CHAPTER 9

BIOLOGICAL, CARBON, AND THEORY ISSUES

OVERVIEW

Lynn Jelinski
Cornell University
WTEC Panel

Biological Aspects

Biology, biophysics, and biomolecules are themes that run through much of the current research on nanoparticles, nanostructured materials, and nanodevices. The structure of the WTEC nanotechnologies study acknowledges and emphasizes the need for interdisciplinary research, especially as it applies to the bio-related aspects of nanotechnology; therefore biological aspects of the study are discussed below within the organizational structure of the entire study.

The relationship between the biological sciences and nanotechnology spans across the missions of a number of federal agencies. For example, NASA is interested in the biomimetic and/or enzymatic removal of carbon dioxide from air, in self-repairing spacesuits and habitats, and in electronic "nose" or sensor technology that can detect adverse chemicals. DOD is interested in biosensors as well, particularly for biological and chemical warfare agents. NSF has programs in molecular self-assembly, in the use of polynucleotide chains as templates for quantum dots, and in oligonucleotide arrays for gene analysis. Biological applications are one of the fastest growing areas of research in NSF's National Nanofabrication Users' Network (NNUN). Biomedical research sponsored by NIH offers a rich opportunity for nanotechnology research. For example, NIH sponsors the University of Michigan's center for neural communications technology, a number of chip technology projects aimed at genomic sequencing, projects involving biosensor development, and projects that involve the measurement of nanoforces and the synthesis of nanocomposites based on bones and teeth.

The complementary interests of the federal agencies illustrated by these examples suggest that it may be fruitful to develop interagency joint proposals to coordinate the funding of nanotechnology research, especially as it pertains to the biological sciences.

Nanotechnology Building Blocks

Synthesis

Modern biotechnology now makes it possible to tap the synthetic machinery of biological systems to produce highly regular materials that might not occur in nature, and/or materials with enhanced properties. Examples include non-native protein polymers with precisely controlled molecular weights, poly(hydroxyalkanoates) that are produced in microbes and plants, and polysaccharides with unusual functionalization (Tirrell et al. 1994; 1995). Furthermore, improved chemistries and separations technologies make it possible to produce unusual DNA and RNA polymers and to obtain purified lipids. These molecules of biological or quasi-biological origin are attractive candidates for building up precisely controlled and complex three-dimensional nanostructures because they usually undergo exquisitely selective binding and obey highly specific rules for self-assembly. These positive qualities notwithstanding, it is important to keep in mind that many biomolecules are fairly nonrobust, and techniques will be required to overcome this problem.

Seeman and coworkers (p. 1771) have been investigating the ability of DNA molecules to form complex three-dimensional objects, with the goal of forming 2-D and 3-D periodic structures with defined topologies. DNA is ideal for building molecular nanotechnology objects, as it offers synthetic control, predictability of interactions, and well-controlled "sticky ends" that assemble in highly specific fashion. Furthermore, the existence of stable branched DNA molecules permits complex and interlocking shapes to be formed. Using such technology, a number of topologies have been prepared, including cubes (Chen and Seeman 1991), truncated octahedra (Zhang and Seeman 1994), and Borromean rings (Mao, Sun, and Seeman 1997). The Friedlander work (p. 83) on the synthesis of nanoparticles and their aggregation describes nanochains as a new type of polymer. See the section below, Consolidated Materials and Parts, which describes "biological bar magnets," which are simply nanochains.

Role of Nanoparticles in Health and Pollution

Although beyond the scope of this review, it is important to keep in mind the potential role of atmospheric nanoparticles in photocatalytic and thermal production of atmospheric pollutants (Chianelli p. 133). Atmospheric aerosols in heavily polluted areas have the potential to accelerate ozone formation reactions; furthermore, because they are respirable, they could represent a health hazard.

These aerosols generally contain two major components; one is composed of amorphous carbon that has fullerene-like particles dispersed in it. The second is inorganic and consists of oxides and sulfides supported on clay minerals. In particular, the iron oxide, manganese oxide, and iron sulfide nanoparticles have band-gaps that could enhance the photocatalytic adsorption of solar radiation. In addition, these materials are acidic and may be coated with water, which would enhance their catalytic ability to crack hydrocarbons and create free radicals (Chianelli p. 133). At present this is an underexplored area of research that bears scrutiny.

Assembly

Research frontiers that exploit the capacity of biomolecules and cellular systems to undergo self-assembly have been identified in two recent National Research Council reports (NRC 1994; 1996). Examples of self-assembled systems include monolayers and multilayers, biocompatible layers, decorated membranes, organized structures such as microtubules and drug-delivery systems, biomineralization, and the intracellular assembly of CdSe semiconductors and chains of magnetite.

Biological materials undergo self-assembly in a hierarchical manner, beginning with monomer molecules (e.g., nucleotides and nucleosides, amino acids, lipids), which form polymers (e.g., DNA, RNA, proteins, polysaccharides), then assemblies (e.g., membranes, organelles), and finally cells, organs, organisms, and even populations (Rousseau and Jelinski 1991). Consequently, biological materials assemble on a very broad range of organizational length scales, and in both hierarchical and nested manners (Aksay p. 79).

Research stemming from the study of self-assembling surfaces (e.g., alkylthiols and other biomembrane mimics on gold) led to the discovery of "stamping" (Kumar and Whitesides 1993). This method, in which an elastomeric stamp is used for rapid pattern transfer, has now been driven to < 100 nanometer scales and extended to non-flat surfaces and is called "soft lithography." The exciting and far-reaching applications made possible by soft lithography are described in Chapter 4 (Whitesides, p. 76).

Self-assembled organic materials such as proteins and/or lipids can be used to form the scaffolding for the deposition of inorganic material to form ceramics such as hydroxyapatite, calcium carbonate, silicon dioxide, and iron oxide. Although the formation of special ceramics is bioinspired, the organic material need not be of biological origin. An example of this is the production of template-assisted nanostructured ceramic thin films (Aksay et al. 1996), which is described in Chapter 7, High Surface Area Materials.

A particularly interesting example of bio-inspired self assembly has been described in a recent article by Stupp and coworkers (1997). This work, in which organic "rod-coil" molecules were induced to self-assemble, is significant in that the molecules orient themselves and self-assemble over a wide range of length scales, including mushroom-shaped clusters, sheets of the clusters packed side-by-side, and thick films, where the sheets pack in a head-to-tail fashion. The interplay between hydrophobic and hydrophilic forces is thought to be partially responsible for the controlled assembly.

Dispersions and Coatings

Drug Delivery

Highly porous materials are ideal candidates for controlled drug delivery (Schnur, Price, and Rudolph 1994) and for tissue engineering (Hubbell and Langer 1995). An example of a controlled drug delivery system comes from the area of microtubules. Phospholipid bilayers can be coaxed to self-assemble into long cylindrical tubes with diameters usually below a micron and lengths up to hundreds of microns (Schnur 1993). During synthesis, drugs can be entrained in these nanotubes, and the final product can be used as a controlled delivery system. Tubules prepared from phospholipid bilayers are ideal for such applications because they are biocompatible.

High Surface Area Materials

Ceramics

Fundamental studies of biomineralization, in which an organic substance (usually protein or peptide or lipid) interacts with an inorganic phase (e.g., calcium carbonate or hydroxyapatite) have led to the bioinspired synthesis of composite materials. The structure and porosity of the inorganic phase can be controlled by templating with an organic surfactant, vesicular arrays, or liquid crystalline materials. Micelle-templated synthesis can produce ceramics with 20-100 Å pore dimensions (Ying p. 96). These tailored pores can be used as catalysts and absorbents, and for gas/liquid separations, thermals, and acoustic insulation. Their selectivity makes them very useful for biochemical and pharmaceutical separations. Bioceramics can also be made that are highly compatible with teeth and bone.

An interesting example of an organic/inorganic composite is the new packaging material that has been developed to replace the polystyrene "clam-shell" for fast food products. Composed of potato starch and calcium carbonate, this foam offers the advantages of good thermal insulation properties, light weight, and biodegradability (Stucky 1997).

Functional Nanostructures

Optoelectronic Devices

Biological molecules and assemblies, such as the photochemical reaction center, are capable of capturing light with good quantum efficiency and transforming it into chemical energy. If properly exploited, such assemblies have potential applications as biomolecule information-processing units.

Bacteriorhodopsin, from the purple membrane bacterium Halobacterium halobium, is one such system that has been studied extensively and has been commercialized into optical holographic memories (Birge 1995). In the bacterium, the protein bacteriorhodopsin self-assembles into ordered lipid patches. The protein absorbs light and undergoes a cycle involving a complex series of intermediates, resulting in a proton being pumped across the membrane. It was information developed from understanding the basic science behind the way that bacteriorhodopsin works that led to the use of bacteriorhodopsin as a biomolecule information processing unit. To be used for information storage, the protein is placed under nonbiological conditions. It is dispersed and immobilized into a matrix (e.g., collagen or another polymeric substance) and held at liquid nitrogen temperatures. At this low temperature, the protein acts as an optically driven bistable switch. One form, the light-adapted form of bacteriorhodopsin, absorbs light at 570 nm. When irradiated with green light at 77K, it switches to a different stable form that absorbs light at 630 nm. Using light of different colors enables one to read and write images onto these memories. By subtracting one memory from the other, these memories are especially useful for real-time, rapid comparison of images.

Molecular Motors

The molecular motors found in biology provide for bacterial locomotion, as well as for the active transport and delivery of molecules. For example, the bacterial flagellar motor, about 20 nm in diameter, is comprised of a complex assembly of more than 10 different proteins (Imae and Atsumi 1989). The role of the motor is to rotate the helical flagella of the bacterium so that it is able to swim. Chemical energy (in this case, protons or sodium) is transduced into mechanical energy.

Other examples of molecular motors include RNA polymerase (Yin et al. 1995), myosin, and kinesin (Seventh Biophysical Discussions 1995). The fuel that powers these motors is ATP. A number of researchers have proposed schemes by which such motors could be used to deliver molecules, one at a time, for the purpose of the ground-up assembly of nanoscale devices (NRC 1996). It is envisioned that the highways could be actin or tubulin, which would need to be immobilized onto a surface. Myosin or kinesin naturally travel along these highways and could be used to deliver molecular "packages" to a specific assembly site. Needless to say, many details and the ultimate feasibility of this vision need to be worked out.

Other Forms of Biological Transport Using Nanoparticles

In the body, the function of the high density lipoproteins is to transport cholesterol. The ~7.5 nm discoidal lipoprotein assemblies are sandwiched between discs of phospholipids, and stacked, poker-chip style. The lipoproteins stabilize the cholesterol particles and assist in their transport. Current research involves manipulating and fusing the assemblies and particles with an atomic force microscope tip (Sligar p. 181).

Nanoscale Silicon Technology

Up until this point, we have focused almost exclusively on nanoparticles, nanostructured materials, and nanodevices from the point of view of their synthesis from the ground up, i.e., starting with the atoms and molecules and building up to particles and objects. It would be myopic to ignore new advances in silicon nano- and micro-fabrication technology in which structures are formed by subtractive techniques. This is especially true in light of the recent successes in immobilizing biological nanoparticles (e.g., enzymes, antibodies, etc.) on these surfaces, leading to functional devices that can be employed as sensors, nanoelectrodes, prosthetic devices, or nanomachines. The following section briefly highlights selected research activities in this area and focuses on soft lithography, biosensors, medical nanomachines, and nano electrodes and capillaries.

Processing using "stamping" or soft lithography. Whitesides (p. 76) and his coworkers have pioneered the technique of soft lithography, which offers enormous promise for the fabrication of structures in the tens of nanometer scales and larger.

Biosensors. The biotin-avadin coupling reaction and the alkylthiol/gold surface functionalization technique (Allara 1996) have proved to be of major importance in coupling biological elements onto nonbiological surfaces. Once coupled to silicon devices, which can be queried by electrical, optical, or chemical means, these biological assemblies can function as highly specific biosensors. There has been a very large body of work on biosensors, often employing antigen-antibody recognition as the sensing mechanism (bioaffinity sensors), or redox enzymes as the sensing element (biocatalytic sensors).

A particularly interesting example comes from the work of Aizawa and coworkers (1996), who have developed an electron transfer pathway of a modified enzyme by self-assembly in a porous gold-black electrode. This sensor uses glucose oxididase, modified with the conductor ferrocene, to detect glucose in solution.

Medical nanomachines (MEMS devices). MEMS (microelectromechanical) devices, built from silicon technology, consist of integrated parts and can act as miniature machines, cogs, actuators, or free-standing capacitors. When properly configured, these devices could be used for biosensors, neural probes for recording and stimulation, and via telemetry for completely implantable microsystems (Wise 1996).

Nano electrodes/capillaries. In order to make progress in the field of nanoparticles and nanotechnology, it will be necessary to develop characterization and measurement devices. There have been many recent advances in the technology surrounding nano electrodes, microcapillaries, and microfluidics (Hietpas et al. 1996).

Consolidated Materials and Parts

Titanium Nanostructures

The commercially available titanium nanostructures also offer advantages in health-related applications, as they are able to withstand stresses in the body that pure titanium is unable to sustain.

Molecular and Quantum Computation

The smallest possible computer would ideally be able to perform computations on a molecular scale. Even though the computation may be carried out on a molecular scale, the issue becomes one of having enough molecules to obtain sufficient signal-to-noise ratio to read out the answer. Consequently, at least at present, these computations must be carried out in bulk or with extremes in temperature. There have been two recent developments along these lines; both developments are in very nascent stages.

Adleman (1994) has shown how the rules of DNA self-assembly, coupled with polymerase chain reaction (PCR) amplification of DNA, can lead to a molecular computer of sorts. The system was used to solve the Hamiltonian path problem, a classic and difficult (NP complete) mathematical problem that involves finding a path between vertices of a graph. The starting and ending vertices of each edge of the graph were encoded as the first and second halves of a strand of DNA. A solution to the problem (i.e., what is the path between two specific vertices?) was obtained by using PCR primers for the two vertices. Others have extended these ideas and shown how one can make DNA add (Guarnieri et al. 1996). Although these are exciting demonstrations, at present this technology has a number of drawbacks, including the labor and time it takes to analyze the results of the computation and the uncertainties associated with wet chemistry.

Quantum computation offers the possibility of ultrafast computation, but it suffers from the conflict between needing to be able to manipulate quantum degrees of freedom while preventing decoherence from taking over (Gershenfeld and Chuang 1997). Approaches to quantum computation have produced a two-bit quantum computer using a single trapped and cooled ion of beryllium, but they require enormous experimental gymnastics (Monroe et al. 1995). Quantum computing has now been demonstrated on bulk molecules using multiple pulse nuclear magnetic resonance techniques to produce coherences in liquids (Gershenfeld and Chuang 1997).

Biological Bar Magnets

It has been well-documented that a very large number of organisms have the ability to precipitate ferrimagnetic minerals Fe3O4 and Fe3S4. In addition, linear chains of membrane-bound crystals of magnetite, called magnetosomes, have been found in microorganisms and fish (Kirschvink et al. 1992). For example, the Fe3O4 domain size in the organism A. magnetotactum is ca. 500 Å, and a chain of 22 of these domains has a magnetic moment of 1.3 x 10-15 A/m2. It is not clear what the biological function of these magnetosomes is, or if or how they could be exploited for non-biological applications. These magnetosomes are an example of the new nanochain form of nanoparticle polymer that is covered by Froes (p. 105).

Carbon

Materials such as carbon nanotubes, fullerenes, nanoparticles, and porous carbon are scientific drivers. They combine one-dimensional properties, such as electronic structures, Coulomb blockade phenomena, and quantum phonon effects, with the mechanical properties of possessing high stiffness yet being bendable (Dresselhaus p. 169).

Nanotubes

Depending upon the method of preparation, nanotubes can be insulators, semiconductors, or conductors. Until recently, nanotubes were produced by methods such as the carbon-arc dischard method, which produced randomly oriented tubes of variable dimensions that were contaminated with carbon particles. However, now Smalley and colleagues (Collins et al. 1997) has prepared all chiral, similar diameter nanotubes. Potential applications include field emission and STM tips, gas storage materials, materials for the manipulation of nanostructures, fillers for conductive plastics, and high power electrochemical capacitors. More recently, Kroto and Walton and colleagues (Terrones et al. 1997) have developed a laser etching method to prepare bundles of aligned carbon nanotubes that are free from contaminating carbon particles. These tubes were produced by pyrolyzing 2-amino-4,6-dichloro-s-triazine on a laser-etched cobalt catalyst on a silicon wafer.

Fullerenes

Polymerized fullerenes, when half-doped with potasium, become superconducting. For example, K3C60 shows isolated phonon modes.

Carbon Nanofibers

Starting with ethylene gas, one can prepare carbon nanofibers that have widths that vary from 2.5 nm to 1 micron and lengths from 5 to 100 microns. Applications include selective absorption agents, molecular sieves, catalyst supports, and electrodes in electronic storage devices. They are especially good for practical hydrogen gas storage systems because the spacings are right; they can store 30 liters per gram of molecular hydrogen. The projection is that the Daimler Benz hydrogen car will be able to travel approximately 5,000 miles on 25 liters of hydrogen fuel (Baker 1997; also p. 172).

Enabling Technologies

Continued progress in nanotechnology and nanoparticles will require certain enabling technologies. These include (see also Koehler and Vermont pp. 25-29) instrumentation such as optical traps, laser tweezers, and "nano-pokers" to measure femtoNewton forces (Svoboda and Block 1994).

There is also a need to move detection away from the ensemble, to the single molecule scale. This includes driving instrumentation toward single molecule spectroscopy, single spin detection (Rugar et al. 1994), chemical analysis of nanoliter volumes (Hietpas et al. 1996), NMR microcoils, nanoscale electrode arrays, and chemical sensing and detecting technology (McConnell 1996), separations technology, chemical analysis of single cells (Hietpas et al. 1996), new biological transformations, and chemical probes of nanostructures.

Theory

Enhanced computational infrastructure, both hardware and algorithm development, will be required to investigate supramolecular assemblies and to understand interactions that occur over a wide variety of time and length scales. At present we are fairly well-equipped to handle quantum mechanical calculations. At the next level of computational complexity, the current molecular dynamics force fields and atomic charges can handle up to about a million particles and still retain their accuracy. The next scale of complexity, mesoscale modeling, currently requires the use of pseudo atoms. Much more research is required to improve the accuracy of finite element calculations and the modeling of materials applications (Goddard 1997; also p. 197).


There is a critical need for molecular level theory to predict structures, proteins, and dynamics. Especially important are issures of reliability, which means that is is going to be important to operate from first principles.

Mechanisms that encourage the development of theory and computation include the SBIR programs, good coupling between academia and industry, and hardware available through the national NSF centers. Much of the progress in theory and computation is advanced by commercialization.

Notes

1References with page numbers but not years of publication are to the authors contributing to this report and the beginning page numbers of their papers. Further references on specific subjects may be found in the individual papers.

References

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Published: January 1998; WTEC Hyper-Librarian
170 9. Biological, Carbon, and Theory Issues 170 L. Jelinski 161