protein memory 2.ppt (Size: 148 KB / Downloads: 352) protein memory .

doc (Size: 163 KB / Downloads: 226)

ABSTRACT The ability of molecules to serve as computer switches will offer appreciable re duction in hardware size, since there are they very small. The use of a hybrid t echnology in which the molecules and semiconductors combine and share the duty w ill appreciably improve the speed and reduce the size of computers. Several biological molecules are being considered for use in computers, but the bacterial protein - bacteriorhodopsin (bR) has generated much interest among sci entists. Bacteriorhodopsin is a protein found in the purple membrane of several species of bacteria, most notably Halo bacterium halobium. This particular bacte rium lives in salt marshes where there is high salinity and temperature. Bacteri orhodopsin, the basic unit of protein memory does not break down at high tempera tures. Survival in such an environment implies that the protein can resist therm al and photochemical damages. The bacteriorhodopsin is one of the most promising organic materials. Seven helix-shaped polymers form a membrane structure, which contains a molecule known as retinal chromophore. The chromophore absorbs light of a certain color and is therefore able to switch to another stable state in a ddition to its original state. Only blue light can change the molecule back to i ts original state. With fast random access capability, good reliability and transportability protei n memories enhance the multimedia capabilities of computer to a great extent. Al so the advantages of optical data storage accrue to such memories. Enormous acce ss to information and manipulation and storage of data in minimal time add to th eir reliability. Unlike disk memories where physical contact with the magnetic h ead is required to read/write information, protein memories use laser beams, whi ch improve their life with reduction in wear and tear. 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, ye ars later; more early scholars invented writing to convey what was being said. Pi ctures gave way to letters which represented spoken sounds. Eventually clay tabl ets 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 compu ters began to come into general use. Evolution of Storage Media: Computers have gone through their own evolution in storage media. In 1956, resea rchers at IBM developed the first disk storage system. This was called RAMAC (Ra ndom Access Method of Accounting and Control) Since the days of punch cards, computer manufacturers have strived to squeeze mo re data into smaller spaces. That mission has produced both competing and comple mentary data storage technology including electronic circuits, magnetic media li ke hard disks and tape, and optical media such as compact disks. Today, companies constantly push the limits of these technologies to improve the ir speed, reliability, and throughput -- all while reducing cost. Standard compa ct disks are also gaining a reputation as an incredibly cheap way of delivering data to desktops. They are the cheapest distribution medium around when purchase d in large quantities (Rs. 18/- per 700 MB disk). Holostore Technology: Practically, researchers believe that Holographic data storage system in which t housands of pages (blocks of data), each containing million bits, can be stored within the volume of a sugar cube, have a storage capacity of 10 GB per cubic ce ntimeter

Fig: Structure of bR the basic unit of protein memory This figure is still very impressive compared to today's magnetic storage densit ies, which are around 100 Kb per square centimeter (not including the derive mec hanism). At this density a block of optical media roughly the size of a deck of playing c ards would be able to house a terabyte of data. Because such system can have no moving parts and its pages are accessed in parallel, it is estimated that data t hroughput on such system can hit 1 Gbps or higher. In holographic recording appl ications, longer interaction lengths imply increased angular selectivity and als o higher data storage capacity. These advantages are in addition to the ability to synthesize a much larger cross sectional area then is currently attainable us ing bulk materials. Holostore leverages the imaging properties of light and its ability to launch. T he reading out of images instead of single bits serially provides a tremendous i mprovement in the bandwidth. The ability for light to be launched through space and deflected easily will eliminate the need for rotation of the medium. The cap ability of coherent light to interfere and to form holograms provides a convenie nt way to address a storage medium in three dimensions, while only scanning the beams in two dimensions. Holography records the information from a three-dimensional object in such a way that a three dimensional image may subsequently be constructed. Holographic mem ory uses lasers for both reading and writing the blocks of data into the photose nsitive material. A digital hologram is formed by recording the interference pat tern between a discretely modulated coherent wave front and a reference beam on a photosensitive material. Molecular Memory: With the advances in Molecular electronics, it is possible to implement a protot ype memory subsystem that uses molecules to store digital bits. The molecule in question here is the protein called bacteriorhodopsin. Its photo cycle, the sequence of structural changes, a molecule undergoes in reaction to light, makes it an ideal AND data storage gate, or flip-flop. According to the t oday's research, the bR (where the state is 0) and the Q (where the state is 1) intermediates are both stable for many years. The reason for considering the molecular memory is that it is protein based and therefore is inexpensive to produce in quantity. Secondly, the system has abilit y to operate over a wider range of temperatures than semiconductor memory Protein-Based Memory: Need For Protein Memory: 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. Currently, RAM is available in modules called SIMMs or DIMMS. These modules can be bought in various capacities from a few 100KB to about 128 MB. These modules are generally 7.5ns. Whereas a 5cu.cm block of bacteriorhodopsin studded polymer could theoretically store 512GB of information. When this comparison is made, t he advantage becomes quite clear. Also, these bacteriorhodopsin modules could al so theoretically run 1000 times faster. More on Protein-Based Memory: Researchers are looking at protein-based memory to compete with the speed of ele ctronic memory, the reliability of magnetic hard disks and the capacities of opt ical/magnetic storage. There have been many methods and proteins researched for use in computer applications in recent years. The most promising approach is of 3D Optical RAM storage using the light sensitive protein bacteriorhodopsin. Bacteriorhodopsin is a protein found in the purple membranes of several species of bacteria, most notably Halobacterium halobium. These particular bacteria live in salt marshes. Salt marshes have very high salinity and temperatures can reac h 140oF (60oC). Unlike most proteins, bacteriorhodopsin does not break down at t hese high temperatures. Early research in the field of protein-based memories yielded some serious probl ems with using proteins for practical computer applications. Among the most seri

ous of the problems was the instability and unreliable nature of proteins, which are subject to thermal and photochemical degradation, making room-temperature o r higher-temperature use impossible. Scientists stumbled upon bacteriorhodopsin, a light-harvesting protein that has following properties which make it a prime candidate for computer applications. Long-term stability and resistance to thermal and photochemical degradation A cyclicity (the number of times it can be photo-chemically cycled) which exceed s 106, a value considerably higher than most synthetic photo chromic materials High quantum yields (efficient use of light) which permits the use of low light levels for switching/activating Ability to form thin films or oriented polymer cubes containing bacteriorhodopsi n with excellent optical properties Bacteriorhodopsin can be used in any number of schemes to store memory, most sig nificant reasons being cost, size and very high memory density. Photo cycle: Bacteriorhodopsin is a complex protein that includes a light absorbing component known as Chromophore. It absorbs energy from light, triggering a complex series of internal motions that results in structural changes. These changes alter pro teins optical and electrical characteristics. The initial resting state for bacteriorhodopsin is called bR. When bR is exposed to green light, in the range of approximately 550nm, it shifts to the K state. This K state is an unstable state. So the bacteria cannot remain in this state f or long thus, K relaxes forming M. This M state is similar to K and is unstable. So it again relaxes forming the O state. This state is quite stable. If the O state is not exposed to a red light source, it will eventually relax ba ck to the bR state. However, if it is exposed, it will then undergo a reaction a called a branching reaction. The O state will shift to the P state and then to th e Q state a form that remains stable almost indefinitely for years. Blue light w ill, however, convert Q back to bR. Of the six states bR, K, M, O, P and Q only the most stable ones are particularly useful. The relative stability of some of the intermediate states determines their usefu lness in computing applications. The initial state of the native protein, often designated bR, is quite stable. Some of the intermediates are stable at about 90 K and some are stable at room temperature, lending themselves to different types of RAM. One stable state is assigned 0 and other 1. Usually O state represents 0 and Q state represents 1. Photo cycle of bacteriorhodopsin Two Photon Method: The two photon method is superior to a single photon method when using three dim ensional memory. This is because a single photon would excite all of the molecul es that it came into contact with, where a two photon method would only excite t he molecules at the location where they intersect. A two photon mechanism is able to excite molecules inside the volume of memory, without exciting the surface molecules. Each photon itself does not have enough energy to excite the molecules to the next higher energy state. Also no real sta te exists at the energy of either photon alone. Absorption will occur if the sum of the energies of each photon is equal to or greater than the energy gap of th e transition, and only in the volume where the two photons overlap. This process would allow reading and writing anywhere in the volume of the RAM w here the sequential method must start at the surface of the RAM. At the point of absorption where the two photons intersect, a molecular change will occur in th at micro volume. This will distinguish it from the rest of the unexcited molecul es. The two molecular structures provide for a read and write state, or 0 and 1 state in the RAM. 3 - Dimensional Optical Memories: Basically, the unit is a thin wafer of protein, sandwiched between glasses and s ealed off with two Teflon gaskets and black anodized aluminum. The protein wafer is formed by creating a matrix of bacteriorhodopsin strands within a polymer ge l. The ribbon-like nature of the protein naturally lends itself to the formation of this matrix. It also makes it easier for the device to read the data.

The first step involved in creating a non-linear bacteriorhodopsin-based would b e forming a cubic protein matrix. This task is somewhat more daunting than formi ng a thin wafer of bacteriorhodopsin, but not substantially so. The same techniq ue of lining up the protein strands with in the polymer gel is used, only now it is extended volumetrically. After the matrix is created, it is then placed with in the cubic cuvette. The cuvette uses a sealing polymer and a conductive indium -tin oxide coating to protect the protein matrix. The major component in the pro cess lies in the use of a two-photon laser process to read and write data. Furthermore, at the base of the cuvette is a temperature base plate capable of h eating or cooling the bacteriorhodopsin. This alters the physical properties of the bR when needed and cools the matrix when the cuvette becomes hot. The storage capacity in two-dimensional optical memories is limited to approxima tely 1/lambda2 (lambda = wavelength of light), which comes out to approximately 108 bits per square centimeter. Three-dimensional memories, however, can store d ata at approximately 1/lambda3, which yields densities of 1011 to 1013 bits per cubic centimeter. Sandwich The principle of organic memory is as simple as it is brilliant. A polymer film which is contacted by a passive matrix emits light on to the memory medium-a pro tein film. The light causes the proteins to switch between two stable states. Th e states can be distinguished above all by those colors which they absorb and th ose which they let pass. Once they have been changed, the states remain stable e ven without light. The data is then read with less intense light, that doesnt cha nge the memory content. In one state the protein absorb more light, in other les s. Another polymer layer, also matrix regulated, acts as a photo detector and me asures the light which has been diffracted by the proteins. A single matrix element of the opticom memory is supposed to have a dimension of less than 100nm. The entire layer is 350nm thick. This is 10 to 100 times small er than the common size of microchips. Thus the usual lithographic procedures co uld not be sued in the production process. Dimensions that small could actually be achieved if the matrixs strip conductors are made of (conductive) polymers. Th e polymer chains, which are only a few nm thick, but quite long, line themselves up under certain conditions, thus serving as one of the matrix lines. The secon d polymer layer could also possibly be structured by exposure to UV light. The catch with organic memory is the connections of this matrix. Every single st rip conductor of the matrix must be connected to and powered by a transistor. Th e dimensions of modern transistors in 0.25 aem technology pose an obstacle of a few micrometers to the measurements of opticoms dream memory with 100nm line inte rvals. In addition, the mini strip conductors have to contact the giant transist or connectors in a confined area. Opticom polymer memory: a matrix addresses the light emitting polymers. The ligh t writes on the proteins in the middle of the sandwich at a cross point. The low er polymer layer absorbs light thus reading the memory content Data Writing Technique Bacteriorhodopsin, after being initially exposed to light (in our case a laser b eam) will change to between photo-isomers during the main photochemical event wh en it absorbs energy from a second laser beam. This process is known as sequenti al one-photon architecture, or two-photon absorption. While early efforts to mak e use of this property were carried out at cryogenic temperatures (liquid nitrog en temperatures), modern research has made use of the different states of bacter iorhodopsin to carry out these operations at room-temperature. The process break s down like this: Upon initially being struck with light (a laser beam), the bacteriorhodopsin alt ers its structure from the bR native state to the O state. After a second pulse of light, the O state then changes to the P form, which quickly reverts to a ver y stable Q state, which is stable for long periods of time (even up to several y ears). The data writing technique proposed by Dr. Berge involves the use of a three-dim ensional data storage system. In this case, a cube of bacteriorhodopsin in a pol

ymer gel is surrounded by two arrays of laser beams placed at 90 degree angles f rom each other. One array of lasers, all set to green (called "paging" beams), a ctivates the photo cycle of the protein in any selected square plane, or page, w ithin 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 struc ture. The P intermediate then quickly relaxes to the highly stable Q state. We t hen 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 analog ous to the binary switching system which is used in existing semiconductor and m agnetic memories. However, because the laser array can activate molecules in var ious places throughout the selected page or plane, multiple data locations (know n as "addresses") can be written simultaneously - or in other words, in parallel . 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 s tate of bacteriorhodopsin. To read multiple bits of data in parallel, we start j ust as we do in the writing process. First, the green paging beam is fired at th e square of protein to be read. After two milliseconds (enough time for the maxi mum amount of O intermediates to appear), the entire red laser array is turned o n at a very low intensity of red light. The molecules that are in the binary sta te 1 (P or Q intermediate states) do not absorb the red light, or change their s tates, as they have already been excited by the intense red light during the dat a writing stage. However, the molecules which started out in the binary state 0 (the O intermedia te 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 ms, a rate of 10MB per second for each page of memory. Data Erasing Technique Erasing the data is even simpler. One method would be to simply fire a deep blue paging beam through the cube. This would erase an entire page of data in one sh ot. If data in one row or one location is to be erased, simply fire two low intensit y orthogonal laser beams in the cubic matrix. Where they meet, the intensity of the beam will be doubled. Thus, it would provide the necessary intensity to chan ge the state of the molecule back to bR. The other locations hit by the low inte nsity beams would begin to absorb the light. But, the intensity would not be eno ugh to cause a state shift. Latest Developments The latest news about the protein memories is rather unbelievable. Evidently, fo r the cost of a few cents, a Norwegian company can produce a memory module with a capacity of up to 170,000 gigabytes, which could fit on a bank card. Various newspapers and magazines have reported the achievements of Oslo-based Op ticom, a company which conceivably could upset the entire industry with their ma mmoth memory made of polymers. Polymers are the stuff that panty hose and plasti c bags are made of. The first series product of so-called organic memory should be on the market this coming year. Conclusion Small enough to be incorporated onto standard computer boards, these optical com puter memory systems will be interfaced to advanced computer architectures for h igh-speed processing. Indeed, we are on the threshold of a new exciting era in t he wonderful world of computing. And every possibility is there, that in the nea r future we will be able to carry a small encyclopedic cube containing all the i nformation we need and retrievable at the speed of light!!! References

http://www.cem.msu.edu http://www.ieee.org http://www.sciamarchive.com Protein-Based Optical Computing and Memories, Berge, Robert R., scientific Ameri can magazine March 1995. Electronics for You Magazine March 2001, Vol. 33, No. 3. Steve Redfield and Jerry Willenbring "Holostore technology for higher levels of memory hierarchy," IEEE potentials, 1991, PP. 155-159 Najeeb Imran, "Optical computing," IEEE potentials, Dec 1992, PP. 33-36 Tom Thom son, "What's Next, "Byte, April 1996, PP. 45-51 CONTENTS 1. INTRODUCTION 2. EVOLUTION OF STORAGE MEDIA: 3. HOLOSTORE TECHNOLOGY 4. MOLECULAR MEMORY 5. PROTEIN-BASED MEMORY 6. PHOTO CYCLE 7. TWO PHOTON METHOD 8. 3 - DIMENSIONAL OPTICAL MEMORIES 9. SANDWICH 10. DATA WRITING TECHNIQUE 11. DATA READING TECHNIQUE 12. DATA ERASING TECHNIQUE 13. DATA ERASING TECHNIQUE 14. LATEST DEVELOPMENTS 15. CONCLUSION 16. REFERENCES Reference: http://www.seminarprojects.com/Thread-protein-memory#ixzz1YsqbcVGE