Thursday, August 7, 2008

Seminar report - Protein memory

Protein memory

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 protein-Bacteriorhodopsin (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 project’s 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 protein’s 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.

As per the photo cycle of bR shown in figure below, a branching reaction was identified. This is identified by the P and Q states. The resting state of the molecule, the bR state, can be elevated to the K state by the primary photochemical event. The other transitions are caused by thermal reactions and result once again in the resting state, bR. The entire photo cycle takes about 6-10 milliseconds depending on the temperature. The interesting reaction which creates this branched photo cycle happens when the last intermediate state, O, is converted by light to P which subsequently decays to Q. P and Q are the only states involved in the branched reaction and it exists as its own entity to the original photo cycle. The Q state is the one used for recording data and is created by a sequential one-photon process. This implies that the timing of the reaction must be precisely controlled. The material must be illuminated a second time while the molecules are in the O state about 2ms after the initial writing pulse. At the room temperature lifetime of the written state is roughly five years.

6. Proposed photo cycle for computing needs

The relative stability of some of the intermediate states determines their usefulness in computing applications. The initial state of the native protein, often designated bR, is quite stable. Some of the intermediates are stable at about 80K and some are stable at room temperature, lending themselves to different types of RAM. For computers, the two or three most stable states of the protein would be used to record data in binary form. This is the proposed photo cycle for computing needs.

7. Bacteriorhodopsin Structure

Bacteriorhodopsin is a photo chemically active protein found in the purple membrane of the bacteria Halo bacterium salinarium, which was known as Halo bacterium halobium. The polypeptide chain is made of seven closely spaced alpha-helical segments looped across the lipid bilayer. The interhelical space contains the all-trans-retinal chromophore which is linked to lys-216 on helix G as a protonated Schiff base.

Photo chemically active means that it reacts to light. It has a photochemical reaction cycle, or photo cycle. This cycle basically transports protons from inside the cell to outside the cell in the bacteria Halo bacterium halobium. The native photocycle has several spectroscopically unique steps, bR --> K <--> L <--> M1 --> M2 <--> N <-->O, which occur in a roughly linear order. The bR state is the protein in its native state and each intermediate is represented by a letter of the alphabet. However, the important, main photochemical event in this cycle is a trans to cis photoisomerization around the thirteenth Carbon atom to the fourteenth carbon double bond in the chromophore.

At around the temperature of 80 K, the native protein undergoes this photocycle andswitches between a green absorbing state and a red absorbing state. At approximately room temperature, the protein switches between a green absorbing state and a blue absorbing state. In both the ground (green) and excited (red or blue) states, the chromophore displays several metastable configurations. The main event follows these steps:

1. A change in the shape of the conformational potential energy surface resulting from electron excitation

2. A conformational change

3. A non-radiative decay to the ground state

"Ball and Stick" molecular structure of the transmembrane protein Bacteriorhodopsin is shownbelow. Bacteriorhodopsin is quite similar to rhodopsin, the light-detecting pigment found in theretinas of vertebrates (like humans)).

8. Bacteriorhodopsin as Computer Memory

Many of the erstwhile memory devices based on Bacteriorhodopsin could operate only at extreme cold temperatures of liquid nitrogen, where light-induced switching between ‘bR’ and the intermediate state ‘K’ could be controlled. These devices were much faster than conventional semiconductor-based devices, as these exhibited the speed of a few trillionths of a second. Today, most Bacteriorhodopsin based devices function even at room temperature, switching between ‘bR’ and another intermediate stable state ‘M’.

If a number of Bacteriorhodopsin molecules are arranged in a three-dimensional fashion, high-speed, high-density, low-cost memories with vast capacities that can handle large volumes of data can be realized. Such memories offer over 300-fold improvement in storage capacity over their two-dimensional counterparts. Read/Write operations on these can be performed with the help of colored lasers that are fixed at such points as to direct the beams through the required points in the plane of the cube.

Such memory cubes must be extremely uniform in their composition and must be homogeneous to ensure good results, since excess of defect of molecules in one particular region tends to distort the stored information and render the memory cube useless. The entire process of data storage or retrieval can be carried out in few milliseconds. The speed of these memories depends on the number of cubes operating in parallel.

9. Data Writing Technique

Bacteriorhodopsin, after being initially exposed to light (in our case a laser beam), will change to between photoisomers during the main photochemical event when it absorbs energy from a second laser beam. This process is known as sequential one-photon architecture, or two photon absorption. While early efforts to make use of this property were carried out at cryogenic temperatures (liquid nitrogen temperatures), modern research has made use of the different states of bacteriorhodopsin to carry out these operations at room-temperature. The process breaks down like this:

Upon initially being struck with light (a laser beam), the bacteriorhodopsin alters its structure from the bR native state to a form we will call the O state. After a second pulse of light, the O state then changes to a P form, which quickly reverts to a very stable Q state, which is stable for long periods of time (even up to several years).

The data writing technique proposed by Dr. Birge involves the use of a three dimensional data storage system. In this case, a cube of bacteriorhodopsin in a polymer gel is surrounded by two arrays of laser beams placed at 90 degree angles from each other. One array of lasers, all set to green (called "paging" beams), activates the photo cycle of the protein in any selected square plane, or page, within the cube. After a few milliseconds, the number of intermediate O stages of bacteriorhodopsin reaches near maximum. Now the other set, or array, of lasers - this time of red beams - is fired.

The second array is programmed to strike only the region of the activated square where the data bits are to be written, switching molecules there to the P structure. The P intermediate then quickly relaxes to the highly stable Q state. We then assign the initially-excited state, the O state, to a binary value of 0, and the P and Q states are assigned a binary value of 1. This process is now analogous to the binary switching system which is used in existing semiconductor and magnetic memories. However, because the laser array can activate molecules in various places throughout the selected page or plane, multiple data locations (known as "addresses") can be written simultaneously - or in other words, in parallel.

10. Data Reading Technique

The system for reading stored memory, either during processing or extraction of a result, relies on the selective absorption of red light by the O intermediate state of bacteriorhodopsin. To read multiple bits of data in parallel, we start just as we do in the writing process. First, the green paging beam is fired at the square of protein to be read. After two milliseconds (enough time for the maximum amount of O intermediates to appear), the entire red laser array is turned on at a very low intensity of red light. The molecules that are in the binary state 1 (P or Q intermediate states) do not absorb the red light, or change their states, as they have already been excited by the intense red light during the data writing stage.

However, the molecules which started out in the binary state 0 (the O intermediate state), do absorb the low-intensity red beams. A detector then images (reads) the light passing through the cube of memory and records the location of the O and P or Q structures; or in terms of binary code, the detector reads 0's and 1's. The process is complete in approximately 10 milliseconds, a rate of 10 megabytes per second for each page of memory.

Clearly, there are many advantages to protein-based memory, among the most significant being cost, size, and memory density. However, there are still several barriers standing in the way of mass-produced protein-based memories.

11. Data Erasing Technique

Blue light erases the encoded data. The P and Q states absorb the blue light to return to their original bR state. Individual data can be erased using a blue laser or a global wipe can be performed with an incoherent blue source. Erasure is a highly efficient process and the memory cuvette must be shielded for protection.

12. Bacteriorhodopsin Memory Cell by Bob Birge

Even smaller objects might serve as storage devices or replace conventional

semiconductor memory. Professor Robert R. Birge, director of the W. M. Keck Center for Molecular Electronics, has implemented a prototype memory subsystem that uses molecules to store digital bits.

Birge selected bacteriorhodopsin because its photo cycle, a sequence of structural changes that the molecule undergoes in reaction to light, makes it an ideal AND data-storage gate, or flip-flop. According to Birge, the bR (where the state is 0) and the Q (where the state is 1) intermediates are both stable for many years. This situation is due, in part, to the remarkable stability of the protein, which appears to have evolved to survive the harsh conditions of a salt marsh.

Using the purple membrane from the bacterium Halo bacterium Halobium, they have made a working optical bistable switch, fabricated in a monolayer by self-assembly, that reliably stores data with 10,000 molecules per bit. The molecule switches in 500 femtoseconds--that's 1/2000 of a nanosecond, and the actual speed of the memory is currently limited by how fast you can steer a laser beam to the correct spot on the memory.

Birge estimated that the data recorded on the bacteriorhodopsin storage device must “live" around 5 years. Another important feature of the bacteriorhodopsin is that these both states have different absorption spectra. It allows easily defining the current state of the molecule with the help of a laser set for the definite frequency.

They built a prototype of memory system where the absorption spectrum stores data in3-dimensional matrix. Such matrix represents a cuvette (a transparent vessel) filled up with polyacryde gel, where protein is put. The cuvette has an oblong form 1x1x2 inch in size. The protein which is in the bR-state is fixed in the space with gel polymerization. The cuvette is surrounded with a battery of lasers and a detector array based on the device using a principle of CID (Charge Injection Device), they serve for data recording and reading.

When recording data first you need switch on a yellow-wave "page" laser – for converting the molecules into Q-state. The SLM which represents an LCD-matrix creating a mask on the beam way stimulates appearing of an active (excited) plane in the material inside the cuvette. This power active plane is a page of data which can house 4096x4096 bit array. Before returning of protein into the quiescent state (in such state it can remain quite a long time keeping the information) a red-wave recording laser lights on; it's positioned at the right angle to the yellow one. The other SLM displays binary data, and this way creates the corresponding mask on the way of the beam, that's why only definite spots (pixels) of the page will be irradiated.

The molecules in these spots will convert into Q-state and will represent a binary one .The remaining part of the page will come into the initial bR-state and will represent binary zeros. In order to read the data you will need again the "page" laser which converts the read page into Q-state. It is implemented so that in the future one can identify binary one and zero with the help of difference in absorption spectra. 2ms later the page is plunged into low intensive light flux of the red-wave laser. Low intensity is necessary to prevent jumping into Q state. The molecules that represent a binary zero absorb red light, and those that represent a binary one let the beam pass by. It creates a "chess" picture of light and dark spots on the LCD matrix which takes a page of digital information.

For erasing information a short impulse of a cyan laser is enough in order to convert the molecules from Q-state back into bR-state. This beam can be obtained not necessary with the laser: you can erase the whole cuvette with a usual ultraviolet lamp. In order to ensure the entirety of data when erasing only the definite pages there used caching of several adjacent pages. For read/write operations two additional parity bits are also used to prevent errors. The data page can be read without corruption up to 5000 times. Each page is traced by a meter and after 1024 reading the page gets refreshed (regenerated) with a new recording operation.

Considering that a molecule changes its states within 1 ms, the total time taken for read or write operations constitutes around 10 ms. But similar to the system of a holographic memory this device makes a parallel access in the read-write cycle, what allows counting on the speed up to 10 Mbps. It is assumed that combining 8 storing bit cells into a byte with a parallel access, you can reach, then, 80 Mbps, but such method requires a corresponding circuit realization of the memory subsystem. Some versions of the SLM devices implement a page addressing, which in cheap constructions is used when sending the beam to the required page with the help of rotary system of galvanic mirrors. Such SLM provides 1ms access but costs four times more.

Birge states that the system suggested by him is close to the semiconductor memory in operating speed until a page defect is come across. On detecting of a defect it's necessary to resend the beam for accessing these pages from the other side. Theoretically, the cuvette can accommodate 1TBytes of data. Limitation of capacity is mainly connected with problems of lens system and quality of protein.

12.1 Memory Cell Specifications

Bob Birge's bacteriorhodopsin memory cell only costs USD 2 but can store 7 Gbyte.

• Purple membrane from Halo bacterium Halobium

• Bistable red/green switch

• In protein coat at 77K, 107-108 cycles

• 10,000 molecules/ bit

• Switching time, 500 femtoseconds

• Monolayer fabricated by self-assembly

• Speed currently limited by laser addressing

12.2 How fast can data be accessed with this design?

While a molecule changes states within microseconds, the combined steps to perform a read or write operation take about 10 milliseconds. However, like the holographic storage system, this device obtains data pages in parallel, so a 10-MBps rate is possible. This speed is similar to that of slow semiconductor memory.

By ganging up eight storage cells so that entire bytes can be accessed in parallel, Birge believes an 80-MBps data rate is possible. Maintaining this throughput depends on how you implement the memory subsystem. In some versions, the SLM does page addressing. Less expensive designs use galvanometric mirrors that slew the beam to the correct page. While the SLM offers a millisecond response time, it also costs four times as much.

12.3. Data Stability

The data is stable. If you turn off the memory system's power, the bateriorhodopsin molecules retain their information. This makes for an energy-efficient computer that can be powered down yet still be ready to work with immediately because the contents of its memory are preserved.

12.4. Storage Capacity

Theoretically, the cuvette described could hold 1 TB. Practically, Birge has stored about 800 MB on the cuvette, and he hopes to achieve a storage capacity of approximately 1.3 GB. Problems with the lens system and protein quality limit the system to this amount for now.

12.5. Transportation

You can remove the small data cubes and ship gigabytes of data around for storage or backups. Because the cubes contain no moving parts, it's safer than using a small hard drive or cartridge.

12.6. Will the molecular memory be able to compete against the traditional semiconductor memory?

Its construction has undoubtedly some advantages. First, it's based on protein which is produced in large volumes and at low price. Secondly, the system can operate in the wider range of temperatures than the semiconductor memory. Thirdly, data are stored constantly - even in case of power switching off, it won't cause data loss. And at last, bricks with data which are rather small in size but contain gigabytes of data can be placed into an archive for storing copies (like magnetic tapes). Since the bricks do not have moving parts, it's more convenient than usage of portable hard discs or cartridges with magnetic tape.

13. 3-Dimensional Optical Memories

Three-dimensional optical memory storage offers significant promise for the development of a new generation of ultra-high density RAMs (Birge, Computer, 63). One of the keys to this process lies in the ability of the protein to occupy different three-dimensional shapes and form cubic matrices in a polymer gel, allowing for truly three-dimensional memory storage. The other major component in the process lies in the use of a two-photon laser process to read and write data. Storage capacity in two-dimensional optical memories is limited to approximately 1/lambda2 (lambda = wavelength of light), which comes out to approximately 108 bits per square centimeter. Three-dimensional memories, however, can store data at approximately 1/lambda3, which yields densities of 1011 to 1013 bits per cubic centimeter. The memory storage scheme proposed by Robert Birge, is designed to store up to 18 gigabytes within a data storage system with dimensions of 1.6 cm * 1.6 cm * 2 cm. Bear in mind, this memory capacity is well below the theoretical maximum limit of 512 gigabytes for the same volume (5-cm3).

14. Advantages and Applications of

Bacteriorhodopsin

Bacteriorhodopsin is an excellent molecule for photonics. Naturally occurring, the purple pigment grows in salt marshes and has evolved to exist in half-a-dozen stable states within a convenient, reversible photo cycle. This robust system, coupled with the emergence of genetic engineering, forms the basis of a variety of applications and devices based on bacteriorhodopsin that are now beginning to emerge.

The range of potential applications for which bacteriorhodopsin (bR) has been

Investigated is remarkable. It includes:

1) Reversible holographic memory

2) Ultrafast random-access memory

3) Neural logic gates

4) Spatial light modulation

5) Nonlinear optical filters

6) Photonic-crystal band gap materials,

7) Pattern-recognition systems

8) High-contrast displays

9) Optical switches

10) Pico second photo detectors.

Unlike many other biomolecules, which are too unstable to be used in any commercial device, bR is protected against photo-induced breakdown - which is caused by reactive oxygen, singlet oxygen and free radicals - by its structure.

Its robustness results from bR's evolution in the tough salt marsh environment. It has learned to cope with extreme variations in light and heat and its natural function is to provide energy to its host bacterium, Halo bacterium salinarum, in low-oxygen (anaerobic) conditions.

14.1. Erasable Holographic Memory

A holographic interferometry camera uses a film of bacteriorhodopsin as an erasable holographic memory. An associative memory device that builds on holographic properties of thin films of Bacteriorhodopsin has been developed. Associative memories take images of data blocks as input, scan the entire memory independently of a central processor for data block that matches the input, and return the closest match. Such holographic thin films allow multiple images to be stored in the same segment of memory, thereby permitting simultaneous analysis of large sets of data. However, holograms based on Bacteriorhodopsin are erasable.

14.2. Optical chameleon

On absorbing a green photon, the bR molecule undergoes such severe deformation that its absorption maximum shifts 160 nm towards the red and its colour changes from purple to yellow. From this state, bR can be converted back to its purple form using blue light, or into a range of states - that all absorb at different wavelengths - using a red source. The molecule is the ultimate chameleon and its ability to change state is the basis of several photochromic applications, such as data storage and associative memories.

Following the discovery of bR's remarkable light-harvesting and colour-changing behavior in the early 1970s, Soviet bioelectronics researcher Yuri Ovchinnikov became fascinated by the molecule. He convinced the Soviet military of its potential, and millions of roubles were ploughed into "Project Rhodopsin". The material was even listed on the "COCOM" list of protected chemicals under export prohibition.

14.3. Electronic Ink

Illuminating the membrane protein bacteriorhodopsin (BR) triggers a photocycle in which a series of conformational and electronic changes results in the translocation of a proton through a channel in the protein. During one intermediate state of this photocycle, a strong, transient color change is caused by the removal of a proton from the Schiff-base linkage which binds the retinal chromophore to the protein.

In natural or "wild-type" BR, this proton is strongly bound, as indicated by a pK valuein excess of 12, and its removal by chemical or electrical means is difficult. However, there are several variants of BR in which the pK of the Schiff base is drastically lowered, either by genetic alteration of charged groups near the Schiff base or by chemical modification of the retinal chromophore. In one such mutant, D85N BR, we have found that electric fields can cause deprotonation of the Schiff base and a consequent color change (P. Kolodner et al, Proc. Natl. Acad. Sci. USA 93, 11618 (1996)). This protein therefore exhibits a novel form of electrochromism that may find application as "electronic ink" in reflective displays.

14.4. Molecular light conversion

Colored proteins, sometimes called 'electronic ink' yield new optical devices to molecular light conversion.

15. Conclusion

Bacteriorhodopsin has attracted the attention of scientists interested in using biological materials to perform technological functions. Part of the attraction of natural materials is that they often perform very complex functions that cannot be easily synthesized. Evolution has perfected these functions over billions of years, often performing better than human-designed materials ever could.

In the last 25 years, bacteriorhodopsin has excited a great deal of interest among biochemists, biophysicists, and most recently among companies seeking to build battery conserving, long-life computer displays. If controllable, quick-change proteins like bacteriorhodopsin could also be used in a kind of electronic writing.

In addition, the protein's photoelectric properties could be used to manufacture Photo detectors. Bacteriorhodopsin is also an attractive material for all-optical 'light' computers because of its two stable protein forms, one purple and one yellow. Shining two lasers of different wavelengths alternately on the protein flips it back and forth between the two colors. Several research groups have already used bacteriorhodopsin as computer memory and as the light-sensitive element in artificial retinas.

With fast random access capability, good reliability, and transportability protein memories enhance the multimedia capabilities of computers to a great extent. Also, the advantages of optical data storage accrue to such memories. Enormous access to information and manipulation and storage of data in minimal time add to their reliability. Unlike disk memories where physical contact with the magnetic head is required to Read/Write information, protein memories use laser beams, which improves their life with reduction in wear and tear.

Researchers are now closely following the way human brain stores, retrieves, and acts on information, to build a biological computer. They are trying to duplicate the capability of information retrieval by inputting a part of it, or any related aspect, instead of specifying the address of the memory location. Though a group of researchers headed by Robert Birge of Suracuse University, USA, has succeeded in developing similar ones, much work is still required to make a fully operational computer with memory that mimics human brain.

Indeed, we are on the threshold of new and exciting era in the wonderful world of computing. And every possibility is there that in the near future we will be able to carry a small encyclopedic cube containing all the information we need!

16. Reference

1. Proptein Based Computers Birge, Robert R., Scientific American March 1995

2. Molecular and Biomolecular Electronics, Birge, Robert R. Ed., American Chemical Society

3. Organic Chemistry Baker, A. David, Robert Engel.

4. Bacteriorhodopsin as an Intelligent Material, a Nontechnical Summary by Felix T. Hong

5. www.quantum.com (Makers of hard drive)

6. www.che.syr.edu (Department of Chemistry, Syracuse University)

7. www.optics.org

8. www.aps.org

9. www.cem.msu.edu

10. www.nai.arc.nasa.gov

11. http://www.buzzle.com/chapters/science-and-technology.asp

208 comments:

1 – 200 of 208   Newer›   Newest»
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