Molecular 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 that 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 has been a recent development along this line. 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 (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 that it is possible to 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.

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 77 K, it switches to a different stable form that absorbs 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 realtime, 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 is about 20 nm in diameter, and 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), F1-ATPase (Noji et al. 1997), myosin, and kinesin (Seventh Biophysical Discussions 1995). The fuel that powers these motors is ATP (adenosine triphosphate). 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, which naturally travel along these highways, could be used to deliver molecular "packages" to a specific assembly site.

Other Forms of Biological Transport Using Nanoparticles

In the human 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 (ATM) tip (Sligar 1998).


There has been considerable research activity in molecular electronics and bioelectronics, particularly in Japan (Aizawa 1994). Although this area of nanotechnology is still not as well developed as others in this report, it bears watching. For example, Shionoya and coworkers at the Institute for Molecular Science of the Okazaki National Research Institutes in Japan (see site report, Appendix D) have proposed that novel combinations of DNA, metal ligands, DNA templating, and proteins could produce molecular wires; molecular hoops through which DNA could be threaded; and double-stranded peptides whose helix pitch could be controlled by an entrained metal (Figure 7.6). The active site containing the metal could be induced to go from Cu(I)tetrahedral to CU(II)square planar, perhaps by electrons delivered by a scanning tunneling microscope (STM) tip.

Published: September 1999; WTEC Hyper-Librarian