Abstract While magnetic and semi-conductor based information storage devices have been in use since the middle

1950's, today's computers and volumes of information require increasingly more efficient and faster methods of storing data. While the speed of integrated circuit random access memory (RAM) has increased steadily over the past ten to fifteen years, the limits of these systems are rapidly approaching. In response to the rapidly changing face of computing and demand for physically smaller, greater capacity, bandwidth, a number of alternative methods to integrated circuit information storage have surfaced recently. Among the most promising of the new alternatives are photopolymer-based devices, holographic optical memory storage devices, and protein-based optical memory storage using rhodopsin , photosynthetic reaction centers, cytochrome c, photosystems I and II, phycobiliproteins, and phytochrome. This seminar focuses mainly on protein-based optical memory storage using the photosensitive protein bacteriorhodopsin with the two-photon method of exciting the molecules. Bacteriorhodopsin is a light-harvesting protein from bacteria that live in salt marshes that has shown some promise as feasible optical data storage. The current work is to hybridize this biological molecule with the solid state components of a typical computer. Contents 1. Introduction 2. Importance 3. Protein Memories 4. Bacteriorhodopsin as an Intelligent Material 4. 1. Need for Molecular Electronics 4. 2. First Imaging device and Microfilm 4. 3. Intelligent Materials 5. Photo cycle of Bacteriorhodopsin 6. Proposed photo cycle for computing needs 7. Bacteriorhodopsin Structure 8. Bacteriorhodopsin as Computer Memory 9. Data Writing Technique 10. Data Reading Technique 11. Data Erasing Technique 12. Bacteriorhodopsin Memory Cell by Bob Birge 12. 1. Memory Cell Specifications 12. 2. How fast can data be accessed with this design?. 12. 3. Data Stability 12. 4. Storage Capacity 12. 5. Transportation 12. 6. Will the molecular memory be able to compete against the traditional semiconductor memory? 13. 3-Dimensional Optical Memories 14. Advantages and Applications of Bacteriorhodopsin 14. 1. Erasable Holographic Memory

14. 2. Optical chameleon 14. 3. Electronic Ink 14. 4. Molecular light conversion 15. Conclusion 16. Reference 1. Introduction Since the dawn of time, man has tried to record important events and techniques for everyday life. At first, it was sufficient to paint on the family cave wall how one hunted. Then came the people who invented spoken languages and the need arose to record what one was saying without hearing it firsthand. Therefore, years later, earlier scholars invented writing to convey what was being said. Pictures gave way to letters which represented spoken sounds. Eventually clay tablets gave way to parchment, which gave way to paper. Paper was, and still is, the main way people convey information. However, in the mid twentieth century computers began to come into general use . . . Computers have gone through their own evolution in storage media. In the forties, fifties, and sixties, everyone who took a computer course used punched cards to give the computer information and store data. In 1956, researchers at IBM developed the first disk storage system. This was called RAMAC (Random Access Method of Accounting and Control) Since the days of punch cards, computer manufacturers have strived to squeeze more data into smaller spaces. That mission has produced both competing and complementary data storage technology including electronic circuits, magnetic media like hard disks and tape, and optical media such as compact disks. Today, companies constantly push the limits of these technologies to improve their speed, reliability, and throughput -- all while reducing cost. The fastest and most expensive storage technology today is based on electronic storage in a circuit such as a solid state "disk drive" or flash RAM. This technology is getting faster and is able to store more information thanks to improved circuit manufacturing techniques that shrink the sizes of the chip features. Plans are underway for putting up to a gigabyte of data onto a single chip. Magnetic storage technologies used for most computer hard disks are the most common and provide the best value for fast access to a large storage space. At the low end, disk drives cost as little as 25 cents per megabyte and provide access time to data in ten milliseconds. Drives can be ganged to improve reliability or throughput in a Redundant Array of Inexpensive Disks (RAID). Magnetic tape is somewhat slower than disk, but it is significantly cheaper per megabyte. At the high end, manufacturers are starting to ship tapes that hold 40 gigabytes of data. These can be arrayed together into a Redundant Array of Inexpensive Tapes (RAIT), if the throughput needs to be increased beyond the capability of one drive. For randomly accessible removable storage, manufacturers are beginning to ship low cost cartridges that combine the speed and random access of a hard drive with the low cost of tape. These drives can store from 100 megabytes to more than one gigabyte per cartridge. Standard compact disks are also gaining a reputation as an incredibly cheap way of delivering data to desktops. They are the cheapest distribution medium around when purchased in large quantities

($1 per 650 megabyte disk). This explains why so much software is sold on CD-ROM today. With desktop CD-ROM recorders, individuals are able to publish their own CD-ROMs. With existing methods fast approaching their limits, it is no wonder that a number of new storage technologies are developing. Currently, researches are looking at protein-based memory to compete with the speed of electronic memory, the reliability of magnetic hard disks, and the capacities of optical/magnetic storage. We contend that three-dimensional optical memory devices made from bacteriorhodopsin utilizing the two photon read and write-method is such a technology with which the future of memory lies. 2. Importance The demands made upon computers and computing devices are increasing each year. Processor speeds are increasing at an extremely fast clip. However, the RAM used in most computers is the same type of memory used several years ago. The limits of making RAM denser are being reached. Surprisingly, these limits may be economical rather than physical. A decrease by a factor of two in size will increase the cost of manufacturing of semiconductor pieces by a factor of 5. Currently, RAM is available in modules called SIMMs or DIMMS. These modules can be bought in various capacities from a few hundred kilobytes of RAM to about 64 megabytes. Anything more is both expensive and rare. These modules are generally 70ns, however 60nsand 100ns modules are available. The lower the nanosecond rating, the more the module will cost. Currently, a 64MB DIMM costs over $400. All Dimms are 12cm by 3cm by 1cm or about36 cubic centimeters. Whereas a 5 cubic centimeter block of bacteriorhodopsin studded polymer could theoretically store 512 gigabytes of information. When this comparison is made, the advantage becomes quite clear. Also, these bacteriorhodopsin modules could also theoretically run 1000 times faster. In response to the demand for faster, more compact, and more affordable memory storage devices, several viable alternatives have appeared in recent years. Among the most promising approaches include memory storage using holography, polymer-based memory, and our focus, protein-based memory. 3. Protein Memories The ability of molecules to serve as computer switches has been a major area of scientific research since the middle of the last century. Molecular switches, if these become a reality, will offer appreciable reduction in hardware size, since these are themselves very small. One can then imagine of bimolecular computer about 1/20th the size of present-day semiconductor-based computers. Small size and fast operation will account for the development of most modern computers. All though still a distant dream the use of a hybrid technology in which the molecules and semiconductors combine and share duty could be possible in near future. Such technology would appreciably improve the size of computers. Scientists have already sharpened their skills and are now trying to apply their knowledge to bring out the very best in this area. Several biological molecules are being considered for use in computers, but the bacterial proteinBacteriorhodopsin (bR)-has generated much interest among scientists. In the past few decades, much research was carried out in several laboratories in North America, Europe, and Japan, and the scientists become successful in building prototype parallel processing devices, three-dimensional memories, and protein-based neural networks.

Bacteriorhodopsin, a light harvesting bacterial protein, is the basic unit of protein memory and is the key protein in halo bacterial photosynthesis. It functions like a light-driven photo pump. Under exposure to light it transports photons from the hollow bacterial cell to another medium, changes its mode of operation from photosynthesis to respiration, and converts light energy to chemical energy thus can be utilized to frame protein memories. Bacteriorhodopsin grows in salt marshes where temperature can exceed 150 degree Farad for the extended time period and the salt concentration is approximately six times that of the seawater. Survival in such an environment implies that this protein can resist thermal and photochemical damages. Upon absorption of light, it generates a chemical and opmotic potential that serves as energy source, it has the ability to form thin films that exhibit excellent optical characteristics and offer long-term stability. The protein generates photoelectrical signals upon photo conversion and can be used as optical memory. Also, it can be prepared in mass quantities. Interest in Bacteriorhodopsin date back to the early seventies when Walther Stockenius, University of California, and Dieter Osterhelt, Max Plank institute of Biochemistry, discovered that this protein exhibited unusual properties upon exposure to light, soon scientists realized its potential for use in computers. Latest, a team of soviet scientists headed by Yuri a. Oschinivhove, Semyakin Institute of Bioorganic Chemistry, took interest in projects on this protein, termed Project Rhodopsin, which were intended only for military applications. Details of these projects achievements remain yet to be revealed. However, Soviet military was able to make microfiche films out of Bacteriorhodopsin, known as Biochrome. 4. Bacteriorhodopsin as an Intelligent Material Can a single molecule possess intelligence? The answer depends on what one means by intelligence. One tends to associate intelligence with what a human brain can do: perception, memory, thinking, problem solving, learning, innovation, creativity, etc. A personal digital computer can do some of these tasks and, in performing certain types of tasks, appears to surpass the human brain. But in terms of the more sophisticated aspects of intelligence such as pattern recognition in an ambiguous situation and creativity, a personal computer is no match even to a modest human brain. A human can do much more than "walk and chew gum" at the same time. While a human being is listening, talking and thinking, the body parts are quietly performing the diverse tasks of providing oxygen and nutrients to individual cells and managing wastes generated in the process of nutrient utilization, fighting invading microorganisms and repairing damaged parts, all without the conscious intervention of a human being. In the computerese language, what the human body possesses is the capability of massively parallel distributed information processing. In contrast to humans, a personal computer has a "one-track" mind, capable of doing only one thing at a time. However, computers have such astonishing raw power and speed in terms of number crunching and chore management that they gave us the illusion of being capable of doing many things simultaneously and serving many users at the same time (time-sharing). Another important determinant in pursuing improved computer performance is miniaturization. The increasing degree of miniaturization of the individual components (integrated circuits, or simply IC) results in increasing capabilities of each device component, increasing speed of operation of these devices, decreasing consumption of energy, decreasing size and weight of the finished product, and, last

but not least, a decrease in price. It may seem that continuing miniaturization could make possible the implementation of better computer architectures, but physicists and engineers see the dead end as the physical limits imposed by quantum and thermal fluctuation phenomena are rapidly approached and the operation of these miniature devices becomes less and less reliable. 4.1. Need for Molecular Electronics The recognition of these ultimate limits has inspired computer scientists to seek inspiration from biology. This is because a living organism operates with functional elements which are of molecular dimensions (about one thousandth of the size of a transistor) and which actually exploit quantum and thermal fluctuation phenomena. The hope of breaking the barrier of miniaturization seems to lie in the utilization of organic and biological materials, and the exploitation of their chemistry, and in the utilization of radically different computer architectures. This line of thinking has ushered in a new science and technology: molecular electronics, which is sometimes also referred to as nanotechnology. As we shall see, the development of intelligent materials is fundamentally important not just for the goal of further device miniaturization but also for the evolution of the ultimate machine intelligence - the kind of intelligence that allows for learning and innovation, and allows for decision-making in a fuzzy situation when many conflicting requirements coexist. 4.2. First Imaging device and Microfilm Until recently, biomaterials have not been seriously considered for device construction because they were perceived as too fragile and not durable enough. A number of years ago, Nikolai V sevolodov and his colleagues in the Institute of Biological Physics, Pushchino, Russia, excited the biomedical research community by producing the first imaging device and microfilm made primarily of biological materials and entirely organic materials (named the "Biochrom" film). The key substance in this device is Bacteriorhodopsin. More recently, Robert Birge's group at Syracuse University has devoted considerable efforts to developing a high-speed optical random access memory based on bacteriorhodopsin. With the advent of genetic engineering, the intelligence of a bio-molecule originally acquired through evolution can be further improved by breeding it in the laboratory in a much shorter time. Thus, molecular engineering will fast become one of the key technologies for the implementation of molecular electronics. 4.3. Intelligent Materials The concept of intelligent materials was initially proposed to promote the idea of designing/ synthesizing materials with a microstructure so that both sensors and actuators are embedded throughout. For example, in the construction of airplane wings, the purpose is to allow the material to sense the changing loads or the condition of external stress as a result of damages, so as to adjust its mechanical characteristics in order to compensate for the changes. Proteins are particularly suitable to be exploited as intelligent materials, as they have already acquired significant degrees of intelligence through evolution. Proteins could be further modified by genetic engineering to custom-tailor their functional properties to suit the intended technological applications. The use of a bacteriorhodopsin mutant as a reversible holographic medium and the use of chemically modified bacteriorhodopsin for construction of "Biochrom" films are existing successful examples.

The development of intelligent materials is in keeping with the goal of miniaturization at the nanometer scale (one nanometer = one billionth of a meter) (nanotechnology). For example, by allowing sensor/processor/actuator capabilities to be packaged into a single molecule or a supra-molecular cluster, avenues are open in the design of integrated information processing systems with massively parallel distributed processing capabilities. Thus, the progress made in the research of intelligent materials will pave the road towards the development of novel information processing systems so as to overcome the much-dreaded "von Neumann bottleneck" that characterizes conventional computers. 5. Photo cycle of Bacteriorhodopsin Bacteriorhodopsin comprises a light absorbing component known as chromophore that absorbs light energy and triggers a series of complex internal structural changes to alter the proteins optical and electrical characteristics. This phenomenon is known as photo cycle. The initial resting state of the molecule is known as bR. Green light transforms the initial bR state to the intermediate state K. Next K relaxes, forms another intermediate state M and then O converts to another intermediate state P, which then relaxes to a more stable state Q. Blue light converts Q black to the initial state bR. Here the idea is to assign any two long -lasting states to the binary values of 0 and 1, to store the required information.