Foresight Update 29
Page 4
A publication of the Foresight Institute
Jeffrey Soreff's
Technical Progress column is continued from the previous page.
 Single Molecule Diagnostics
One approach to nanotechnology is to construct systems with
scanning probe techniques. This has the advantage of providing
excellent control of the locations of the molecules being
assembled, but it has the disadvantage of being an inherently
serial process. It therefore requires techniques to investigate
very small numbers of molecules, ideally single molecules. The
following five items describe techniques applicable in this
regime.
The first paper in this section extends a spectroscopic technique
to single molecules. Writing in [Science 275:1102-1105--MEDLINE
Abstract], S. Nie and S.R. Emory describe a type of
Raman spectroscopy that is sufficiently sensitive to detect
individual molecules. In their experiments, rhodamine 6G was
bound to silver particles with average diameters of 35 nm. Free
rhodamine 6G absorbs light efficiently. Unfortunately, its
visible absorption (and fluorescence) spectra are fairly broad,
carrying little detailed information. In a normal dye's visible
absorbtion spectrum the incoming light is absorbed by a
transition from one electronic state to another and the effect of
molecular vibrations on the energy difference between the states
spreads out the absorbtion. In Raman spectroscopy, on the other
hand, the energy of the visible photon is split into exciting a
well-defined molecular vibration and a reradiated visible photon.
This process yields much sharper spectra, with much more
information about molecular features. The spectra in the paper
show 6-7 distinct peaks from separate vibrations.
Normally, the "Raman process is an extremely inefficient
process, and its cross sections (~10-30 cm2
per molecule) are about 14 orders of magnitude smaller than those
of fluorescent dyes (~10-16 cm2 per
molecule." Raman scattering is, however, enhanced at certain
surfaces. These authors found that by binding a chromophore to
the surface of a nanoparticle they could enhance it by factors
"as high as 1014 to 1015," making
it feasible to measure the Raman spectrum of individual
molecules. In addition to the enhancement, another feature of the
authors' system is that "photochemical decomposition or
photobleaching is significantly reduced for single molecules
adsorbed on metal nanoparticles because the metal surface rapidly
quenches the excited electronic state and thus prevents excited
state reactions." This is important since it increases the
numbers of photons that can contribute information.
One odd feature of this paper is that the authors found that only
certain Ag particles were optically "hot" (perhaps 1%
to 0.1% of the total), and "only one out of 10,000 surface
sites on a hot particle shows efficient enhancement." The
authors suggest a number of ways to better control the
fabrication of their nanoparticles, including some scanning probe
methods.
This technique looks primarily attractive as a diagnostic
technique for determining whether an attempt to produce a
chemical change to a single molecule with an STM or AFM probe has
been successful. Vibration spectroscopy of organic molecules has
been a powerful analytical technique for decades. Making it
feasible for individual molecules will add a valuable tool for
the development of nanotechnology.
The second paper in this section extends what might be considered
a hydrodynamic diagnostic to individual molecules. Writing in [Science
275:1106-1109 21Feb97--MEDLINE
Abstract], X.-H. Xu and E.S. Yeung describe detecting
the diffusion of individual fluorescent rhodamine-6G molecules.
In one mode, they imaged the fluorescence in a 4-um thick layer
of rhodamine solution confined between a cover slip and a prism.
In another mode, they imaged it in a 0.15 um thick layer excited
with the evanescent wave from a totally internally reflected
laser. In both modes, they used sufficiently low concentrations
of rhodamine (5 nM in the first case, 100 nM in the second) that
molecules were isolated, even accounting for diffusion in a
100-200 msec exposure window. The authors measured the
distribution of the fluorescence for each molecule and calculated
diffusion coefficients for them. In addition to the rhodamine-6G
experiment, the authors bound rhodamine to a 30-base strand of
DNA. It had a reduced diffusion rate, as expected. This technique
may be useful as a diagnostic for structures available in very
small quantities, measuring the diffusion rate of a handful of
structures built with scanning probe techniques, for example,
perhaps to detect if an assembly step had succeeded.
The third item in this section describes the steady advances in
application of electron imaging to determination of the structure
of small numbers of particles. A trio of papers in Nature
describe the determination of the hepatitus B virus by electron
cryomicroscopy. B. Böttcher et. al. [Nature 386:88-91
6Mar97--MEDLINE
Abstract] and J.F. Conway et. al. [ibid. 91-94--MEDLINE
Abstract] wrote the detailed papers with D. J. De
Rosier writing a commentary on them [ibid. 26-27]. This technique
involves solving a structure by taking many electron micrographs
(done at cryogenic temperatures, hence the name) rather than by
growing a crystal and diffracting X-rays with it. From a
biological point of view this technique is notable primarily
because it permits the structural analysis of things such as
membrane proteins and ribosomes which are difficult or impossible
to crystallize. From a nanotechnological viewpoint, it is notable
because it allows 3D structural analysis from a small number of
particles. In B. Böttcher et. al.'s paper 6,400 images were
used, and J.F. Conway et. al. used 600. If a structure is being
built by a scanning probe technique, these numbers of copies are
substantial but conceivable, while diffraction techniques
requiring macroscopic quantities of structures are not. Note that
electron micrographs contain information about the interior of
objects, so, for example, they could provide valuable
confirmation of a successful alignment of two interior subsystems
in a structure, even if the structure's surface is being
monitored with an AFM while it is being assembled. The Böttcher
team achieved 0.74 nm resolution while the Conway team achieved
0.9 nm resolution. De Rosier writes that: "Structural
analysis by electron cryomicroscopy of two-dimensional crystals
now extends to essentially atomic resolution, of 3 to 4 Ä,"
even with only thousands of units in the crystal.
The fourth item in this section describes imaging a single
molecule's motion during the course of a reaction. In [Science
275:1882 28Mar97], E. Stokstad describes a film made by P.
Hansma et. al. of an enzyme actually working its way down a DNA
strand. The enzyme was an RNA polymerase. The scene was imaged
with a tapping mode AFM. A difficult part of the experiment was
to attach the DNA sufficiently firmly to the substrate that it
would not be pushed away by the AFM or diffuse away but
sufficiently loosely that the polymerase could still operate.
Stokstad writes: "After several attempts, the team found
that zinc ions added to the water would loosely attach the
molecules to the sample dish." Hansma suggests that "an
AFM movie might reveal subtle changes in the shape of the RNA
polymerase as it passes over different letters of the genetic
code on its way down a DNA strand." As far I am aware, this
would be a novel sensing architecture, using a hybrid of a
biochemically produced molecule acting as both an atomically
precise sensor and a mechanical sample feed mechanism, together
with a AFM used as a sensitive, but less precisely fabricated,
readout mechanism.
The last item in this section describes a technique that can
detect single charges, and which places an amplifier in submicron
proximity to the system under study. Writing in [Science
276:579-582 25Apr97--MEDLINE
Abstract], M.J. Yoo et. al. describe a high resolution
electrometer that uses a single electron transistor (SET) as a
sensing element on the very tip of a scanning probe. They
detected charge distributions on a surface by scanning it with a
tip terminated in a 100 nm patch of aluminum. Two tunnel
junctions were made to this patch, and the current through it
measured. The current varies approximately sinusoidally with the
potential of the patch, including the potential induced from
charges on the sample surface. It "passes through a full
period each time the electric field lines terminating on the
island induce a charge of exactly one additional electron."
In this paper, this charge is primarily induced by the bias on
the source and drain electrodes coupled to the island. The effect
of the sample charges is to shift the phase of the variation. The
phase shift can detect a signal of as little as 1% of an
electron's charge. The SET is biased with ~1mV, switching
currents of around ~1nA, so the signal power from the SET is
~1pW. The SET island capacitance was ~0.1fF, so the input signal
energy was only around ~10-22 J and there is power
gain for any scanning speed below 1010 pixels/sec.
This is useful because one limitation in rapidly retrieving
information stored in atomically precise structures is the
available signal power from these structures. In both STMs and
AFMs micron scale structures (FETs and cantilevers respectively)
must be driven by atomic structures, while this tiny SET avoids
this requirement.
The fabrication of the SET is surprisingly simple.
"Fabrication of the SET involves the evaporation of three
separate areas of a thin (10 to 20 nm) aluminum film onto a
specially shaped glass fiber...The films for source and drain
leads spread out from the edges of the tip and extend up the side
of the fiber to electrical contacts...The three electrode shapes
are defined by natural shadowing." I would have expected a
much more complex process to be necessary to avoid shorting at
such fine geometries. The success of this instrument suggests the
possibility of many other uses for this technique. The authors
have essentially gotten two voltage sources to within 100
nm of a sample on a single tip, while conventional STM tips only
get one close to the sample. One might apply the same probe
fabrication technique to dual tunnelling instruments, lateral
conduction measurements on low conductivity samples, lateral
electrostatic deflection of surface molecules or a variety of
other fabrication or sensing experiments.
This electrometer requires operation at 2K in order for the
coulomb blockade effect to make the SET operate. Scaling down the
SET both improves resolution (currently set to 100 nm by the SET
size) and increases operating temperature. The authors write:
"Even room-temperature operation, although ambitious, is
conceivable, requiring the development of molecular- or even
atomic-sized SET tips."
Single Electronics in Esprit
An article by A. Hellemans in [Science 275:920
14Feb97] covers a new $3.7 million subproject in the EU's Esprit
program. The project, "Fabrication and Architecture of
Single-Electron Memories", intends to store bits with single
electrons. Eight research labs are participating. The long term
goal of the project is to build large scale memory chips, 1012
bit devices by 2015. The short term goal for "the initial
3-year contract is a 4 X 4 array of single-electron devices on a
substrate of silicon." The researchers expect to place
charges on conducting islets a few nanometers in size. While this
project does not not directly attempt to control the placement of
atoms to atomic precision, a successful single electron memory
would allow routine contruction of precision electrostatic
patterns that might then drive assembly of large patterns of
charged structures. In addition, routine use of these memories
would create incremental economic incentives for precision
fabrication from the low nanometer scale down to atomically
precise fabrication.
Abzymes
One approach to nanotechnology is to synthesize successively
larger, more complex structures by parallel techniques drawn from
chemistry and biochemistry. A key capability necessary for this
approach is the use of very selective catalysts to perform
reactions on selected sites on substrates while avoiding them on
chemically similar sites in other locations. For a number of
years, researchers have been using catalytic antibodies, abzymes,
as one of the approaches towards building selective catalysts.
The following two papers describe some recent advances in this
area.
Writing in [Science 275:945-948 14Feb97--MEDLINE
Abstract], K.D. Janda et. al. describe a novel
selection mechanism for catalytic antibodies which captures the
genes for the antibody as a result of the reaction itself rather
as a result of binding to a transition state analog. In the
particular reaction that they studied, a hydrolysis of a
glycosidic bond, they synthesized a variation of the substrate
which reacted with the abzyme to form a covalent bond connecting
it to a solid support. More precisely, the substrate contained a
phenol with an ortho difluoromethyl substituent. They write:
"On enzymatic clevage, the difluoromethyl moiety generates a
reactive quinone methide species at or near the active site [of
the abzyme], thereby alkylating any nucleophile [in the enzyme,
and capturing it]." The other end of the phenol was
connected to a solid substrate through a disulphide bond. Thus,
the catalysis itself bound the enzyme to the solid support. The
authors also modified the abzymes themselves to carry the
information needed to make additional copies of them. They used
genetic engineering techniques to package the antibody genes into
a phage, and to bind the phage to the antibody. After reaction
with the substrate, phage, abzyme, and phenol are all left
attached to an insoluble support, while non-catalytic members of
the library were washed away. The authors then cleave the
disulphide bond by reduction with DTT, and the freed phages are
"amplified through infection of E. coli." This method
can thus "detect catalysis in single phage particles",
allowing for the direct screening of a very large number of
potential abzymes in parallel. The authors write: "The
advantage of purely chemical systems [such as this one] is one of
generality in that many desired reactions do not yield
intermediates or products that perturb cellular machinery, and
thus biologically based selection systems cannot be used."
On the other hand, this technique does require that the target
reaction be modifiable into a form that captures the abzyme with
the irreversible formation of a covalent bond, which may not be
feasible for some reactions of interest.
J.-B. Charbonnier et. al., writing in [Science 275:1140-1142
21Feb97--MEDLINE
Abstract] did an experiment that describes an improved
procedure for finding catalytic antibodies, but may also probe
the limits of this technology. The antibodies were generated in
the usual way, by immunizing a mouse with a transition state
analog for the reaction to be catalyzed. In this case, the
reaction was an ester hydrolysis and the transition state analog
was a phosphonate. The usual process is to screen "the
immune response [library of antibodies] for binding to the hapten
[transition state analog] and then testing the best scoring
clones for catalytic activity." Instead, this group used a
procedure called "catELISA, in which product-specific
antibodies are used to detect the appearance of product after
immobilised substrate is exposed to the supernatant of culture
hybridoma cells." They were able to screen all 1570 clones
derived from a mouse, of which 9 scored positive for catalysis,
"a figure to be compared to 970 hapten-binding clones"
which would otherwise have needed to be tested again for
catalytic ability. The authors purified and crystallized the
three most reactive antibodies complexed together with the
transition state analog. They found a great deal of structural
convergence of these abzymes, to the extent that "the
conformations of the catalytic residues are similar." They
write that: "The central question now is whether the
mechanism we observe is a dead end or a point on the pathway
which can be further refined." They suggest that further
cycles of mutation and selection may improve it. It will be
interesting to see if its catalytic efficiency can indeed be
increased.
Jeffrey Soreff is a researcher at IBM with an interest in
nanotechnology.
 Media
Watch
Newsweek
continued its look toward the 21st Century by identifying
nanotechnologist K. Eric Drexler
as one of "100 people to watch as America prepares to pass
through the gate to the next millennium." He was one of 15
selected by editors in the Science & Medicine category, and
one of only five of those not associated with medical research.
"Drexler studies the possibilities of molecule-size machines
that might repair cells and build microscopic computers. He
chairs Palo Alto's Foresight Institute," the magazine said. Newsweek
selected its roster not by identifying "the great and
powerful, or the beautiful and celebritous," but rather
"personalities whose creativity or talent or brains or
leadership will make a difference in the years ahead."
Scientific American continues
its gradual retraction of its April 1996 ad hominem critique of
molecular nanotechnology with a new posting on the magazine's
electronic version on the World Wide Web. The article by
contributing writer Alan Hall summarizes work by Al Globus and
his colleagues at NASA. (Globus is cochair of the upcoming Fifth Foresight Conference on
Molecular Nanotechnology ) "Globus and his colleagues at
Ames's Numerical Aerospace Simulation Systems Division are among
a growing number of investigators who now believe that atom-scale
factories will one day produce new structural materials and
advanced computer components, and may even act as tiny
repairmen," Hall wrote. He reported on the NASA team's
designs for molecular gears, their thoughts about "matter
compilers" and the possibilities of "smart
materials" that could heal themselves if torn or broken.
"There is no question that real nanomachines are probably
decades away. But more and more, research is demonstrating that
such things are possible—possibly sooner than most of us
think," Hall concluded.
Shortly after the article appeared, NASA issued a substantial press
release from its Washington headquarters describing the
team's work.
Sky (the monthly
in-flight publication of Delta Airlines with 500,000 copies in
print and a total readership exceeding 1 million) devoted part of
its March 1997 issue to "The Future Of The Future: Peering
Into The Nanofuture." Author Robert Ebisch surveyed current
micromachines created using lithographic techniques, and
dismissed them as "crude monkey tricks compared with what is
to come, if the core concepts of future nanotechnology are on
target." He extensively quoted Ralph Merkle (computational
nanotechnologist at Xerox Corp. and cochair of the upcoming Fifth Foresight Conference on
Molecular Nanotechnology), cited Eric Drexler's Engines of Creation, and
discussed resistance in the old line science community to its
concepts. "A complete scandal," MIT professor Marvin
Minsky is quoted as saying of the April 1996 Scientific
American article on nanotechnology. Ebisch surveyed
recently reported advances in the field, both in protein
engineering and mechanical construction, and quoted Minsky that
"it shows there's no technical reason why the stuff can't be
done."
Popular Mechanics
carried a brief item in the Tech Update column of its July
1997 issue about recent fullerene tube developments at Rice
University and in Switzerland, and reported that "Nanotube
cable...between 10 and 12 times stronger than steel" would
make feasible a "space elevator" using a cable
suspended from a geosynchronous satellite. "Even if a space
elevator is never built, researchers say nanotubes will find
their way into a variety of aerospace applications. They could
also be used in bulletproof vests, sports equipment and
automotive parts. Electrically conductive nanotubes could wire
computer chips," the article said.
Knight-Ridder Newspapers
science correspondent Robert Boyd authored a solid basic survey
of nanotechnology carried by member newspapers in late March. The
chain owns major dailies including the San Jose
Mercury, Miami Herald, Detroit Free
Press and Philadelphia Inquirer, and dozens
of smaller papers. Boyd quoted Merkle, Nobel Laureate Richard
Smalley of Rice University, Paul Green of Nanothinc, and
Foresight executive director Chris Peterson. Nanotechnology is
"a very broad field, and it is, in many ways, the ultimate
playground" of science, Smalley is quoted as saying. The
story also referred to research by Al Globus and his NASA
colleagues. It echoed may of the themes in a February 20 story in
the Inquirer by Reid Kanaley, which was discussed in
MediaWatch.28.
The electronic computer is now 50
years old. Noting the anniversary both of its invention and of
the formation of the Association for Computing Machinery, (ACM) Electronic
Engineering Times used a review of
the first half century to look forward to the next. At ACM's anniversary
meeting in San Jose, plenary speakers discussed advancing the
state of silicon chip architecture, the physical limits imposed
on Moore's Law as circuit dimensions continue to shrink, and even
the continued viability of the basic von Neumann computing
architecture (in which a sequence of operations retrieves data
from a central memory, processes it and then returns the result).
Caltech electrical engineering professor Carver Mead discussed
analog approaches to computing "inspired by biology's mode
of information processing: neural networks. Departing once again
from the conventional wisdom, Mead...now predicts that
analog/neural systems represent the future of computing,"
the magazine wrote.
Associated Press Science
Editor Matt Crenson wrote in February about a laboratory
demonstration of the Casimir Effect—virtual photons that
"spontaneously burst into existence like kernels of popping
corn and then disappear almost instantly, (which) ought to push
two narrowly separated metal plates together." Dutch
physicist Hendrik Casimir postulated the effect in 1948, based on
quantum electrodynamics, but nobody had set out to verify it
until a University of Washington physicist did so last summer.
Although too weak to be significant at macro scales, the Casimir
force may need to be taken into account in nanomachines, Crenson
wrote. "Right now the possibilities of nanotechnology are as
endless as the imagination of the field's most enthusiastic
proponents. But in the future, nanotechnology will rely on
understanding the Casimir force and similar effects," he
said.
From Foresight Update 29, originally
published 30 June 1997.
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