Potential Roles for Diatomists in Nanotechnology
Richard Gordon
Departments of Radiology and Electrical & Computer Engineering
University of Manitoba
Health Sciences Centre. GA216, 820 Sherbrook Street
Winnipeg, MB R3A 1R9 Canada
Phone: (204) 789-3828, Fax: (204) 787-2080
E-mail: GordonR@ms.Umanitoba.ca
John Parkinson
Etc.
Manuscript started June 1, 2002. Version 9, February 9, 2003. Prepared for a
special issue of J. Nanosci. Nanotech. 3.
Abstract
Diatoms produce diverse three dimensional structures that may be of value
in growing components for nanotechnology, as an alternative to present
lithographic techniques. Vapor replacement of the silicon permits the
conversion of diatom silica valves and other structures to metal/ceramics,
with no loss of structure. The literature on diatom nanotechnology is
reviewed, along with suggestions on how diatomists might enhance this
emerging technology. There is need for a systematics based catalog of parts,
improved diatom culture techniques, better understanding of the mechanisms
of diatom morphogenesis and motility, and genetic manipulation,
mutagenesis and selection (as via a compustat). We also need a diatom
genome project based on species that would be valuable for nanotechnology.
Introduction
In 1988, while I was probably the world’s only Professor of Botany and
Radiology, I received an invitation to an IEEE (Institute of Electrical and
Electronics Engineers) meeting in New Orleans from a former postdoctoral
student, Rangaraj M. Rangayyan. He and I had worked on enhancement of
mammograms and computed tomography via teleradiology a few years
earlier ((Rangayyan, Dhawan & Gordon, 1984)). My scientific hobby of
diatoms had brought me into the Department of Botany, as I had been
working on and off on their morphogenesis and motility for some years. So I
put together a two page paper for the Microscopic Imaging session chaired
1
by Karan Kaler, reporting on work with another then recent postdoc,
Baltazar Aguda, but added an engineer’s slant:
Diatom morphogenesis: natural fractal fabrication of a complex
microstructure
Abstract: “Diatom shells are intricate structures made by single algal cells
with a spacing between parts of about 0.1 µm. They appear to be formed by
instabilities in diffusion-limited precipitation of amorphous, colloidal silica.
The patterns are apparently modified by surface diffusion during their
formation. They present a possible means of microfabrication of intricate
structures.” ((Gordon & Aguda, 1988))
This was expanded 11 years later by the imaginative postdoctoral fellow
John Parkinson, this time addressed to a more specifically nanotechnology
audience ((Parkinson & Gordon, 1999)). Beyond micromachining: the
potential of diatoms has already been cited at least 11 times (((Coradin,
Durupthy & Livage, 2002)); ((Falciatore & Bowler, 2002)); ((Guetens et al.,
2000)); ((Kröger et al., 2000)); ((Kröger, Deutzmann & Sumper, 2001b));
((Lowe, 2000)); ((Noll, Sumper & Hampp, 2002)); ((Sandhage et al., 2002));
((Scala & Bowler, 2001)); ((Zurzolo & Bowler, 2001))).
One might wonder why people in nanotechnology would bother with
diatoms, since they are made of silica, rather than elemental silicon, the
staple of the electronics industry. I wondered too, and then a remarkable
paper arrived by Kenneth H. Sandhage and his colleagues ((Sandhage et al.,
2002)). Inspired by Beyond micromachining, they added one major step:
replacement of all the silicon atoms with magnesium atoms. This was done
by placing diatom valves (Aulacoseira obtained from diatomaceous earth) in
a magnesium gas at 900oC for 4 hours. The wonderful result is that the
structure is preserved during this process, much like the (not necessarily
slow: ((Drum, 1968))) process of fossilization. In this case, the SiO2 was all
replaced by MgO:
“…the silica could also be converted into a wide variety of other ceramics
or ceramic/metal composites with desired electronic, optical, thermal, or
chemical properties… it seems likely that future genetic engineering could
yield frustules with tailored, non-natural shapes and features ((Parkinson &
Gordon, 1999))” ((Sandhage et al., 2002)).
An advantage of diatoms is that they allow direct fabrication of three
2
dimensional structures, instead of the layer by layer manipulation common
in present day nanotechnology, which is based primarily on the lithographic
methods used to make microelectronics ((Madou, 2002)). Furthermore,
diatoms reproduce, and so can outperform any factory production method
via exponential growth of their numbers ((Sandhage et al., 2002)). Diatom
parts could also be used as molds ((Blanco et al., 2000)). The diatom valve is
flexible, without being brittle ((Sterrenburg & Tiffany, 2003)), and it will be
interesting to measure its strength, in silica and substituted materials, using
micromanipulation techniques (((Harper & Harper, 1967)); ((Rappaport,
1996))), or to calculate it, which would be a challenge to finite element
methods ((Entwistle, 1999)). One might speculate that aberrant diatoms will
have weaker valves. The degree of silicification of diatom valves can vary in
nature for a species, some diatoms have only minimally silicified valves, and
in Cylindrotheca, only the raphe is silicified, the remainder of the valve
being purely organic.
The study of diatoms may now take center stage in nanotechnology and
biotechnology. It all depends on just how versatile they are, and how much
effort we put into mastering their domestication. Here are opportunities for
diatomists to apply their skills:
1.
2.
3.
4.
5.
Nanotechnologists need a catalog of parts that diatoms make that
might be useful, and which species of diatoms make them. Parts
include pores of many shapes, costae, raphes, whole valves, girdle
bands, strutted processes, rimoportulae, labiate processes, setae,
spines, hollow spines, etc. Some parts come prefit together, such as
marginal spines in certain colonial diatoms.
Culture of diatoms with interesting parts may have to be
standardized and scaled up. In particular, we may have to learn how
to prevent diatom malformations, common in culture ((Estes &
Dute, 1994)), from occurring (except when they are exactly what we
want).
Quantitative control of silicification, by making silica the limiting
nutrient ((Gensemer, Smith & Duthie, 1993)), gives us a degree of
control of the morphogenetic process.
Silica starvation synchrony ((Okita & Volcani, 1978)) could be used
to mass produce parts whose silicification is stopped early, such as
nascent valves not yet released from their silicalemmae.
Auxospores ((Håkansson & Chepurnov, 1999)) and resting spores
((Oku & Kamatani, 1995)) may provide unique diatom parts, and we
3
need to master how to bring on these life cycle stages and diatom
sex for recombination ((Falciatore & Bowler, 2002)).
6. Inclusions of salt crystals ((Gordon & Brodland, 1990)) and
manipulation (or poisoning, as with germanium or aluminum
((Vrieling et al., 1999))) of the physicochemical conditions in the
silicalemma should provide altered valve geometries ((Vrieling ,
Gieskes & Beelen, 1999)).
7. Separation techniques for the isolation and purification of specific
diatom parts will be needed.
8. Given that many diatoms decrease in size through succeeding
generations ((Pfitzer, 1869)) ((Kling, 1993)), we may have to either
focus on those few species that somehow avoid this, or sort diatoms
or components by size.
9. If we want diatoms to make parts for us that are not in their present
repertoire, we need to find out how far they can be pushed by
domestication (forced evolution towards desired characteristics), as
with a compustat ((Gordon, 1996a)), or by selection in the presence
of physical forces ((Gordon et al., 1996)).
10. Diatom paleontologists ((Stoermer & Smol, 1999)) may be able to
extend the parts list, and challenge us to recover lost morphogenetic
capabilities by selective breeding and mutagenesis of extant species
for “throwbacks”.
11. Since the molecular biology of diatoms (reviewed in ((Falciatore &
Bowler, 2002))) is now well under way (((Hildebrand et al., 1993));
((Roessler, 2000))), including genetic transformation (((Apt, KrothPancic & Grossman, 1996)); ((Dunahay, Jarvis & Roessler, 1995));
((Falciatore et al., 1999)); ((Zaslavskaia et al., 2000))), we may find
means of genetically manipulating diatoms to produce silica parts
with desired characteristics.
12. Much may be learned by the further analysis of just how diatoms
create silica structures. This field has advanced from simple
precipitation models (albeit with instabilities in diffusion limited
precipitation: ((Schultze, 1863a)); ((Schultze, 1863b)); ((Gordon &
Drum, 1994))), to the role of the cytoskeleton ((Parkinson, Brechet
& Gordon, 1999)), to the molecular analysis of silica transport and
“prepatterning” organic molecules (((Brott et al., 2001)); ((Fischer
et al., 1999));
((Hildebrand, Dahlin & Volcani, 1998));
((Hildebrand et al., 1997)); ((Kröger & Wetherbee, 2000)); ((Kröger,
Bergsdorf & Sumper, 1996)); ((Kröger, Deutzmann & Sumper,
1999)); ((Kröger et al., 2000)); ((Rhodes, 2000)); ((Kröger,
4
13.
14.
15.
16.
Deutzmann & Sumper, 2001a)); ((Kröger, Deutzmann & Sumper,
2001b)); ((Kröger et al., 1997)); ((Martin-Jezequel, Hildebrand &
Brzezinski, 2000)); ((Naik et al., 2002)); ((Sowards et al., 2001));
((Wenzler et al., 2001))), whose place in the overall spatiotemporal
morphogenesis of diatom valves and other parts is far from
understood ((van de Poll, Vrieling & Gieskes, 1999)). These
molecules are already in use to produce holograms ((Brott et al.,
2001)).
The optical properties of diatoms have yet to be explored, except for
speculations that the valve and spines form an antenna for visible
light (Ryan W. Drum, personal communication). With
metal/ceramic substitutions ((Sandhage et al., 2002)) the refractive
index would change, altering optical characteristics. Perhaps diatoms
could become components in optical computing ((Karim & Awwal,
1992)). The remarkable regularity of striation in some genera makes
the valves act as small diffraction gratings ((Sterrenburg, 1991)).
This idea was also raised in an apparently unsuccessful grant
application that I reviewed, but is certainly worth pursuing.
Diatom adhesion to surfaces is strong, a major factor in biofouling
((Johnson, Hoagland & Gretz, 1995)). These glues, deposited by us,
or diatoms directed by us to specific locations, might prove useful in
bonding nanotechnology components.
It may now be time to launch a diatom genome project around
diatom nanotechnology objectives. Selection of appropriate diatoms
should be based on phylogenetic, molecular evolution ((Kooistra &
Medlin, 1996)) and taxonomic criteria, and on (preferably small)
genome size ((Falciatore & Bowler, 2002)). Here is an opportunity
for rational choice of a model organism or two, rather than locking
in on someone’s favorite beast which may be evolutionarily
specialized (as happened with Drosophila and zebrafish). One
diatom, the morphologically simple Thalassiosira pseudonana, is
now being sequenced (((Hildebrand, 2000); ((Schwartz, 2001)).
If we succeed in morphologically and/or genetically modifying
diatoms, given that they are at the bottom of many food chains or
webs, attention will have to be paid to the accidental release of
altered diatoms into the environment (Liz Kalaugher, personal
communication). The ubiquity of some species presents the
possibility of worldwide impact, which we should evaluate before it
happens.
5
17. If diatoms are to be used for microencapsulation of drugs
((Sandhage et al., 2002)), then we have to worry about
biocompatibility or silicosis ((Harber et al., 1998); (Hughes et al.,
1998)).
Finally, motile diatoms can lift 1000x their own weight (((Harper & Harper,
1967)); ((Gordon & Drum, 1970))) via a still puzzling raphe mechanism
((Drum & Gordon, 2003)) that appears to be over 99% energy efficient
((Gordon, 1987)). Some diatoms move and then adhere tightly to surfaces
((Wang et al., 2000)). If we understood their chemotactic ((Cooksey &
Cooksey, 1988)), phototactic ((Nultsch, 1975)) and adhesion
((Wigglesworth-Cooksey & Cooksey, 1992)) behavior better, we might be
able to get diatoms to move into specified positions, say on micropatterned
substrates ((Chen et al., 1997)), and then in place convert them into
organized arrays of nanotechnology components.
Some engineers are trying to grow computers the way embryos grow
((Mange et al., 2000)) ((Gordon, 2001e)). Diatoms give us a handle on
morphogenesis at the finer, subcellular level (cf. ((Gordon, 1999)); ((Harold,
2001))). There is much work ahead, but there is no reason that diatomists
couldn’t take the lead, teaming up with the engineers who are trying to grow
nanotechnology.
Acknowledgments
I would like to thank Diana Gordon, Isabelle Harouche, Thierry Lebeau,
Blake Podaima, Kenneth H. Sandhage and Frithjof A.S. Sterrenburg for their
comments.
6
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