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20-10-2009, 01:36 AM
Post: #1
protein memory
i needpics related to data write and data read techniques in bacteriorhodopsin protein .
so pls mail me urgently.

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20-10-2009, 02:58 PM
Post: #2
RE: protein memory
Protein Based Memory Storage

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 paper focuses mainly on protein-based optical memory storage using the photosensitive protein bacteriorhodopsin with the two-photon method of exciting the molecules, but briefly describes what is involved in the other two. 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. Along with that this paper is explaining some currently existing projects.

Internal revolution and External Evolution in Memory Research



Protein Based Memory Storage

Introduction:
From the time of homosafien, 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, yearâ„¢s later, more early 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 . . .

Evolution of Memories:
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

Protein Based Memory Storage 6 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.

Current Vs Latest:
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 more dense 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. All Dimms are 12cm by 3cm by 1cm or about 36 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.



Protein Based Memory Storage

Protein-Based Memory:
There have been many methods and proteins researched for use in computer applications in recent years. However, among the most promising approaches, and the focus of this paper, is 3-Dimensional 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 Halo bacterium halobium. This particular bacteria lives in salt marshes. Salt marshes have very high salinity and temperatures can reach 140 degrees Fahrenheit. Unlike most proteins, Bacteriorhodopsin does not break down at these high temperatures. Early research in the field of protein-based memories yielded some serious problems with using proteins for practical computer applications. Among the most serious of the problems was the instability and unreliable nature of proteins, which are subject to thermal and photochemical degradation, making roomtemperature or higher-temperature use impossible. Largely through trial and error, and thanks in part to nature's own natural selection process, scientists stumbled upon Bacteriorhodopsin, a light-harvesting protein that has certain properties which make it a prime candidate for computer applications. While Bacteriorhodopsin can be used in any number of schemes to store memory, we will focus our attention on the use of Bacteriorhodopsin in 3-Dimensional Optical Memories.



Protein Based Memory Storage

BACTERIORHODOPSIN PHOTOCYCLE
Bacteriorhodopsin is a photochemically active protein found in the purple membrane of the bacteria Halobacterium salinarium, which was known as Halobacterium 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. Photochemically active means that it reacts to light. It has a photochemical reaction cycle, or photocycle. This cycle basically transports protons from inside the cell to outside the cell in the bacteria Halobacterium 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.

This is the chromophore At around the temperature of 80 K, the native protein undergoes this photocycle and switches 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:


Protein Based Memory Storage 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 The single critical step in the proton pumping ability of the protein is the transfer of the Schiff base proton do D85, and piece of the protein, in the L --> M reaction. Absorption of light leads to rapid photoisomerization in the excited state because the barrier to conformation al change in that state is negative. In a manner of thinking, the conformational motion of the excited state acts to gate the conformational motion of the ground state. In the L state, the Schiff base exhibits strong H-bonding with close water molecules and distorts the chromophore near the Schiff base. The two necessary coordinators for these water molecules are the anionic Asp85 and Asp212. That coincides with the Trp182 interacting with the retinal skeleton by the 9-methyl group. These events bring about the deprotonation of the Schiff base. Also in the L intermediate state, the backbone has good local structural flexibility. This is evidenced by the many different change in the peptide C to O double bond stretching vibrational frequencies. Some of these frequency variations correlate to the O to H single bond stretching vibrational frequencies. This indicates that the structural changes can come from changing interaction with water molecules. A network of H-bonding including bonds between water and peptides, exists between two pieces of the protein, Asp85 and Asp96. This network exhibits changes most often in the bR to L transformation, which would be the first step in writing to a block of bacteriorhodopsin memory. In the K intermediate, an H-bonding change of the peptide C to O double bond of a valine residue, called Val49, occurs. This stays on in the L intermediate, but is gone in the M intermediate. This is affected by a mutation in the protein. Water appears to affect the C to O double bond affects the protein at specific regions. Some, which exhibit O to H single bond stretching frequencies, interact with the C to O double bond of the Val49 piece. 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.


Protein Based Memory Storage

10

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 photocycle for computing needs:

The photocycle for computer memory An interesting intermediate in the photocycle is the O intermediate. The O intermediate is an all-trans structure like the native protein state. The native state is a light-adapted state. The O state is the red absorbing state. The M state, or unprotonated Schiff base, does not accumulate in the photocycle. This is strange since this protein transports protons. This could mean two things. The first is that the M state cannot be observed because the kinetics is set against its build-up. The other is that the Schiff base does not deprotonate and the transport is based on a completely different mechanism than the wild type protein. The two kinetic reasons for this lack of M are that the rate of decay of M is faster than the rate of formation or that the L <--> M and M <--> N equilibrium are tilted away from the M state

3-Dimensional Optical Memories:
Three-dimensional optical memory storage offers significant promise for the development of a new generation of ultra-high density RAMs. 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

Protein Based Memory Storage 11 photon laser process to read and write data. As discussed earlier, 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 which we will focus on, proposed by Robert Birge in Computer (Nov. 1992), 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 the same volume (5-cm3).

Data Writing Technique:
Bacteriorhodopsin, after being initially exposed to light (in our case a laser beam), will change to between photo isomers 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 write process



Protein Based Memory Storage 12 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.

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.

The read process

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.



Protein Based Memory Storage

13

Advantages:
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. For three-dimensional memory to work, all of the molecules need to be reached without altering any other molecules. This is done with a process called two-photon interaction.

Single Vs Two Photons:
First, let's consider why we even need to use two photons. Let's try to do this with a single photon. A chunk of bacteriorhodopsin-laden polymer would be the memory in this example. The source of light in this example would be a laser of appropriate wavelength to excite the bacteriorhodopsin from the bR to the M or Q state. As a person was using this computer, the RAM would begin to be used up. The surface of the chunk of polymer with our favorite protein would slowly get used up. Eventually, the need to use the memory storage capacity inside the chunk of polymer would arise. No big deal, you're thinking. Just shine the laser on the molecules inside. the chunk. Okay. Let's try it. Zap!! we've encoded on the in sided of the chunk. Now, it's time to read the entire RAM for some computations you need to do for chemistry class. The computer starts reading the RAM and all of a sudden it can't go any further because the memory has been corrupted. This corruption was due to the use of a single photon to change the state of the bacteriorhodopsin. A two photon method would reduce this type of corruption. The two photons would each have only part of the energy needed to change the state of the bacteriorhodopsin. Therefore they would pass through the polymer until they coincided at a point and changed a molecule of bacteriorhodopsin. The single photon method would not be a good choice for a threedimensional memory. A single photon would excite all of the molecules that are in its path. If the surface of the chunk of polymer was used to store something for the computer, that information would be corrupted by the photon as the computer attempted to write to some of the molecules in the inside of the polymer. The photon would also excite all of the molecules in its path through the polymer chunk.



Protein Based Memory Storage

14

Projects:
Bacteriorhodopsin Optical Memory
¢ ¢ ¢ ¢ ¢ ¢

Purple membrane from Halo bacterium, Halobium. Bi-stable red/green switch In protein coat at 77K, 107-108 cycles 10,000 molecules/bit Switching time, 500 femto seconds Monolayer fabricated by self-assembly ,Speed currently limited by laser addressing As an example of current work, consider the molecular optical memory research underway by Prof.

Robert Birge and his group at Syracuse University. Using the purple membrane from the bacterium Halo bacterium Halobium, they've made a working optical bi stable switch, fabricated in a monolayer by selfassembly, that reliably stores data with 10,000 molecules per bit. The molecule switches in 500 femto seconds--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.

Lest you think this is some far out distant future research topic, here's an ad from a couple weeks ago by a company in West Germany offering bacteriorhodopsin for sale, listing under applications, ``Optical data processing, optical switches, holography, information processing, nonlinear optics, and light sensors.''



Protein Based Memory Storage

15

New
Protein based storage...is an experimental means of storing data. Using proteins that respond to light from bacteria found in salt water, a small cube can store large amounts of data. By using lasers the protein can be changed depending on various wave lengths, allowing them to store and recall data. As a result protein can be used to store enormous amounts of data using lasers to read and write binary code. With this new found technology scientists are now developing a larger more efficient storage media.

The students from Fowler High School, Syracuse New York, have created this presentation with help from the Living School Book of Syracuse University and the W. M. Keck Center for Molecular Electronics to show the possibilities of protein memory.

Conclusion:
This paper focuses mainly on protein-based optical memory storage using the photosensitive protein Bacteriorhodopsin. Bacteriorhodopsin is a light-harvesting protein from bacteria that live in salt marshes that has shown some promise as feasible optical data storage. The present research work is to hybridize this biological molecule with the solid state components of a typical computer.

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16-02-2010, 07:17 AM
Post: #3
RE: protein memory

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ABSTRACT
The ability of molecules to serve as computer switches will offer appreciable reduction in hardware size, since there are they very small. The use of a hybrid technology in which the molecules and semiconductors combine and share the duty will 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 scientists. Bacteriorhodopsin is a protein found in the purple membrane of several species of bacteria, most notably Halo bacterium halobium. This particular bacterium lives in salt marshes where there is high salinity and temperature. Bacteriorhodopsin, the basic unit of protein memory does not break down at high temperatures. Survival in such an environment implies that the protein can resist thermal 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 addition to its original state. Only blue light can change the molecule back to its original state.
With fast random access capability, good reliability and transportability protein memories enhance the multimedia capabilities of computer 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 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, yearâ„¢s later; more early 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.
Evolution of Storage Media:
Computers have gone through their own evolution in storage media. 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. 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 (Rs. 18/- per 700 MB disk).
Holostore Technology:
Practically, researchers believe that Holographic data storage system in which thousands 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 centimeter
Fig: Structure of bR the basic unit of protein memory
This figure is still very impressive compared to today's magnetic storage densities, which are around 100 Kb per square centimeter (not including the derive mechanism).
At this density a block of optical media roughly the size of a deck of playing cards 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 throughput on such system can hit 1 Gbps or higher. In holographic recording applications, longer interaction lengths imply increased angular selectivity and also higher data storage capacity. These advantages are in addition to the ability to synthesize a much larger cross sectional area then is currently attainable using bulk materials.
Holostore leverages the imaging properties of light and its ability to launch. The reading out of images instead of single bits serially provides a tremendous improvement 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 capability of coherent light to interfere and to form holograms provides a convenient 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 memory uses lasers for both reading and writing the blocks of data into the photosensitive material. A digital hologram is formed by recording the interference pattern 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 prototype 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 today'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 ability 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, the advantage becomes quite clear. Also, these bacteriorhodopsin modules could also theoretically run 1000 times faster.
More on Protein-Based Memory:
Researchers 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. 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 reach 140oF (60oC). Unlike most proteins, bacteriorhodopsin does not break down at these high temperatures.
Early research in the field of protein-based memories yielded some serious problems with using proteins for practical computer applications. Among the most serious of the problems was the instability and unreliable nature of proteins, which are subject to thermal and photochemical degradation, making room-temperature or 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 exceeds 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 bacteriorhodopsin with excellent optical properties
Bacteriorhodopsin can be used in any number of schemes to store memory, most significant 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 proteinâ„¢s 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 for 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 back 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 the Q state “ a form that remains stable almost indefinitely for years. Blue light will, 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 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 90K 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 “ dimensional memory. This is because a single photon would excite all of the molecules that it came into contact with, where a two “ photon method would only excite the 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 state 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 the 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 where 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 that micro volume. This will distinguish it from the rest of the unexcited molecules. 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 sealed off with two Teflon gaskets and black anodized aluminum. The protein wafer is formed by creating a matrix of bacteriorhodopsin strands within a polymer gel. 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 be forming a cubic protein matrix. This task is somewhat more daunting than forming a thin wafer of bacteriorhodopsin, but not substantially so. The same technique 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 within 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 process 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 heating 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 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.
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 protein film. The light causes the proteins to switch between two stable states. The states can be distinguished above all by those colors which they absorb and those which they let pass. Once they have been changed, the states remain stable even without light. The data is then read with less intense light, that doesnâ„¢t change the memory content. In one state the protein absorb more light, in other less. Another polymer layer, also matrix regulated, acts as a photo detector and measures 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 smaller than the common size of microchips. Thus the usual lithographic procedures could not be sued in the production process. Dimensions that small could actually be achieved if the matrixâ„¢s strip conductors are made of (conductive) polymers. The 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 second 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 strip conductor of the matrix must be connected to and powered by a transistor. The dimensions of modern transistors in 0.25 aem technology pose an obstacle of a few micrometers to the measurements of opticomâ„¢s dream memory with 100nm line intervals. In addition, the mini strip conductors have to contact the giant transistor connectors in a confined area.

Opticom polymer memory: a matrix addresses the light emitting polymers. The light writes on the proteins in the middle of the sandwich at a cross point. The lower polymer layer absorbs light thus reading the memory content
Data Writing Technique
Bacteriorhodopsin, after being initially exposed to light (in our case a laser beam) will change to between photo-isomers 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 the O state. After a second pulse of light, the O state then changes to the 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. Berge 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.
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 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 shot.
If data in one row or one location is to be erased, simply fire two low “ intensity 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 change the state of the molecule back to bR. The other locations hit by the low intensity beams would begin to absorb the light. But, the intensity would not be enough to cause a state shift.
Latest Developments
The latest news about the protein memories is rather unbelievable. Evidently, for 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 Opticom, a company which conceivably could upset the entire industry with their mammoth memory made of polymers. Polymers are the stuff that panty hose and plastic 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 computer memory systems will be interfaced to advanced computer architectures for high-speed processing. Indeed, we are on the threshold of a new 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 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 American 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 Thomson, "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

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05-05-2010, 03:48 PM
Post: #4
RE: protein memory
Hi,

In the reading process of protein memory, first green laser is turned on to select a page and then red laser to read particular byte or whatever.
But my doubt is the molecules which are already in Q state doesnt absorb red light and it is imaged on a detector. the molecule which are in O state absorbs light. So how does we distiguish between 0 and 1 on the detector?

can anyone pls mail me the clear picture of read and write process .

Thanks in advanceSmile






Regards,
Pallavi

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05-06-2011, 02:50 PM
Post: #5
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