Protein memory(seminar report)


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Protein memory(seminar report)

  1. 1. PROTEIN BASED MEMORY STORAGE DEVICES 1 1. INTRODUCTION Since the dawn of time, man has tried to record important events and techniquesfor everyday life. At first, it was sufficient to paint on the family cave wall how onehunted. Then came people who invented spoken languages and the need arose to recordwhat one was saying without hearing it firsthand. Therefore, years later, earlier scholarsinvented writing to convey what was being said. Pictures gave way to letters whichrepresented spoken sounds. Eventually clay tablets gave way to parchment, which gaveway 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 thecomputer information and store data. In 1956, researchers at IBM developed the first diskstorage system. This was called RAMAC (Random Access Method of Accounting andControl). Since the days of punch cards, computer manufacturers have strived to squeezemore data into smaller spaces. That mission has produced both competing andcomplementary data storage technology including electronic circuits, magnetic media likehard disks and tape, and optical media such as compact disks. Today, companiesconstantly push the limits of these technologies to improve their speed, reliability, andthroughput -- all while reducing cost. The fastest and most expensive storage technologytoday is based on electronic storage in a circuit such as a solid state "disk drive" or flashRAM. This technology is getting faster and is able to store more information thanks toimproved circuit manufacturing techniques that shrink the sizes of the chip features. Plansare underway for putting up to a gigabyte of data onto a single chip. Department of Electronics and Communication, LMCST
  2. 2. PROTEIN BASED MEMORY STORAGE DEVICES 2 Magnetic storage technologies used for most computer hard disks are the mostcommon and provide the best value for fast access to a large storage space. At the lowend, disk drives cost as little as 25 cents per and provide access time to data in tenmilliseconds. Drives can be ganged to improve reliability or throughput in a RedundantArray of Inexpensive Disks (RAID). Magnetic tape is somewhat slower than disk, but it issignificantly cheaper per megabyte. At the high end, manufacturers are starting to shiptapes that hold 40 gigabytes of data. These can be arrayed together into a Redundant Arrayof Inexpensive Tapes (RAIT), if the throughput needs to be increased beyond thecapability of one drive. For randomly accessible removable storage; manufacturers arebeginning to ship low-cost cartridges that combine the speed and random access of a harddrive with the low cost of tape. These drives can store from 100 megabytes to more thanone gigabyte per cartridge. Standard compact disks are also gaining a reputation as an incredibly cheap way ofdelivering data to desktops. They are the cheapest distribution medium around whenpurchased in large quantities ($1 per 650 megabyte disk). This explains why so muchsoftware is sold on CD-ROM today. With desktop CD-ROM recorders, individuals areable to publish their own CD-ROMs. With existing methods fast approaching their limits, it is no wonder that a numberof new storage technologies are developing. Currently, researches are looking at protein-based memory to compete with the speed of electronic memory, the reliability of magnetichard-disks, and the capacities of optical/magnetic storage. We contend that three-dimensional optical memory devices made from bacteriorhodopsin utilizing the twophoton read and write-method is such a technology with which the future of memory lies. Department of Electronics and Communication, LMCST
  3. 3. PROTEIN BASED MEMORY STORAGE DEVICES 3 2. PRESENT MEMORY STORAGE DEVICES The demands made upon computers and computing devices are increasing eachyear, speeds are increasing at an extremely fast clip. However, the RAM used in mostcomputers is the same type of memory used several years ago. The limits of makingRAM denser are being reached. Surprisingly, these limits may be economical ratherthan physical. A decrease by a factor of two in size will increase the cost ofmanufacturing of semiconductor pieces by a factor of 5. Currently, RAM is available in modules called DIMMs and SIMMs .Thesemodules can be bought in various capacities from a few hundred kilobytes of RAM toabout 64 megabytes. Anything more is both expensive and rare. These modules aregenerally 70ns; however 60ns and 100ns modules are available. The lower thenanosecond rating, the more the module will cost. Currently, a 64MB DIMM costs over$400. All DIMMs are 12cm by 3cm by 1cm or about 36 cubic centimeters. Whereas a 5cubic centimeter block of bacteriorhodopsin studded polymer could theoretically store512 gigabytes of information. When this comparison is made, the advantage becomesquite clear. Also, these bacteriorhodopsin modules could also theoretically run 1000times faster. In response to the demand for faster, more compact, and more affordablememory storage devices, several alternatives have appeared in recent years. Among themost promising approaches include memory storage using protein-based memory. Department of Electronics and Communication, LMCST
  4. 4. PROTEIN BASED MEMORY STORAGE DEVICES 4 3. PROTEIN-BASED MEMORY There have been many methods and proteins researched for use in computerapplications in recent years. However, among the most promising approaches, themain one is 3-Dimensional Optical RAM storage using the light sensitive proteinbacteriorhodopsin. Bacteriorhodopsin is a protein found in the purple membranes of several speciesof bacteria, most notably Halobacterium halobium. This particular bacterium lives insalt marshes. Salt marshes have very high salinity and temperatures can reach 140degrees Fahrenheit. Unlike most proteins, bacteriorhodopsin does not break down atthese high temperatures. Early research in the field of protein-based memories yielded some seriousproblems with using proteins for practical computer applications. Among the mostserious of the problems was the instability and unreliable nature of proteins, which aresubject to thermal and photochemical degradation, making room-temperature or higher-temperature use impossible. Largely through trial and error, and thanks in part tonatures own natural selection process, scientists stumbled upon a light-harvestingprotein that has certain properties which make it a prime candidate for computerapplications. While bacteriorhodopsin can be used in any number of schemes to storememory, we will focus our attention on the use of bacteriorhodopsin in 3-DimensionalOptical Memories. Department of Electronics and Communication, LMCST
  5. 5. PROTEIN BASED MEMORY STORAGE DEVICES 5 4. DEVELOPMENT IN THE FIELD OF MOLECULAR ELECTRONICS There is a revolution fomenting in the semiconductor industry. It may take 30years or more to reach perfection, but when it does the advance may be so great thattodays computers will be little more than calculators compared to what will come after.The revolution is called molecular electronics, and its goal is to depose silicon as kingof the computer chip and put carbon in its place. The perpetrators are a few cleverchemists trying to use pigment, proteins, polymers, and other organic molecules tocarry out the same task that microscopic patterns of silicon and metal do now. For years these researchers worked in secret, mainly at their blackboards,plotting and planning. Now they are beginning to conduct small forays in thelaboratory, and their few successes to date lead them to believe they were on the righttrack. "We have a long way to go before carbon-based electronics replace silicon-basedelectronics, but we can see now that we hope to revolutionize computer design andperformance," said Robert R. Birge, a professor of chemistry, Carnegie-MellonUniversity, Pittsburgh. "Now its only a matter of time, hard work, and some luckbefore molecular electronics start having a noticeable impact." Molecular electronics isso named because it uses molecules to act as the "wires" and "switches" of computerchips. Wires may someday be replaced by polymers that conduct electricity, such aspolyacetylene and polyphenylenesulphide. Another candidate might be organometalliccompounds such as porphyrins and pthalocyanines which also conduct electricity.When crystallized, these flat molecules stack like pancakes, and metal ions in theircenters line up with one another to form a one-dimensional wire. Many organic molecules can exist in two distinct stable states that differ in somemeasurable property and are interconvertable.These could be switches of molecularelectronics. For example, bacteriorhodopsin, a bacterial pigment, exists in two opticalstates: one state absorbs green light, the other orange. Shinning green light on thegreen-absorbing state converts it into the orange state and vice versa. Birge and hiscoworkers have developed high density memory drives using bacteriorhodopsin. Department of Electronics and Communication, LMCST
  6. 6. PROTEIN BASED MEMORY STORAGE DEVICES 6 "Electron transport in photosynthesis one of the most important energy generatingsystems in nature, is a real-world example of what were trying to do," said Phil Seiden,manager of molecular science, IBM, Yorkstown Heights, N.Y. Birge, who heads theCenter for Molecular Electronics at Carnegie-Mellon, said two factors are driving thisdeveloping revolution, more speed and less space. "Semiconductor chip designers are always trying to cram more electroniccomponents into a smaller space, mostly to make computers faster," he said. "Andtheyve been quite good at it so far, but they are going to run into trouble quite soon." Afew years ago, for example, engineers at IBM made history last year when they built amemory chip with enough transistors to store a million bytes if information, themegabyte. It came as no big surprise. Nor did it when they came out with a 16-megabytechip. Chip designers have been cramming more transistors into less space since JackKilby at Texas Instruments and Robert Noyce at Fairchild Semiconductor first showedhow to put multitudes on electronic components on a slab of silicon. But 16 megabytesmay be near the end of the road. As bits get smaller and loser together, "crosstalk"between them tends to degrade their performance. If the components were pushed anycloser they would short circuit. Physical limits have triumphed over engineering. That iswhen chemistry will have its day. Carbon, the element common to all forms of life, willbecome the element of computers too. "That is when we see electronics based oninorganic semiconductors, namely silicon and gallium arsenide, giving way toelectronics based on organic compounds," said Scott E. Rickert, associate professor ofmacromolecular science, Case Western Reserve University, Cleveland, and head of theschools Polymer Micro device Laboratory. "As a result," added Rickert, "we could seememory chips store billions of bytes of information and computers that are thousandstimes faster. The science of molecular electronics could revolutionize computer design." Department of Electronics and Communication, LMCST
  7. 7. PROTEIN BASED MEMORY STORAGE DEVICES 7 5. WHY BACTERIORHODOPSIN? Bacteriorhodopsin (BR), a photon-driven proton pump, is a transmebraneprotein found in the purple membrane of the archaeon, Halobacterium halobium. TheBR is organized with polyprenoid lipid chains in the hydrophobic moiety on a highlyordered two-dimensional lattice in the membrane. Enormous interest has beengenerated by application of the structural and dynamic properties of the BR protein inbioelectronics devices. Embedding bacteriorhodopsin in membrane films is essential toachieve functionality of such devices. Although some prototype devices have beenfabricated, instability of the membranes is acknowledged as a major impediment to thedevelopment of BR-based devices. Whereas there has been much biotechnologicalexperimentation on the properties and functionalities of the BR protein, comparativelylittle attention has been paid to the critically important supporting lipid matrices inwhich BR functions. Archaeal membranes consist predominantly of isoprenoid chainsether-linked to an alcohol such as glycerol. These isoprene structures are unique and arenot prone to decomposition at high temperatures. That isoprene molecular fossils havebeen found in geologic Miocene deposits attests to the extreme durability and stabilityof these structures. In viable organisms BR functions in high efficiency at temperaturesas high as 140˚C, in near-saturating concentrations of salt, and in highly acidicenvironments. Specific lipids of the purple membrane are required for normalbacteriorhodopsin structure, function, and photo cycle kinetics.At ambienttemperatures,the membranes are in a liquid crystalline state that provides optimalfunctioning of the BR..Adaptations of the membrane lipids allow maintenance of theliquid crystalline state even as the indigenous conditions change. Nevertheless, as aconsequence of light absorption, BR initiates a photo cycle through structurallydistinctive conformations, causing tractable optical and electronic properties of theprotein. The characteristics of the lipids in the membrane dictate the large-amplitudemotions of BR,and by consequence the broad utility of bR in bioelectronic devices.Theresearch to be developed under this topic would have military and civilian importance.Some of the bionanotechnological applications that are anticipated include: ultra rapidoptical data acquisition with parallel processing capabilities and extreme high densityholographic 3-dimensional data and image storage. Department of Electronics and Communication, LMCST
  8. 8. PROTEIN BASED MEMORY STORAGE DEVICES 8 6. BACTERIORHODOPSIN OPTICAL MEMORYFollowing are the features of Bacteriorhodopsin Optical Memory:-1. Purple membrane from Halobacterium Halobium2. Bistable red/green switch3. In protein coat at 77K, 107-108 cycles4.10,000 molecules/bit5. Switching time, 500 femtoseconds6. Monolayer fabricated by self-assembly7. Speed currently limited by laser addressing Using the purple membrane from the bacterium Halobacterium Halobium, Prof.Robert Birge and his group at Syracuse University have made a working opticalbistable switch, fabricated in a monolayer by self-assembly, that reliably stores datawith 10,000 molecules per bit. The molecule switches in 500 femtoseconds--thats1/2000 of a nanosecond, and the actual speed of the memory is currently limited byhow fast you can steer a laser beam to the correct spot on the memory. Department of Electronics and Communication, LMCST
  9. 9. PROTEIN BASED MEMORY STORAGE DEVICES 96.1 THE STRUCTURE OF BACTERIORHODOPSIN Bacteriorhodopsin - as all retinal proteins from Halo bacterium - folds into aseven-Tran membrane helix topology with short interconnecting loops. The helices(named A-G) are arranged in an arc-like structure and tightly surround a retinalmolecule that is covalently bound via a Schiff base to a conserved lysine (Lys-216) onhelix G. The cross-section of BR with residues important for proton transfer and theprobable path of the proton are shown in Fig.1. The 3D structure is also available.Retinal separates a cytoplasmic from an extra cellular half channel that is lined byamino acids crucial for efficient proton transport by BR . The Schiff base betweenretinal and Lys-216 is located at the center of this channel. To allow vectorial protontransport, de- and reprotonation of the Schiff base must occur from different sides ofthe membrane. Thus, the accessibility of the Schiff base for Asp-96 and Asp-85 mustbe switched during the catalytic cycle. The geometry of the retinal, the protonation stateof the Schiff base, and its precise electrostatic interaction with the surrounding chargesand dipoles tune the absorption maximum to fit its biological function. Fig. 1: The 3D structure of Bacteriorhodopsin Department of Electronics and Communication, LMCST
  10. 10. PROTEIN BASED MEMORY STORAGE DEVICES 106.2 BACTERIORHODOPSIN PHOTOCYCLE Fig 2:Bacteriorhopsin Photocycle Bacteriorhodopsin comprises of a light absorbing component known asCHROMOPHORE that absorbs light energy and triggers a series of complex internalstructural changes to alter the protein’s optical and electrical characteristics. Thisphenomenon is known as photocycle. In response to light Bacteriorhodopsin “pumps”proton across the membrane, transporting charged ions in and out of the cell.Bacteriorhodopsin goes through different intermediates during the proton pumpingcycle. These stages have been labelled K, L, M, N and O, each one easily identifiablebecause Bacteriorhodopsin changes colour during each stage of the process. The nativephoto cycle has several spectroscopically unique steps, bR --> K <--> L <--> M1-->M2 <--> N <-->O, which occur in a roughly linear order The photo cycle ofbacteriorhodopsin or its cycle of molecular states depend on the luminous radiation thatit absorbs. The initial state known as bR evolves into state K under the effect of greenlight. From there it spontaneously passes to state M then to state O (relaxationtransitions). Department of Electronics and Communication, LMCST
  11. 11. PROTEIN BASED MEMORY STORAGE DEVICES 11 Exposure to red light from O state will make the structure of the bacteriumevolve to state P then spontaneously to state Q, which is a very stable state. Some of the intermediates are stable at about 80K and some are stable at roomtemperature, lending themselves to different types of RAM. Nevertheless, radiationfrom blue light can take the molecule from state Q back to the initial state bR. Any twolong lasting states can be assigned the binary value 0 or 1, making it possible to storeinformation as a series of Bacteriorhodopsin molecules in one state or another.Genetic engineering has been used to create bacteriorhodopsin mutants with enhancedmaterials properties. Three-dimensional optical memory storage offers significant promise for thedevelopment of a new generation of ultra-high density RAMs. One of the keys to thisprocess lies in the ability of the protein to occupy and form cubic matrices in a polymergel, allowing for truly three-dimensional memory storage. The other major componentin the process lies in the use of photons to read and write data. As discussed earlier,storage capacity in two-dimensional optical memories is limited to approximately1/lambda2 (lambda = wavelength of light), which comes out to approximately 108 bitsper square centimeter. Three-dimensional memories, however, can store data atapproximately 1/lambda3, which yields densities of 1011 to 1013 bits per cubiccentimeter. The memory storage scheme which we will focus on, proposed by RobertBirge in Computer (Nov. 1992), is designed to store up to 18 gigabytes within a datastorage system with dimensions of 1.6 cm * 1.6 cm * 2 cm. Bear in mind, this memorycapacity is well below the theoretical maximum limit of 512 gigabytes for the samevolume (5-cm3). Department of Electronics and Communication, LMCST
  12. 12. PROTEIN BASED MEMORY STORAGE DEVICES 126.3 DATA WRITING TECHNIQUE Bacteriorhodopsin, after being initially exposed to light (in our case a laserbeam), will change to between photo isomers during the main photochemical eventwhen it absorbs energy from a second laser beam. This process is known as sequentialone-photon architecture, or two-photon absorption. While early efforts to make use ofthis property were carried out at cryogenic temperatures (liquid nitrogentemperatures), modern research has made use of the different states ofbacteriorhodopsin to carry out these operations at room-temperature. Fig 3. Data Writing TechniqueThe process breaks down like this: Upon initially being struck with light (a laser beam), the bacteriorhodopsinalters its structure from the bR native state to a form we will call the O state. After asecond pulse of light, the O state then changes to a P form, which quickly reverts to avery stable Q state, which is stable for long periods of time (even up to several years). Department of Electronics and Communication, LMCST
  13. 13. PROTEIN BASED MEMORY STORAGE DEVICES 13 The data writing technique proposed by Dr. Birge involves the use of a threedimensional data storage system. In this case, a cube of bacteriorhodopsin in apolymer gel is surrounded by two arrays of laser beams placed at 90 degree anglesfrom each other. One array of lasers, all set to green (called "paging" beams), activatesthe 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 bacteriorhodopsinreaches 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. 6.4 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. Department of Electronics and Communication, LMCST
  14. 14. PROTEIN BASED MEMORY STORAGE DEVICES 14 Fig 4.Data Reading Technique 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 0s and 1s. The process is complete in approximately 10 milliseconds, a rate of 10 megabytes per second for each page of memory. 6.5 DATA ERASING TECHNIQUE To erase data; a brief pulse from a blue laser returns molecules in the Q state back to the rest state. The blue light doesnt necessarily have to be a laser; you can bulk-erase the cuvette by exposing it to an incandescent light with ultraviolet output. 6.6 REFRESHING THE MEMORY In Protein memory the read/write operations use two additional parity bits to guard against errors. A page of data can be read nondestructively about 5000 times.Each page is monitored by a counter and after 1024 reads, the page is refreshed by a new write operation. Department of Electronics and Communication, LMCST
  15. 15. PROTEIN BASED MEMORY STORAGE DEVICES 15 7. MERITS Fig 5.Birge’s Memory cell • This is based on a protein that is inexpensive to produce in quantity. • .The system has the ability to operate over a wider range of temperatures than the semiconductor memory. • The data is stable, i.e. the memory system’s power is turned off, the molecules retain their information. • This is portable, i.e. we can remove small data cubes and ship GBs of data around for storage or backups • Data can be stored for years without any refreshment. Department of Electronics and Communication, LMCST
  16. 16. PROTEIN BASED MEMORY STORAGE DEVICES 16 8. APPLICATIONS Most successful applications of bacteriorhodopsin have been in the development of holographic and volumetric three- dimensional memories. Other applications of Bacteriorhodopsin are:-• When nutrients get scarce, this Bacteriorhodopsin becomes a light- converting enzyme. Its a protein powerhouse that in times of famine flips back and forth between purple and yellow colours. If controllable, this could be valuable in building battery conserving and long lasting computer display panels.• Protein’s photoelectric properties could be used to manufacture photo detectors.• Bacteriorhodopsin could be used as light sensitive element in artificialretinas.• German scientists have used holographic thin films of bacteriorhodopsin to make pattern-recognition systems with high sensitivity and diffraction-limited performance.• Nano biotechnology based medical diagnostics may use this proteins in imaging devices.• Molecules can potentially serve as computers switches because their atoms are mobile and change position in a predictable way. By directing the atomic motion two discrete states can be generated in a molecule, which can be used to represent either 0 or 1. This results in reduction of size, that is, a bimolecular computer in principle is one-twentieth of t h e size of the present day computer. Department of Electronics and Communication, LMCST
  17. 17. PROTEIN BASED MEMORY STORAGE DEVICES 17• bR has all desired properties for usage in associative memory applications. 9. RESEARCH DEVELOPMENT Branched- photocycle memory is developed at the W.M. Keck Centre forMolecular Electronics at Syracuse University. This memory stores from 7 to 10gigabytes (GB) of data in a small 1 × 1 × 3-cm3 cuvette containing the protein in apolymer matrix Data are stored by using a sequential pair of one-photon processes,which allows the use of inexpensive diode lasers to store one bit into the long-lived Qstate. The read/write/erase process is fairly complicated. The 10-GB data cuvettes usedin the 3-D memory described above can withstand substantial gravitational forces andare unaffected by high-intensity electromagnetic radiation and cosmic rays. They caneven be submerged under water for months without compromising the reliability of thedata. 3-D protein memory cuvettes are already being designed and optimized forarchival data storage in office environments. Many millions of dollars have been spenton this research and development. We have learned a great deal in recent years aboutproteins and its applications. Department of Electronics and Communication, LMCST
  18. 18. PROTEIN BASED MEMORY STORAGE DEVICES 18 10. CONCLUSION Birge’s system, which he categorizes as a level-1 prototype (i.e., a proof ofconcept), sits on a lab bench. He has received additional funding from the US Air force,Syracuse University, and the W.M.Keck foundation to develop a level-2 prototype.Such a prototype would fit and operate within a desktop personal computer. “We are ayear or two away from doing internal testing on a level-2 prototype”, says Birge.“Within three or five years, we could have a level-3 beta-test prototype ready, whichwould be a commercial product.” Department of Electronics and Communication, LMCST
  19. 19. PROTEIN BASED MEMORY STORAGE DEVICES 19 REFERENCES1. www.cem.msu.edu2. www.wikipedia.com4. Samuel Styne Protein-Based Three-Dimensional Memory, American Scientist, pp.328-355, July-August 2002.5. Fedrro McKenzie, A model with Protein Storage, Int. J. Quantum Chem., vol. 95, pp. 627–631, 2003.6. D. A. Thompson and J. S. Best, “The future of magnetic storage technology,” IBM J. Res. Develop., vol. 44, pp. 311–322, 2000.7. Marques Da Silva, “Bacteriorhodopsin as a photochromic retinal protein optical memories,” Chem. Rev. vol.100, pp. 1755–1776, 2000. Department of Electronics and Communication, LMCST