Bioelectronics and Protein-based Devices


'Robert R. Birge Robert R. Birge

Molecules form the basis of life, and when combined to form biological organisms, yield highly sophisticated systems which perceive, manipulate, self-repair, think, calculate and feel. Although digital computers can carry out calculations with a speed and precision far superior to humans, in the other five areas, even simple biological systems are superior. In short, biology has achieved through billions of years of evolution, complex systems that have unique attributes that have to date escaped duplication within the realm of semiconductor and software systems.

Chess enthusiasts were recently surprised and perhaps dismayed to watch IBM's Deep Blue computer beat the world's leading [human] chess master, Garry Kasporov [for details see http://www.chess.ibm.com/home/html/ b.html]. It now seems clear that a computer will soon be able routinely to beat the best human chess masters. Such an accomplishment should not be regarded as an example of artificial intelligence. Chess is a game, and follows well-defined rules. Such constraints permit programmers to test all possible moves, and make decisions based on rule-based logic. While the hardware and software responsible for Deep Blue's accomplishments are very impressive, they do not combine to yield artificial intelligence.

Thus nature still retains the edge over human engineering in many aspects of global computational/intellectual endeavors. Many scientists, and most humanists, will argue that human engineering will never achieve the level of creation and creativity that is evidenced by the human brain, and nature in general. Many scientists and engineers, however, believe that given enough CPU power, memory and data bandwidth, there is no limit as to what can be accomplished. We make no attempt here to arbitrate between these two conflicting views of evolutionary versus human engineering. Rather, we suggest that if our goal is to compete with nature, we need to learn as many of its secrets and make use of its materials and methods to the extent possible.

During the past two decades, my research group has been exploring the potential use of biological systems in computer architectures. Our approach is often called biomimetic, in that we try and use native and genetically engineered proteins in architectures that are often designed to mimic the way nature does things. We seek to make both associative memories, that mimic the data storage and retrieval capabilities of the human brain, and volumetric memories, that can store both image and digital data within three-dimensional solids of a protein matrix. Working prototypes are now in the second generation, but much remains to be accomplished before commercial systems will be available. Here, we give a brief outline of how our devices work and a progress report. We will also explore what impact such systems may ultimately have on computer artists.

Interest in exploring the computer applications of bioelectronics dates back to the early 1970s and the discovery by Walther Stoekenius and Dieter Oesterhelt at Rockefeller University, New York, of a bacterial protein that has unique photophysical properties. The protein is called bacteriorhodopsin and it is grown by a salt-loving bacterium that populates salt marshes. In the native organism, this photosynthetic protein allows the bacterium to grow when the concentration of oxygen is insufficient to sustain respiration. Upon the absorption of light, the protein pumps a proton across the membrane and drives the synthesis of ATP. The name bacteriorhodopsin derives from its photochemical similarities to rhodopsin, the visual pigment in the eye. Russian scientists were the first to recognize and explore the potential of this protein in optical computing.

Funded by "Project Rhodopsin", and headed by the late Yuri Ovchinnikov Russian scientists at five laboratories, explored the use of this protein in photochromic and holographic devices. Ovchinnikov was not only a highly respected molecular biologist, but also had the ear of the Soviet military leaders. He convinced them that Soviet science could leap-frog the west in computer technology by exploring bioelectronics and garnered significant funding for his Project. Many of the applications were military and the details of this ambitious project may never be fully known. Informal reports from Russian scientists currently in the U.S. indicate the successful creation of sophisticated optical computing architectures that carried out real-time data transformations. Nevertheless, the unusual photochemical and holographic properties of this protein were published and stimulated the international research effort that continues today.

Bacteriorhodopsin is a membrane bound protein with seven alpha-helical segments that span the membrane. A light absorbing group [called the chromophore] embedded inside the protein matrix converts the light energy into a complex series of molecular events that pump the proton. Scientists using the protein for bioelectronic devices exploit the fact that this complex series of thermal reactions results in dramatic changes in the optical and electronic properties of the protein [Fig. 2].

The excellent holographic properties of the protein derive from the large change in refractive index that occurs following light activation. Furthermore, bacteriorhodopsin converts light into a refractive index change with remarkable efficiency [approximately 65%]. The size of the protein is ten times smaller than the wavelength of light which means that the resolution of the thin film is determined by the diffraction limit of the optical geometry rather than the "graininess" of the film. [The Soviet military exploited this property by making thin films of bacteriorhodopsin, called Biochrome, for use as microfiche recording materials.] Also, the protein can absorb two photons simultaneously with an efficiency that far exceeds other materials. This latter capability allows the use of the protein to store information in three dimensions [see below]. In addition, the protein gives off an electrical signal that changes polarity as a function of its current conformation, or state. This latter characteristic can be used to design memories that use light to write the information and electronics to monitor the data. Finally, the protein was designed by nature to function under conditions of high temperature and intense light, a necessary requirement for a salt marsh bacterial protein.

When the protein absorbs light, it undergoes a complex photocycle which generates intermediates with absorption maxima spanning the entire visible region of the spectrum [Fig. 2]. Many of the early optical devices and memories based on bacteriorhodopsin operated at liquid nitrogen temperature and utilized photochemical switching between the bR and K states. While these devices were efficient and potentially very fast [the bRgK interconversions take place in a few picoseconds], the use of cryogenic temperatures precluded general application. Most current devices operate at ambient or near ambient temperature and utilize the following two states: the initial green – red absorbing state [bR] and the long-lived blue absorbing state [M]. The forward reaction only takes place via light activation and is complete in ~50 ms. In contrast, the reverse reaction can be either light activated or can occur thermally. The light activated M > bR transition is a direct photochemical transformation.

The thermal M > bR transition is highly sensitive to temperature, environment, genetic modification and chromophore substitution. This sensitivity is exploited in many optical devices based on bacteriorhodopsin. Another reaction explored here is a photochemical branching reaction from the O intermediate to form P. This intermediate subsequently decays to form Q, a species that is unique in that the chromophore breaks the bond with the protein but is trapped inside the binding site. The Q intermediate is stable for extended periods of time [years] but can be photochemically converted back to bR. This branching reaction has great potential for long term data storage as discussed below.

ASSOCIATIVE MEMORIES MIMIC THE WAY THE HUMAN BRAIN STORES AND RETRIEVES INFORMATION.

STORING DATA IN THREE DIMENSIONS.

DATA ARE WRITTEN IN PARALLEL VIA A BRANCHING REACTION.

DATA ARE READ IN PARALLEL ONE PAGE AT A TIME.

DATA ARE ERASED IN MULTIPLE PAGE SETS USING INCOHERENT BLUE LIGHT.