Chapter 6: Bioelectronics and Protein-Based Optical Memories and Processors

Duane L. Marcy, Bryan W. Vought, Robert R. Birge

Overview

Molecular computing is defined as the encoding, manipulation, and retrieval of information at a molecular or macromolecular level. Bioelectronics (or biomolecular electronics) is a subfield of molecular electronics that investigates the use of native, as well as modified biological molecules (chromophores, proteins, etc.), in place of the organic molecules synthesized in the laboratory. Because natural selection processes have often solved problems of a similar nature to those that must be solved in harnessing organic compounds, and because self-assembly and genetic engineering provide sophisticated control and manipulation of large molecules, bioelectronics has shown considerable promise. The ability to explore new architectures unique to molecular-based systems has a potential equal to that provided by molecular-scale engineering and miniaturization.

Semiconductor electronics is a well-established technology for developing computing systems. Therefore one should not consider that bioelectronics could instantly replace semiconductor electronics as a tool for developing computing systems, but that it will become a more competitive technology as the trend advances toward more powerful computers. The continuing push toward miniaturization and high speed as evidenced by Moore's Law is driving the semiconductor industry toward the limits of lithographic manipulation of bulk materials and into the domain of the molecular world. Experts in the semiconductor industry predict that standard roomtemperature silicon CMOS will reach its scalable limit within the next two decades and after that, new inventions, particularly new "transistors" as well as new computer architectures, will be needed to circumvent currently known material, device, and circuit limits (Meindl 1993). When the requirement to directly manipulate compounds at the molecular level is reached, technologies such as bioelectronics will become more viable. For this reason, this chapter begins by comparing bioelectronics to semiconductor electronics as the molecular limit is approached.

A bioelectronic material that has gathered considerable interest is the protein bacteriorhodopsin. The salt marsh bacterium Halobacterium salinarium uses the protein in a process that converts light energy to chemical energy, and therefore it has many unique optoelectronic properties. The properties important for employing bacteriorhodopsin in computing systems will be discussed. Bacteriorhodopsin has found many applications as a storage and computing material. Several systems in the field of optical memories and optical processors that have been prototyped or envisioned are described in this chapter.

Finally, the fact that bacteriorhodopsin is a biological substance opens the door for a unique method of material optimization. Although the optimization of inorganic materials requires detailed knowledge of the structure and properties of that material before modifications can be made to improve its performance in an application, a biological material can be modified simply based on its performance. Through genetic mutation, changes in a material can be tested to see if they decrease or increase the performance of the material in the application. The mutations that improve the system can then be further modified, forcing an accelerated version of evolution to take place. Evolution, which has worked so well in making the material perform its function in the living organism, is now applied to make the material work in the application of interest. This can all take place without detailed knowledge of the structure or properties of the material. Genetic engineering as applied in this manner is described in the final section of this chapter.