechnology. The machines and processes shown in this article are not filling journals or being made daily in laboratories.

How small are atoms really? Kenneth Ford says,

"To arrive at the number of atoms in a cubic centimeter of water (a few drops), first cover the earth with airports, one against the other. Then go up a mile or so and build another solid layer of airports. Do this 100 million times. The last layer will have reached out to the sun and will contain some 1016 airports (ten million billion). The number of atoms in a few drops of water will be the number of airports filling up this substantial part of the solar system. If the airport construction rate were one million each second, the job could just have been finished in the known lifetime of the universe (something over ten billion years)."[1]


The origins of nanotechnology, whether 'normal nanotechnology' or Molecular Nanotechnology, are often linked to Richard Feynman's historic 1959 lecture, There's Plenty of Room at the Bottom, but the origins can be traced further back. Colin Milburn in his book Nanovision, for example, correctly argues that Feynman 'merely' articulated existing ideas in the science fiction of the time.

Feynman's path to nanotechnology consisted on having remotely controlled arms building smaller ones, successively until the nanoscale. The closest parallel to this idea is Robert Heinlein's 1942 Waldo, in which a homonymous robot does this until its copies are small enough to perform sub-cellular surgery[2]. A coworker at Caltech's JPL, Al Hibbs, had read the story and even filed a patent application for the use of waldoes in space exploration. He talked it over with Feynman and 'delighted' him with the notion of miniature surgical robots.[3]

File:Bush and Von Ehr.jpg
James von Ehr was invited to the Oval Office as President Bush signed the 21st Century Nanotechnology Research and Development Act, on December 3, 2003; officially starting the National Nanotechnology Initiative.

Mechanosynthesis of Diamondoid

Mechanosynthesis is the synthesis of chemical structures catalyzed by mechanical pressure and constraints, or, simply, the use of mechanical force to direct and alter the course of chemical reactions. For example, the animations to the left show a reversible mechanosynthethic reaction in which an acetylene dimer is placed on a diamond C(100) surface and then removed, using an atomic force microscope with a special tip geometry.

Mechanosynthesis of diamond, specifically, is the synthesis through this mechanical chemistry of diamond, a stiff polycyclic structure.

The evidence for mechanosynthesis can be traced back to the historic 1989 spelling of the IBM logo using 35 Xenon atoms in a surface of Nickel by Don Eigler and Erhard K. Schweizer. However, this experiment took place a few degrees above absolute zero, and no covalent bonds were formed.

In 2003, Oyabu et al.[4] first demonstrated mechanosynthesis on a Silicon surface using an atomic force microscope to remove an atom from the surface, then place it again on the same position, again at liquid helium temperatures.

File:Mechanosynthesis of Si.gif
'Si' spelt on a Silicon surface using mechanosynthesis
Mechanosynthethic Reactions
File:Drexler Arm assembly line.jpg
A Drexler Arm in an assembly line configuration.

Minimal Toolset for Positional Diamond Mechanosynthesis

The landmark paper by Ralph Merkle and Robert Freitas, published in 2008 by the Journal of Computational and Theoretical Nanoscience, shows a minimal set of tools that can be used to synthesize unstrained diamond of arbitrary size, and also synthesize copies of itself. Each tooltip is designed to work on a flat surface of (Initially) Hydrogen-terminated diamond and can be moved attached to a Scanning Probe Microscope to control their motion. Bootstrap strategies -- Through which ordinary tools are used to produce the simplest tips, which are then used to produce the rest of the set -- are provided, along with reaction sequences for the construction of diamond and fullerene.

The paper is: Robert A. Freitas Jr., Ralph C. Merkle, "A Minimal Toolset for Positional Diamond Mechanosynthesis," J. Comput. Theor. Nanosci. 5(May 2008):760-861; and is available here.


File:Mechanosynthesis of fullerene.jpg
Mechanosynthesis of an atomically-precise nanotube

The rapid, atomically-precise construction of macroscale objects of varied molecular structures is the eventual goal of molecular nanotechnology. The paper presents the more modest and specific objective of ultra-high-vacuum-based diamondoid mechanosynthesis using the positional control granted by an Scanning Probe Microscope.

Following the 1992 publication of Drexler's Nanosystems, in which some basic mechanosynthethic reaction pathways and sketches of possible tooltips, in 1997 Merkle outlined the "hydrocarbon metabolism", a set of reaction pathways for DMS, which used nine different tooltips and several intermediate tooltips, some of which were not defined entirely, and used at least six different elements and one unspecified transition metal, and yet another unspecified "vitamin molecule" possibly requiring additional elements. Moreover, most reaction sequences were not completely specified and reaction closure was not 100%. It did not specify how the toolset may be constructed or what handle structures may have been required.

The Minimal Toolset paper proposes a 100% process closure which can be achieved using a minimal set of tools for mechanosynthesis, consisting of three primary tools: Hydrogen Abstraction (HAbst), Hydrogen Donation (HDon), and Dimer Placement (DimerP). These are assisted by six auxiliary tools, the discharged versions of Hydrogen Abstraction (AdamRad) and Hydrogen Donation (GeRad), and intermediate structures: Methylene (Meth), Germylmethylene (GM), and Germylene (Germ). And finally, a Hydrogen Transfer tool that is a compound form of the HAbst and GeRad tools.


Tool Fabrication





Ethylation, Propylation, and Related Reactions

Hydrocarbon Chains

Molecular Assembler

Patterned Atomic Layer Epitaxy

Patterned Atomic Layer Epitaxy (PALE) consists of using a Scanning Tunneling Microscope on a Hydrogen-terminated Silicon surface to remove individual Hydroge atoms. A variety of cases can be injected into the chamber, where they deposit on the depassivated area of the surface. Silylene (SiH2), in particular, will deposit and add a new layer to the crystal on the depassivated site.

Vertical growth is simple to achieve, but 3D, moving objects can be built using the same method: Grow a bed of Germanium, then grow the Silicon structures on top, and etch away the Ge to remove the structures and machines.

Epitaxial Assembler

Atom Holography

Biological Nanomanufacturing

Artificial Ribosomes

DNA Origami




Foresight Institute



  • Mechanosynthesis
  • PALE
  • Nanomechanical Molecular Machinery


Richard Smalley

Richard Jones

George Whitesides


The opening quote,

Drexler’s thesis is merely the source of the disease. What I’m really sick of are ding dongs trying to tell me toothpaste or golf balls is nanotech.

is actually correct, since it was Drexler who first started the hype with Engines of Creation, a book that later proved to be much more abstract and fantastic than his more down-to-Earth work on the chemistry of mechanosynthesis. It is true that Drexler's thesis is the 'source of the disease', for his ideas where bandwagoned from the start. The second sentence is something we can all share.

The idea was first postulated by Richard Feynman and popularised by the work of science fiction that Eric Drexler used as a Ph.D. thesis. Nanotechnology fanboys — as opposed to the people who actually work with the stuff — have a habit of downplaying Feynman's origination of the idea and playing up Drexler, possibly because the latter is far more indulgent of their fantasies.

The first part needs a correction: Drexler's thesis is okay, it's Engines that's the problem. Compare the predictions he makes in Engines to the machines he discusses in Nanosystems, and you'll see a large gradient between the fantasy of the nano-future and the actual simulations and calculations.

The rest is just all ad-hominem so there really isn't much to disprove. Drexler's thesis is available online, and I have yet to see someone find an error in Nanosystems, besides the diamond surface friction calculations which came from simple scaling law analysis (With considerations for the nanoscale). The individual, atomically-precise machines (The small bearing, the planetary gear) were 'validated' by molecular dynamics. Validated in quotes because force fields are cool and all but it is improper to use anything less than quantum chemistry as proof of.

In the woo world (i.e., science fiction), nanomachines will be able to repair a body from almost complete mush into a fully functioning human.

Reviving cryonics patients through nanotechnology is one aspect of Freitas' work on nanomedicine that may not be feasible. Cells, unlike ordinary machines, do not shatter into discrete components that can be glued together, and it may be overkill to use nanomechanical arms to repair cells, a process which will quite probably be easier to achieve through biological means. They refer to the state of cryopreserved patients as 'mush', which shows they really are just trendy pseudo-skeptics: Cryonics works. As for revival, see the relevant section.

The popular conception of nanotechnology is K. Eric Drexler's concept of nanobots, like industrial robots scaled down a billion times. This is entirely made of bollocks and would violate physics, chemistry, and thermodynamics.

All Drexler talked about were nanoscale robot arms.

As for violations of physics, chemistry and thermo: The last item refers, probably, to the idea that a 'self-replicating nanobot' (A term created by the nonsensical bandwagon that spawned from Engines of Creation) would essentially burn due to the waste heat of rapid self-replication. Though nobody has actually done the math I bet it would be a problem. Thankfully, Drexler's vision of nanotechnology is not about self-replicating nanobots, so we can skip that.

As for chemistry, well, we'll probably be hearing Richard Smalley's arguments against molecular manufacturing, so I'll just let Ralph Merkle refute those.

Now, notice the sources of the statement: The first is an article by Richard Jones, a critic of Drexler's vision of nanotechnology (Who's still cool though). However, he has said that he does not think it's impossible, and he says, answering the question "Does Nanosystems contain obvious errors that can quickly be shown to invalidate it?"

He replies: "No. It’s a carefully written book that reflects well the state of science in relevant fields at the time of writing. Drexler’s proposals for radical nanotechnology do not obviously break physical laws. There are difficulties, though, of two types. Firstly, in many cases, Drexler used the best tools available at the time of writing, and makes plausible estimates in the face of considerable uncertainty. Since then, though, nanoscale science has considerably advanced and in some places the picture needs to be revised. Secondly, many proposals in Nanosystems are not fully worked out, and many vital components and mechanisms remain at the level of “black boxes”." For a shorter explanation, he does not think it's impossible, merely pushing against the grain, and in this we can all sort of agree. The second link is a blog that repeats essentially the whole thing. The only technical point that is correcet is that Drexler's machines '[look] rather like a meter-scale object', which is related to Jones' earlier point.



  • Needs:
    • Efficiency
      • Anything above 10,000 makes rotating/translating slow as fuck
      • the diamond creation screen is slow as fuck as well
      • port it from python to some other language
    • Up-to-date libraries and installation instructions
    • More molecular machine parts for the parts library
  • Provides:
    • Fast design of molecular machine parts
    • Might lead to the equivalent of .stl files for the nanoscale

Freitas Process

  • Summary
  • Needs:
    • an AFM
    • a UHV chamber
    • loads of cash
    • CVD equipment
  • Provides:
    • Experimental evidence for mechanosynthesis
    • A basic tool for the construction of some simple molecular features and patterning of surfaces


  • Currently it's looking for feasible than direct-to-diamondoid for the production of dry nanomachines
  • Needs:
    • a UHV chamber
    • an STM
  • Provides:
    • Experimental validation for the ideas of mol nano
    • A rapid, easy-to-parallelize tool for the construction of some nanoscale (And even macroscale machines)
      • You could synthesize some incredibly precise NEMS and MEMS wheels on a bed of Germanium which is etched away, allowing you to push them together with an AFM or similar

General Audience

Engines of Creation: The Coming Era of Nanotechnology by [[Eric Drexler]], 1986
By the 'father' of nanotechnology, this book describes nanotechnology as a kind of radical biology, greatly extended in its capabilities, efficiency and the range of products it can produce, and most importantly, being computer-controlled. This brilliant work heralds the new age of nanotechnology, which will give us thorough and inexpensive control of the structure of matter. Drexler examines the enormous implications of these developments for medicine, the economy, and the environment, and makes astounding yet well-founded projections for the future.

Nanotechnology: Molecular Speculations on Global Abundance by Edited by BC Crandall, 1996
The introductory chapter on molecular engineering, written by Crandall, covers an impressive range of ideas and facts and introduces some novel perspectives. He begins by explaining measurement systems and physical scales, and then introduces atoms and molecules, giving both scientific basics and historical perspective, and segueing into the most relevant facts from biochemistry and molecular biology.







Opinion, Politics & Websites:





  • NanoEngineer
  • Gwyddion
  • QuteMol
  • Gabedit QC-GUI
  • NanoDynamics
  • Gaussian
  • MPQC


In Popular Culture

The Universal Constructor from Deus Ex was a Molecular Assembler, as were the Seed and the Feed from TDA.


See Also


  1. Kenneth W. Ford, "The Large and the Small," in Timothy Ferris, ed., The World Treasury of Physics, Astronomy, and Mathematics (Boston: Little, Brown and Company, 1991), 22. First published in Kenneth W. Ford, The World of Elementary Particles (Cambridge: Cambridge University Press, 1958).
  2. Waldo (short story). Wikipedia. Link.
  3. Ed Regis. Nano: The Emerging Science of Nanotechnology. June 1995.
  4. Noriaki Oyabu, Oscar Custance, Insook Yi, Yasuhiro Sugawara, Seizo Morita, “Mechanical vertical manipulation of selected single atoms by soft nanoindentation using near contact atomic force microscopy,” Phys. Rev. Lett. 90(2 May 2003):176102; abstract, APS story.