Foresight Update 23
A publication of the Foresight Institute
by Jeffrey Soreff
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Scanning Tunneling Microscope Techniques
Scanning tunneling microscopes have been used to to modify
individual molecules. Their main advantage is that they allow
modifications at precisely chosen locations. Their main
disadvantage is that they operate on only one molecule at a time.
The first paper mentioned below describes a technique which may
extend the range of structures that can be built with an STM,
while the second demonstrates the stability of a type of switch
that can now be built with an STM.
An advance in controlling the environment of a scanning tip,
which may be applicable to fabrication, came from J. D. Noll, P.
G. Van Patten, M. A. Nicholson, K. Booksh, and M. L. Myrick,
writing in [Rev. Sc. Instrum. 66: 4150-4156
Aug95]. They built a fluid cell for a scanning tunneling
microscope that allowed them to exchange fluids during imaging.
The noise due to fluid flow is sufficiently low that they were
able to image graphite with atomic resolution during flow. From a
fabrication viewpoint, their cell should allow a sequence of
liquid phase reactions and scanning probe controlled workpiece
modifications to be applied to a single site. One should, for
instance, be able to adsorb one reagent on a surface, then
locally modify it with the scanning tip, then adsorb a different
reagent, then modify the new layer of the second reagent at the
same site, and so on. The stability of the fluid cell that this
group has demonstrated should allow such a sequence to be
followed without needing to relocate the work site after changing
reagents, as would occur with a more disruptive method for
changing reagents. In the cell described in this paper, a reagent
injected into the fluid stream reached the cell approximately 90
seconds later, and peaked in concentration about 50 seconds after
that, setting a time scale of several minutes for replacing
reagents in this design.
An STM-based approach to nanometer-scale circuits is described by
D. P. E. Smith in [Science 269: 371-373
21Jul95]. This paper describes experiments in switching quantum
conduction channels on and off in an STM experiment. The
experiments were performed at 4.6 - 8.6 K, with contact between a
gold ball and a nickel tip (thought to become coated with gold,
producing gold-gold contacts, under experimental conditions). The
key finding is that the contact can form a very stable high
conductance state, with a conductance of 0.977▒0.015 (2e2/h).
This conductance "could be stably measured over one position
for a period greater than 24 hours and is in good agreement with
detailed simulations that find a stable single-atom contact with
a quantized conductance of 0.93▒0.05 (2e2/h)."
The junction could be repeatedly cycled between the conducting
state and a state with about 15 times as much resistance. The
author observed switching speeds as fast as 10Ásec (limited by
sensing electronics), and noted that "Molecular dynamics
simulations have shown that the fastest possible switching time
for single atoms in the point-contact configuration is on the
order of 1 psec." The author also observed switching of a
second conductance channel, but much less stably than the
switching of the first channel. Because a long conductance
channel would make the switching of the second channel more
distinct, "...the single-channel constriction probably
corresponds to a single atom." Presumably the reproducible
cycling between states of a single channel shows that one of the
bonds to an atom at the channel constriction can be repeatedly
broken and reformed without damaging nearby bonds enough to
change the resistance. In addition "The QPC [quantum point
contact] switch displays power gain and can be used to make an
oscillator (by feeding the output signal back into the control
input) or to drive a series of other QPC switches."
Single Electron Circuits
Logic devices are necessary components of intelligent
manufacturing systems. The paper described below shows one
approach to using small numbers of electrons to operate
electronic circuitry, including logic devices.
W. R÷sner, F. Hofmann, T. Vogelsang, and L. Risch write of a
technique for simulating certain classes of single electron
circuits in [Microelec. Eng. 27: 55-58 1995].
They model their circuits as a set of electrical nodes, tied
together by capacitors and tunnel junctions, with a charge on
each node due to a small number of electrons.
Their modeling process calculates the electrostatic voltages on
each of the nodes. For each tunneling junction, it then
calculates the change in energy that would be produced by a
single tunneling event through the junction. Based on this energy
change and the resistance of the junction, they then calculate
the rate at which electrons tunnel through it. The actual
transition is then selected with a probability proportional to
its rate. Because this analysis is applied to circuits with very
small capacitances, the unfavorable changes in energy due to the
movement of individual electrons are accounted for, so
"Coulomb blockade" effects are properly modeled. Using
their program, the authors have modeled the voltage transfer
curve of a logic inverter, and have also simulated a ring
oscillator built with 3 stages of inverters. This simulated
oscillator operated at a frequency of 20GHz with a power
consumption of 3nW. While this dissipation is larger than that
possible with fully atomically precise fabrication, it looks like
an attractive intermediate target.
The authors describe some limitations to this modeling technique.
It neglects the energy level structure within the conducting
regions that form the nodes of the circuits. They note that this
is acceptable as long as the regions are a few nm in size, which
makes the energy level separations smaller than the voltages used
in the circuits (67 mV was used in the inverter simulation). In
terms of fabrication, this makes the circuits designed with this
paradigm relatively insensitive to the atomic scale details of
their conducting regions. The calculation of the tunneling rates
is also approximate, depending only on the characteristics of a
single junction at a time. This is accurate as long as the
junction resistance is large compared to the quantized resistance
h/e2 = 25.8kohms. In terms of fabrication, this makes
the circuit independent of quantum phase relationships across
several circuit elements. These circuits do need
atomically precise control of their tunnelling junctions, since
the detailed bond geometry in the junction sets the tunnelling
resistance. The circuits might be good targets for a hybrid
technique where the tunnel junctions are built with atomic
precision by classical chemistry, and are then attached to
capacitors and interconnections built by STM lithography.
The self-assembled route to nanotechnology requires extending
synthetic structures to larger sizes in order to form working
mechanisms. This, in turn, requires highly specific synthetic
steps to maintain tolerable yields of large, complex structures.
These requirements are generally better satisfied by enzymatic
(or catalytic antibody) reactions than by classical chemistry.
Applications in molecular manufacturing have additional
requirements. They also require stiff structures, partially to
reduce the effects of thermal noise on mechanisms and (in the
more extreme case of polymers with freely turning bonds) to keep
the task of predicting folding possible. In addition, it is
important that there be enough flexibility in the synthesis
techniques to permit the design of a useful range of structures.
The papers described below extend biosynthetic capabilities in
A new DNA technology that extends the range of metabolic products
available is described by M. Rouhi in [C&EN p9
2Oct95]. ChromaXome cofounder K. A. Thompson explains "...if
you take DNA and paste it to DNA from another source or from
other places in the same bacteria, then you get a chemical that's
built from a combination of pathways..." From the point of
view of nanotechnologists, these might provide building blocks
which are not otherwise available. P. B. Fernandes (a vice
president at Bristol-Myers Squibb) says "The diversity from
natural products is much more than you can buy from synthetic
A specific example of which pathways might be usefully combined
is explored by R. McDaniel, S. Ebert-Khosla, D. A. Hopwood, and
C. Khosla writing in [Nature 375: 549-554
15Jun95]. They describe the biosynthesis of polyketides, polymers
of -(C=O)-CH2-, and their derivatives. The polyketide backbone,
without modification, would have many bonds about which it could
twist, and would not be a particularly good candidate for
building stiff structures. Fortunately, polyketide derivatives
include compounds where the backbone has been cyclized into sets
of fused aromatic rings. One of the new products that the article
focuses on (designated SEK26) is a substituted anthraquinone (a
three ring structure). The authors give a set of design rules for
which gene clusters can be combined to give a functional
synthetic pathway. At present, 8 backbones are available, with
the prospect that "enzymes that catalyze downstream
cyclizations and late-step modifications, such as group transfer
reactions and oxidreductions commonly seen in naturally occurring
polyketides, can be studied along the lines presented here and
elsewhere." Hopefully, some of the products of these
enzymatic pathways may include stiff, fused ring structures,
valuable for constructing atomically precise mechanisms, that are
not available from classical organic chemistry. Alternatively,
the active sites of the enzymes which synthesize stiff, fused
ring structures may serve as a model for extending an early,
protein-based nanotechnology towards the diamondoid structures
that exhibit better mechanical properties and wider design
Turning to a broader range of biochemically catalyzed reactions,
P. G. Schultz and R. A. Lerner, writing in [Science 269:
1835-1842 29Sep95] describe the state of the art in catalytic
antibodies. Catalytic antibodies are raised by provoking an
immune response to a compound that resembles the transition state
of a reaction that one wants to accelerate. In catalysis, the
antibody binds to the transition state of the reaction,
stabilizing it, lowering the activation energy of the reaction,
and accelerating the reaction. One of the early reactions to be
catalyzed was ester hydrolysis. The transition state for hydroxyl
attack on an ester has a tetrahedral carbon at the carboxyl
position. Analogous phosphonates have sufficiently similar
tetrahedral geometries and charge distributions that antibodies
to them can catalyze hydrolysis of esters.
Shultz and Lerner describe a variety of reactions which are now
possible with catalytic antibodies. One of their examples is the
catalysis of a Diels-Alder addition ("...in its simplest
form...the reaction of butadiene and ethylene to yield
cyclohexene..."). This is particularly notable because no
natural enzymes are known which catalyze this reaction. More
generally, Shultz and Lerner describe catalysis of a class of
reactions known as pericyclic reactions, only one of which is
known to have an enzyme that catalyzes it. "These reactions
have not only received a great deal of theoretical and
mechanistic attention from chemists, they have also found many
applications in organic synthesis." In addition to the
Diels-Alder reaction, they describe catalysis of the Cope
rearrangement, an intramolecular rearrangement which moves two
double bonds and a single bond in a six-atom group.
Another class of reactions that Shultz and Lerner cover is the
catalysis of reactions involving reagents ("cofactors")
that are not present under physiological conditions. The examples
that they give are catalysis of the oxidation of an organic
sulfide by periodate and the reduction of a number of ketones by
cyanoborohydride to the corresponding alcohols with "96%
enantiomeric excess." In the corresponding uncatalyzed
reaction, there would be, of course, no selectivity between
Some reactions that can now be catalyzed have sufficiently
unstable transition states that they do not occur at any
appreciable rate in the absence of catalysis (although undesired
side reactions of the same reagents may occur without catalysis).
An example of a cyclization is given where the product formed in
the presence of the catalytic antibody is essentially absent in
the normal reaction products. Another example is given where a
cyclization product is formed in 98% yield where the uncatalyzed
reaction yields an impure mixture of many products. The authors
write "These studies will undoubtedly lead to efforts aimed
at larger multiring cyclization reactions."
The facility that these antibodies provide to nanotechnologists
is the ability to produce more selective reactions than classical
organic chemistry allows. Since the antibodies can bind all over
the surfaces of their substrates, they can geometrically orient
the reactants, confining them to just one of a number of
potentially competing reaction pathways. This can potentially
allow us to build structures which are unreachable (in reasonable
yields) through classical techniques.
Another approach to controlling stiff, polycyclic structures
from a technology base which initially controls only flexible
compounds is to control the formation of the polycyclic
structures in crystal lattices. A. Berman, D. J. Ahn, A. Lio, M.
Salmeron, A. Reichert, and D. Charych, writing in [Science
269: 515-518 28Jul95], describe controlling the
crystallization of calcite with an organic monolayer. Their
experiments grew calcite crystals on an acidic PDA
(polydiacetylene) film. The monomer that they used was CH3-(CH2)11-CC-CC-(CH2)8-COOH.
Polymerization of this compound yields long polymer chains within
the PDA monolayer. In these experiments the calcite crystal's a
axis was aligned "parallel to the polymer backbone
direction" (within the plane of the film). By comparison, in
previous examples of crystal nucleation on thin films "The
crystal axes in the plane of nucleation do not appear to be
aligned with a structural parameter of the nucleation
surface." The authors state that "the total control
exerted over their [the crystals'] orientation is to our
knowledge unprecedented in crystal growth at the in vitro
organic-inorganic interface." In order to use these crystals
for atomically precise mechanisms, it would now be desirable to
extend this work to control the absolute position, as well as the
orientation, of these crystals, perhaps by performing the
analogous experiments on proteins that mimic a finite,
well-defined area of the PDA membrane.
An important capability in approaching nanotechnology is to be
able to evaluate the results of attempts to build target
structures. A three dimensional reconstruction of the structure
of the ribosome at 25┼ resolution is described by J. Frank, J.
Zhu, P. Penczek, Y. Li, S. Srivastava, A. Vershoor, M.
Radermacher, R. Grassucci, R. K. Lata, and R. K. Agrawal in [Nature
376: 441-444 3Aug95]. The analysis technique that they
used combined 4,300 electron micrographs of separate ribosomes.
The computational power brought to bear on the problem was
remarkable. For instance, "The orientation of each
projection was determined individually by matching it to computed
projections of the previous 29┼ model..." This analytical
technique may prove useful for determining if some self-assembly
step succeeded or failed. It retains one of the strongest points
of x-ray diffraction, the ability to use information from many
molecules, without requiring the ability to precisely align all
of the molecules in a crystal, as x-ray diffraction requires.
The specific results of this group allow them to identify "a
channel in the small ribosomal subunit and a bifurcating tunnel
in the large subunit which may constitute pathways for the
incoming message and the nacent polypeptide chain,
respectively." As this model is extended towards molecular
precision, it may allow us to improve the yield of our in vitro
peptide synthesis techniques, or possibly to extend the
capabilities of ribosomes in intact organisms. Either of these
developments would broaden the range of proteins available to us
for constructing novel structures.
Jeffrey Soreff is a researcher at IBM with an interest in
by Elizabeth F. Enayati
It was a pleasure addressing those of you who attended the Foresight
Conference on Molecular Nanotechnology in mid-November. Your
questions, as usual, were thought- provoking and perceptive. I
enjoyed the dialog. Unfortunately, there was more to discuss than
time available for my presentation. This column will fill in the
Primarily, you should be aware of a few pending bills that may
have additional impact on emerging technology, such as
nanotechnology. The House Bill HR 1733, sponsored by Rep. Carlos
J. Moorhead (R-CA) and Patricia Schroeder (D-CO), proposes to
amend the patent term from its present 20 years from the U.S.
priority filing date, to 20 years from the filing date of the
issued patent. This is a subtle, yet significant difference; 20
from priority means that the 20 year term may be measured from an
earlier patent application from which the issued patent is
derived; whereas 20 years from the filing date of the issued
patent merely considers the date on which the issued patent was
filed, independent of when the parent case was filed. To overcome
issues of "submarine patents", this bill includes a
mandatory publication of patent applications at 18 months from
the priority filing date.
For example, an applicant files a "parent" application
on June 30, 1995, and subsequently files on July 30, 1996, a
"continuation" or a "divisional" application
based on the parent case. Under the existing law (as amended
post-GATT) the issued patent would have a term of 20 years from
June 30, 1995, but under the Moorhead/Schroeder Bill, the patent
would have a term of 20 years from July 30, 1996, with a
publication occurring December 30, 1996.
Another House Bill HR 359, sponsored by Rep. Dana Rohrabacher
(R-CA) proposes to change the patent term to the longer of 17
years from issuance or 20 years from the U.S. priority filing
date. However, because it does not address concerns over
"submarine patents", it is not expected to succeed.
Another controversial pending House Bill is HR 2235, also
sponsored by Moorhead. That Bill proposes to grant certain rights
to prior users of patented technology. Such a provision exists
under most foreign patent systems, and is notably absent from the
U.S. system. The Bill proposes to grant a royalty-free right to a
prior user to continue using the patented invention if the prior
user has been using it in good faith, and only continues to use
technology for the use existing at the time the patent issues.
Obviously, this Bill raises both significant concerns and
potential for small companies, individual inventors, and emerging
This last topic is worth discussing, and I welcome your comments.
I will address this issue, incorporating your comments, in the
Elizabeth Enayati is a patent law specialist with the Palo
Alto law firm Weil, Gotshal & Manges.
Her e-mail address is firstname.lastname@example.org,
or phone (415) 926-6248, or fax (415) 854-3713. She can also be
reached by mail c/o Foresight Institute, P.O. Box 61058, Palo
Alto, CA 94306.
[Editor's Note: See later columns for Elizabeth
A U.S. Department of Science?
"There is something very wrong with American
science." This provocative claim was offered by George A.
Kenworth II, White House Science Advisor under the Reagan
Administration, while addressing the House Science Committee last
June. "Preserving the status quo has become the overarching
goal, replacing the pursuit of excellence," he continues. In
addition, U.S. science suffers from "a deeply ingrained lack
of [public] accountability" and "ingratitude for two
generations of unparalleled federal largesse.
"A major overhaul is needed." And the restructuring
implicit in the creation of a Department of Science (DOS)
"is the only way I know to restore coherent policies,
research dedicated to excellence, and the public trust,"
Kenworth told the committee.
Robert S. Walker (R-Pa.), chair of the committee, anticipates
drafting a bill to establish a DOS to the U.S. Congress. He
estimates that the coordination and streamlining of policy made
possible by merging many research responsibilities could, over
seven years, save Uncle Sam more than $2 billion and eliminate
more than 5,000 federal jobs.
While the proposal won overwhelming endorsement from most
committee members present - and from all invited witnesses - the
June 28th hearing also highlighted some major issues that must be
resolved before the long-term implications of such a
restructuring can be evaluated. Turf battles are expected.
One issue sure to kindle protectionist passions among people
currently engaged in federal research and development (R&D)
is how much applied research - the "D" in R&D - a
DOS should undertake. Today, nearly 80% of the federal R&D
budget goes to applied research, including technology
Some people anticipate a DOS would probably spell an end to the
White House Office of Technology Policy (OSTP), but one of the
chief advantages of a DOS would be to merge science policy making
and program implementation into a single structure. [Science
News, 148: 59-60]
In the U.K., an ambitious program to harness science,
engineering and technology for increasing the competitiveness of
that nation's businesses is now ready to disseminate and
implement a number of recommendations. These recommendations are
based on a massive consultation exercise spanning 15 sectors of
British industry. One of the more concrete proposals is for the
creation of a national institute for applied catalysis.
The program is known as "Technology Foresight," and was
one of several announced in a 1993 document titled
"Realizing Our Potential: A Strategy for Science,
Engineering, and Technology." It was the first major policy
review in the area for 20 years. "The program is a new
departure," says John Brophy, research general manager for
BP Chemicals, Sunbury on Thames, England. "It identifies
national priorities for the scientific infrastructure to channel
research in the direction of industry." Brophy is vice
chairman of the Technology Foresight Panel on Chemicals. He
explains "Our panel recommends that we retain a large
element of that, but also ensure that the science base, working
with industry, is prepared for and aware of market opportunities
when they arise."
Top priority areas include genetic and biomolecular engineering,
sensors and sensory information processing, and environmentally
sustainable technology. Catalysis, chemical and biological
synthesis, and materials are regarded as intermediate priority
areas that require further action and development of
"stronger exploitation links." The strategic themes
include the need for a cleaner, more sustainable world, and
advances in materials science, engineering, and technology, with
a particular emphasis on multidisciplinary settings. [C&EN
July 3, 1995, pps. 16-17]
"A Visualization Revolution" is how recent advances
in computing, visualization algorithms, and display technology
are heralded by R&D Magazine, in the October
1995 issue. "Virtual environments" can now be created
which enable researchers to make prototypes and conduct tests and
experiments. A virtual prototyping system, with stereoscopic
computer-driven images projected on two walls and the floor of
the CAVE (Cave automatic virtual environment) has been unveiled
at the National Center for Supercomputing Applications at the
University of Illinois, Urbana-Champaign.
Researchers at Caterpillar Inc., have developed a virtual reality
copy of Caterpillar's Peoria test track. In the CAVE, one can sit
in an instrumented mockup of an earth-moving machine cab.
Listening to lifelike stereo sounds, the driver maneuvers the
computer-driven machine and its earthmoving accessories. With
these simulations, Caterpillar engineers can eliminate the
lengthy process of fabricating steel casting needed for design
studies by changing CAVE's design program, which only takes a few
Recent advances in desktop computing power and visualization of
algorithms mean that supercomputers are no longer always
necessary. An engineer with Pacific Gas & Electric used a
desktop system and graphical analysis program to study the
effects of earthquakes on a building. Using accelerograms to
study the effects of the 7.1 Richter scale Loma Prieta earthquake
on a 34-story steel building in San Francisco, the model resulted
in visualizations of the movement of the 34th floor during Loma
Prieta. These data allow structural engineers to realistically
evaluate the seismic safety of the building. The analyses
included baseline corrections, integration to obtain velocity and
displacement data, cross-section functions, and fast Fourier
transforms to measure the response to earthquake movements.
In line with my unbridled enthusiasm for the Foresight Web
Project, here are two important URLs for Update
Color microscopy imaging is now seen on Web pages to add product
details and provide users with application forums. Many of these
images would interest nanophiles. Point your Web browser to:
Dr. Jamie Dinkelacker leads Apple Computer's development of
multimedia authoring tools for science, math, and medical
education as Senior Engineer Scientist, Technical Manager of the
East/West Authoring Tools Group within Apple's Advanced
Report: Oak Ridge National Laboratory
Dr. Noid Describes
to Minnesota Study Group
by Steven C. Vetter
Newly devised computational algorithms make possible more
complex and useful simulations of nanoscale structures, Dr.
Donald Noid told the second meeting of the Minnesota Molecular
Nanotechnology (MNT) Study Group. Dr. Noid is a physical chemist
from the Department of Energy's Oak Ridge National Laboratory and
pioneer of chaos theory.
Recent molecular modeling work by the Oak Ridge National
Laboratory trio of Donald W. Noid, Bobby G. Sumpter and Robert E.
Tuzan also was described in a recent presentation by Drs. Sumpter
and Noid at Technology 2005, held at Chicago's McCormick
Place convention center. Sumpter and Noid presented the trio's
paper, "Advancing Manufacturing Through Computational
Chemistry," which discusses the path toward convergence of
nanotechnology and computational chemistry.
In the Minnesota presentation, Dr. Noid described his molecular
simulation software and showed a video of the software simulating
several new molecular-scale mechanisms. His algorithm reduced the
computation required from a page full of equations per atom
simulated to just a few lines, he said. This algorithm makes
computational simulation of a many-atom structure possible.
Without it, many of the simulations he has done would be
impractical with currently available computing power.
The new mechanisms simulated and shown on video included:
- A molecular steam engine, consisting of two tubes: a
large diameter one, and a small diameter one inside the
first, with a flared "knot" about midway along
the length. The knot serves as the piston. The space
between the inner and outer tube is thus divided into two
regions. These regions are filled with water molecules.
By heating one end of the larger tube, the water
molecules expand against the knot of the inner tube,
driving the inner tube laterally.
- A tube as a conveyor or pipe for smaller-diameter
buckyballs being carried along by a flow of helium atoms.
One of things he was testing with this simulation was the
propensity of the helium atoms to leak past the
buckyballs. He talked about some counter-intuitive
results he got with these experiments, dealing with the
leakage as a function of the size and stiffness of the
tube. Stiffer tubes leak more, he said.
- Bearing simulations, showing that friction, while
different in each mechanism's details, is very much
present at the molecular level. A bearing consisting of
two concentric graphite tubes was given an initial
rotation. It stopped rotating within a few nanoseconds,
due to friction.
- Another simulation involved bearings being driven by a
laser to simulate a motor. Basically, a small-diameter
graphite tube was placed within a larger graphite tube.
The inner tube had a pair of atoms attached at the end
that provided a dipole moment that the laser could couple
with. Both one-laser and two-laser motors were simulated,
with a variety of radii and other parameter values. It
was clear from graphing the angular momentum as a
function of time that many of these designs were
unreliable. The video of the motor simulation showed
graphite tubes distorting significantly in response to
the force of the driving laser, changing the
characteristic dipole length of the receiver. It will be
interesting to see how well this laser-driven motor works
with a diamondoid bearing, instead of the graphite tubes.
Possible solutions to the problem, which remain to be
explored, include a three-laser motor, and simply
stiffening the tubes, he said.
- Simulation of a diamondoid bearing design known to be
faulty in terms of the stress on the bonds. As expected,
the bearing changed shape radically in response to the
energy stored in the overly-strained bonds.
Noid's videos provide a sense of watching actual atoms. We can
"see" atoms, make things out of them, and see if they
work. He said his software makes simulations more realistic by
taking into account conservation of energy. All other known
molecular dynamics packages have systematic errors under which
energy monotonically increases with time.
Dr. Noid believes that simulations of a mechanism must run for a
fair amount of time, several nanoseconds at least. He has seen a
structure act in a very stable fashion for a long period, then
exhibit anomalous behavior. With his software, you can "fine
tune" the molecular structure with successive iterations to
reduce or eliminate unwanted behavior, in the process developing
"design rules" which, if followed, will result in sound
mechanisms. With this software, it is as if we could suddenly
make any physically possible molecular structure, and let it run
and watch it work or not. This is enormously powerful.
He cited two problems doing large simulations (thousands of atoms
for millions of simulation cycles). First is the substantial
computing power required. His algorithms provide much more
accurate results (especially for long simulation times), and do
it much more efficiently, but the shear size of the computations
required is still significant. Some of his simulations required
as much as a week on up to four IBM RISC 6000 processors (a
mini-supercomputer costing around $60,000 each). Fortunately, his
code is extremely vectorizable, meaning that it can be run on
many processors in parallel very efficiently. This allows
efficient simulation on even the most massively parallel
machines, such as the Paragon.
Another problem with large simulations is the large amount of
data generated. This problem is not unique to molecular
simulations. People have been trying to deal with simulation
results data since the first simulators were used, several
decades ago. He is currently working on ways to "mine"
that data for useful information, using neural nets and other
Steven C. Vetter (email@example.com)
is a co-founder and President of Molecular Manufacturing
Enterprises, Inc., 9653 Wellington Lane, Saint Paul, MN 55125.
MMEI is working with Dr. Noid to make his software more widely
From Foresight Update 23, originally
published 30 November 1995.