Foresight Update 3 (page 2)
A publication of the Foresight Institute
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
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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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
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
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Molecular Modeling on the Mac
Molecular Editor, Version 1.1
[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.]
MicroChem, Version 2.0 [and 2.5]
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.
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
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;
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
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
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[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,
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.
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Foresight thanks Dave Kilbridge for converting Update 3 to html for this
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