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The earliest and still most thorough treatment of molecular nanotechnology is the text Nanosystems: Molecular Machinery, Manufacturing, and Computation (1992), by K. Eric Drexler. Also highly recommended, as brief introductions, "Revolutionizing the Future of Technology" (Revised 2006) and "Productive nanosystems: the physics of molecular fabrication" (2005) both by K. Eric Drexler.
The first journal article published on molecular nanotechnology: "Molecular engineering: An approach to the development of general capabilities for molecular manipulation," Proceedings of the National Academy of Sciences, September 1981, is available at the Institute for Molecular Manufacturing web site.
The key concept in the proposal that molecular nanotechnology will allow the fabrication of complex objects to atomic precision is positional control, sometimes called positional mechanosynthesis. Ralph Merkle has written and made available at his Web site the article Molecular Manufacturing: Adding Positional Control to Chemical Synthesis. An extensive technical bibliography for research on positional mechanosynthesis, covering both theory and experiment, has been compiled by Robert A. Freitas Jr.
Nanotechnology: Research and Perspectives is the proceedings of the First Foresight Conference on Nanotechnology, the first interdisciplinary technical conference on nanotechnology. In addition to considering theoretical aspects of advanced nanotechnology, this conference reviewed the state of the art of several experimental approaches that will be crucial to developing advanced nanotechnology, as of the date of the conference—1989.
The book Nanomedicine, Volume I: Basic Capabilities, by Robert A. Freitas Jr. describes the basic capabilities of molecular machine systems that may be required to develop medical nanorobotic devices. Chapter 2, "Pathways to Molecular Manufacturing" (available on the author's web site at http://www.nanomedicine.com/NMI/2.1.htm and subsequent pages), presents an extensive, thorough, and detailed overview of both experimental and theoretical approaches to developing advanced nanotechnology, as of 1999.
"Building Molecular Machine Systems", by K. Eric Drexler, a pre-print of an article published in Trends in Biotechnology, January 1999, Vol 17 No 1, pp 5-7, considers possible routes from naturally occurring biological molecular machine systems to the artificial molecular machine systems that will make possible advanced nanotechnology.
Chapter 4, "Microscale and Molecular Kinematic Machine Replicators" of Kinematic Self-Replicating Machines by Robert A. Freitas Jr. and Ralph C. Merkle, presents an extensive overview of molecular mechanisms and other approaches to developing the basic capabilities of advanced nanotechnology, as of 2004.
Inexpensive fabrication of manufactured products using molecular manufacturing is only possible using either self replication or exponential manufacturing. Early discussions of molecular manufacturing proposed programmable microscopic machines, termed assemblers, capable of building complex objects to atomic precision. Because assemblers were to be general purpose machines that could be programmed to build a wide variety of materials and machines, it was pointed out that they could therefore be programmed to build copies of themselves, and were therefore potentialy self-replicating. See, for example, the article by Ralph Merkle Self replication and nanotechnology.
More recent studies ["Safe exponential manufacturing" by Chris Phoenix and Eric Drexler, 2004, Nanotechnology 15 869-872.] have shown that it is not necessary for the microscopic machines themselves to be self-replicating in order for macroscopic molecular manufacturing systems to reap the practical and economic advantages of machine replication. A desktop nanofactory would be such a macroscopic molecular manufacturing system. An 86.1 MB movie ["Productive Nanosystems: from Molecules to Superproducts". The file nanofactory.mov is a QuickTime movie. To play, download the file and view it or convert it with the media player appropriate to your system.], depicting an animated view of a nanofactory and demonstrating key steps in a process that converts simple molecules into a billion-CPU laptop computer, is a collaborative project of animator and engineer, John Burch, and pioneer nanotechnologist, Dr. K. Eric Drexler.
Chris Phoenix, Director of Research for the Center for Responsible Nanotechnology, published (2003) a "Design of a Primitive Nanofactory" (see Foresight Update 53). Chris Phoenix and Eric Drexler published (2004) an assessment of the advantages of exponential manufacturing using macroscopic nanofactories compared to small self-replicating machines (see "Gray Goo Begone" in the Media Watch column of Foresight Update 54).
Zyvex Labs provides two very useful background documents on atomically precise manufacturing:
Molecular Nanotechnology: A Realistic Treatment distinguishes molecular nanotechnology from alternate visions of nanotechnology, top-down vs. bottom-up approaches, and describes mechanochemistry, system designs, and business opportunities in molecular nanotechnology.
Atomically Precise Manufacturing: Questions and Answers
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