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Foresight Update 3 (page 2)

A publication of the Foresight Institute

Table of Contents - Foresight Update 3

Nanotechnology Ideas Spreading

Nanotechnology concepts continue to be introduced to diverse audiences. At the Artificial Life Workshop, held at Los Alamos, NM, nanotechnology was compared to the "artificial life" theme. Parallels and differences were pointed out between artificial replicators and living things, with the differences predominating. We hope these issues will be included in the Workshop proceedings and will announce when they're available.

A four-part mini-symposium was given at MIT in January. It was well-attended: some attendees stood for hours to hear the introductory presentation. The group especially enjoyed the extensive discussion of the possible social consequences of nanotechnology.

Nanotechnology systems were by far the smallest systems discussed at the IEEE Micro Robots and Teleoperators Workshop, a meeting focusing on the smallest mechanical parts we can fabricate today. The next largest parts discussed were in the multi-micron range.

IBM has requested several talks on nanotechnology: first at the Almaden Research Center, with an audience including top STM researchers; then at the Watson Research Center, which featured nanotechnology in its Physical Sciences Colloquium and found its auditorium overflowing from the chairs to the stairs. Soon IBM Santa Teresa will have a presentation as part of its Advanced Education Seminar Series.

Chemical engineers heard about nanotechnology at a recent Molecular Thermodynamics Seminar at UC Berkeley. At Johnson Controls in Milwaukee, sensor experts considered long-term business applications.

Computer-oriented audiences continue to show a high level of interest: Apple Computer employees, upon hearing an introductory talk, immediately generated some extreme (but physically reasonable) applications which are too wild-sounding to describe in this staid publication. Other recent audiences include SRI, the well-known think tank in Menlo Park, CA, and leaders of the personal computer industry at Esther Dyson's PC Forum, where nanotechnology was part of the closing talk. The organizers gave each speaker at the Forum a copy of Engines of Creation

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Books of Note

Your suggestions are welcomed on books for this column.--Editor

Tools for Thought, Howard Rheingold, Simon & Schuster, 1985, $9.95 paperback. Fun book covering past, present, and future computer tools for augmenting human mind. Includes hypertext (Nelson, Engelbart, Xanadu), ARPAnet, "epistemological entrepreneurs," future of network culture. Photos, personality profiles. For general reader.

Solid Clues: Quantum Physics, Molecular Biology, and the Future of Science, Gerald Feinberg, Simon & Schuster, 1985, $17.95 hardcover, $8.95 paperback. Feinberg, a Columbia physics professor and FI Advisor, covers a broad range of topics in science, focusing on physics and biology, including careful thinking on where science is going. Rarely does a scientist discuss the future of science: a special treat. Glossary. Accessible (but challenging in parts) to non-technical readers.

Odyssey: Pepsi to Apple ... a journey of adventure, ideas, and the future, John Sculley, Harper & Row, 1987, $21.95 hardcover. A "business" book for those who don't read business books. The story of a top Pepsi executive (read about a strange but amusing corporate domain one hopes never to enter) and how he escaped to Apple Computer to make a difference in the real world. Epilogue on Sculley's dream, the Knowledge Navigator, which sounds like hypertext and hypermedia publishing with some AI.

Computer Lib/Dream Machines, Ted Nelson, Microsoft Press, 1987, $18.95 paperback. Newly revised version of the classic work which revolutionized the way we see computers, by the man who is widely regarded as the father of hypertext.

The Tomorrow Makers, Grant Fjermedal, Microsoft Press, 1988, $8.95. Previously reviewed popular book on robotics, AI, and nanotechnology, now in paperback.

The Ecology of Computation, ed. Bernardo Huberman, Elsevier Science Publishers, 1988, $80. Open-systems perspective on advanced computing. Includes a set of three papers on agoric market-based computation. For the computer literate.

Proceedings of the IEEE Micro Robots and Teleoperators Workshop: an Investigation of Micromechanical Structures, Actuators and Sensors, held Nov. 6-11, 1987, Hyannis, MA. 28 papers on topics such as "gnat robots," micromotors, and "Nanomachinery: Atomically Precise Gears and Bearings." Available through technical libraries or call the IEEE in NYC.

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Media Coverage

Coverage of nanotechnology continues to increase. In January an excellent discussion of nanocomputers appeared in A. K. Dewdney's "Computer Recreations" column of Scientific American. It included a large color illustration of nanomachines clearing fat deposits from a blood vessel. FI's address was given for more information, and we've received over 300 requests so far, with more coming in.

Also in January, nanotechnology was featured in a television special on supercomputers produced by Christian Science Monitor Reports, shown in many U.S. cities on January 30-31. The January 28 San Jose Mercury News discussed nanotechnology on page 2 in an article on scanning tunneling microscopy; the article made the error--first made in a Washington Post story and now common in articles drawing on it--that mechanical nanocomputers will be a trillion times faster than today's machines. Readers are asked to help us make clear that they will be a trillion times more compact, but not much faster.

On February 1 an article by Grant Fjermedal (author of The Tomorrow Makers) appeared in the Seattle Times in connection with a lecture by Eric Drexler at the University of Washington. A brief and fairly inaccurate article appeared in PC Week on February 16. The nanotechnology article in Analog mentioned in our last issue has been voted "best non-fiction article" in the magazine's annual readership poll.

We've had many requests for investment advice drawing on the prospect of nanotechnology. This is not our specialty, but we can report on an investment book that does address the issue: Blood in the Streets, by James Dale Davidson and Sir William Rees-Mogg (Summit Books, 1987) devotes seven pages to the topic, and more to technological change in general and its effects on investment strategies.

Table of Contents - Foresight Update 3

Molecular Modeling on the Mac

by K. Eric Drexler

Molecular Editor, Version 1.1
MicroChem, Version 2.0 [and 2.5]

[Note: Because of rapid progress in molecular modeling software, the application-specific information in this article is largely obsolete. For more recent information, a "Universal Molecular Modeling Software List" is available on the Web as part of the NIH Guide to Molecular Modeling.]

Molecular modeling software systems fall into two categories with widely differing capabilities. Those in the first category enable users to build and display three-dimensional models of molecular structures; those in the second use information about molecular geometries and energies to calculate molecular properties and shapes.

Molecular Editor, from Drexel University, is an example from the first category. It can show a set of points in three dimensional space as seen from any chosen angle, representing atoms at those points as spheres (displayed as shaded circles) and representing bonds between them as lines. It can shade circles and lines to represent different atom and bond types. The program, though, knows nothing about molecular structures other than atomic sizes (which it uses to size its circles). Users are free to draw in nonsensical structures; the documentation notes that the program can be used to teach generalized cartesian geometry.

Figure 1. Two views of the carbon skeleton of a slim shaft structure,
drawn in Molecular Editor. Atoms can be positioned by dragging to a location, by a move-to-origin command, or by entering coordinates. Groups of atoms can be selected and then duplicated, dragged, rotated, or reflected, enabling the user to build up complex, regular structures with reasonable economy of effort (see Figure 1). Since Molecular Editor can read and write coordinates in text files, structures can be calculated elsewhere and imported for display and manipulation. Like most (all?) molecular modeling programs on the Macintosh, Molecular Editor gives an intersecting-spheres representation of bonded atoms: where two spheres should show a line of intersection, one simply sees an overlap, with the circle representing the closer sphere on top.

The program is generally well-executed. Its interface follows Macintosh conventions closely, with no nasty surprises and broad availability of the undo command. On-screen help is extensive, and the documentation is reasonably complete.

The chief drawbacks relate to bugs and speed. Various manipulations are best performed by cutting molecules (or molecular fragments) to the Macintosh clipboard and pasting them into another window for modification. Unfortunately this process sometimes fails to bring some atoms or bonds across (for mysterious reasons), and pasting--especially into a window with another molecule in place--can lead to the equally mysterious formation of improper bonds, sometimes to nonexistent atoms in never-never land outside the window. Such bugs, while frustrating, were rare enough to be tolerable. The speed problems are also tolerable, but the rotation and redisplay of a structure containing a hundred atoms or so can take about a minute. There is reason to think that better code would speed this up considerably.

In general, Molecular Editor is a professionally executed piece of software, though not rock-solid or fast. It generally does what it is supposed to do and costs remarkably little. It is available for $33 (including domestic shipping) from Kinko's Academic Courseware Exchange, 4141 State Street, Santa Barbara, CA 93110; phone 800-235-6919 outside CA, 800-292-6640 inside CA, 805-967-0192 outside U.S. (Macintosh 512e, Plus, SE, or II required; 800K disk).

MicroChem 2.0, from Intersoft, is a more ambitious package in the second category of molecular modeling systems [comments inserted in brackets describe reported changes in version 2.5]. Its organic modeling unit includes several modules that communicate via text-file representations of molecular structure (tables of atom types, coordinates, and bonding relationships) [version 2.5 is reported to provide for more convenient interchange of structures between modules]. The input module enables a user to provide coordinates or crude sketches to describe a molecular structure. The basic molecular mechanics module takes a description of this sort and modifies it, attaching hydrogen atoms to any atom with dangling bonds and adjusting the lengths and angles of bonds in ways that take account of their preferred geometries. Another molecular mechanics module enables users to compare the energies of sets of molecular conformations generated by rotating one part with respect to another around a single bond (holding each part's geometry fixed). Other modules (parts of separately sold "modeling units") include a zeolite maker, a macromolecule maker, and a group additive properties unit for use in drug design.

In general, the implementation of these modules gives a sense of programming resources being stretched too far [though improvements reported in version 2.5 show that further resources are being applied]. The input and display modules have functions that overlap with those of Molecular Editor, but the implementation is poor. The user interface for the input module in particular is painful. All choices are made through menus (with no command-key shortcuts [added in 2.5]) and a click causes an immediate action, with no chance either to see what target is selected beforehand or to undo the operation afterward. Clicking squarely in the middle of an atom can cause an operation on a non-overlapping atom remarkably far away [now said to be fixed]. This combination of circumstances causes real problems with deletion. One first chooses "delete" from the menu, then clicks on the atom to be deleted. All too often, something else then immediately and irretrievably vanishes. Further, one cannot select and move a single atom, much less a group. The display module interface is awkward but less can go seriously wrong here. Still, it fails in the basic task of reliably stacking atom-images in back-to-front order to make foreground atoms obscure background atoms, rather than vice-versa (see Figure 2) [this, too, is said to be fixed].

Figure 2. A segment of the Figure 1 shaft structure, done in MicroChem, showing first the skeleton alone, then the locations of the hydrogens, and finally the results of drawing the atoms. [The atom-stacking bug is reportedly fixed.]

The first of the two molecular mechanics modules takes a crude input structure and adjusts it to minimize its energy. In doing so, however, it ignores interactions between non-bonded atoms; these include electrostatic forces and the van der Waals repulsions that keep two atoms from occupying the same place at the same time. It takes account only of forces resulting from the covalent skeleton of the molecule--forces that are often dominant, especially in conventional chemistry. Faced with bonds in linear or branching molecular structures, it simply constructs a geometry having the preferred bond lengths and angles. Bonds in ring and cage structures, though, are generally distorted; this module calculates the shapes of these looped substructures by an iterative energy-minimization procedure that essentially treats bonds as springs and lets them settle toward their equilibrium configuration.

The neglect of non-bonded interactions may be adequate for many purposes (and it keeps the time required for energy minimization within reasonable bounds) but the design of nanomachines typically involves these interactions in a major way. Non-bonded interactions are surface interactions, and surface interactions are what gears, bearings, and most other mechanisms are about. The second molecular mechanics model can calculate the energy of non-bonded interactions, but only during the rotation of one part of a molecule with respect to another about a bond, while treating the rest of the molecule's covalent framework as rigid. This has its uses, but is inadequate for the design of typical molecular mechanical devices.

And again, problems appear. The first molecular mechanics module first minimizes the energy of looped substructures, then constructs any non-looped structures that need to be added using a simple geometric algorithm. Figure 3 shows a molecule of cubane in two views; the module found the correct form for the looped structure (a regular cube), then constructed irregular, crooked hydrogens around it.

Figure 3. Two views of MicroChem's version of the cubane structure, showing irregular hydrogen placement.

To be useful for the design of simple nanomechanisms, the molecular mechanics modules need to be combined and extended. First, MicroChem needs options permitting energy minimization and calculation using both bonded and non-bonded interactions. Second (and more esoteric), it needs a way to let users specify forces on atoms and constraints on their motion, to allow (for example) calculation of energies for a bearing in a variety of rotational positions. These more elaborate calculations would inevitably be more sluggish, but overnight runs are sometimes acceptable, and the greater abilities of the Mac II and future machines will help. We should eventually get systems adequate for amateur molecular-machine hacking, but in the meantime, there is a need waiting for someone to fill it. [As these bracketed comments show, however, MicroChem itself is evolving at a fair pace.]

The MicroChem Organic Modeling Unit, Version 2.5, is available from Intersoft, Inc., One Concourse Plaza, 4711 Golf Rd., Suite 412, Skokie, IL 60076 (tel. 312-699-4143). Academic license, $295, industrial license, $495. Special prices and arrangements are available for multiple modeling units, multiple licenses, high schools, and classroom use. (Macintosh Plus, SE, or II required; preferably with a hard disk, but at least a second 800K disk drive).

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Upcoming Events

[Very Large] Space Station Design and Development, May 4, Chicago Hilton, $148 prereg., $195 on-site. We've added the "very large" to indicate that space colonies are included; aimed at architects, May 3 evening reception for new International Association for Space Architects. Contact Guidelines, 800-634-7779 outside CA, 415-254-9393 in CA.

Third International Conference on Supercomputing, May 15-20, Boston. Includes a presentation on nanotechnology on May 20. Contact ISI, 813-866-2694.

Space Development Conference, May 27-30, Denver, CO. Co-sponsored by FI, ask for FI discount. Includes one hour on nanotechnology. Registration $60 through May 1. Contact Box 300572, Denver, CO 80218, 303-692-6788.

Gordon Research Conference on Immobilization and Biotechnology, Aug. 8-12, Plymouth, NH. Includes "Nanomachines and Molecular Assembly" on Aug. 9. Preregistration $270-310. Contact 401-783-4011.

Directions and Implications of Advanced Computing, Aug. 21, St. Paul, MN, $50. Plenary speaker is Doug Engelbart, pioneer in hypertext. Sponsored by Computer Professionals for Social Responsibility. Contact DIAC-88, CPSR/LA, PO Box 66038, LA, CA 90066.

AI and Hypertext: Issues and Directions, Aug. 23, St. Paul, MN. Half-day workshop includes hypertext publishing. Limited to 35, position papers due May 2. Sponsored by AAAI. Contact Mark Bernstein, 617-782-9044.

Second Conference on Computer-Supported Cooperative Work, Sept. 26-68, Portland, OR. Includes "technological, sociological, organizational, cognitive, and task domain perspectives." Sponsored by ACM. Contact Suzanne Sylvia, 617-225-1860.

Fourth International Symposium on Molecular Electronic Devices, Oct. 1989, Baltimore/DC area. Watch this column for details.

Table of Contents - Foresight Update 3

Foresight thanks Dave Kilbridge for converting Update 3 to html for this web page.

From Foresight Update 3, originally published 30 April 1988.
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