Computer Memory Based on the Protein Bacterio-rhodopsin
Palash Jain#, Likhit Jain#, Bhavesh Jaiswar#
1palashj1995@gmail.com
2jain.likhit@yahoo.com
3bhavesh.jaiswar@gmail.com
Abstract-There has been many methods researched for use in computer applications in recent years. However, among the most promising approaches, and the focus of this particular paper, is 3-Dimensional Optical Random Access Memory storage using the light sensitive protein bacterio-rhodopsin. Protein memory is an experimental means of storing data. Using proteins that respond to light from bacteria found in salt water can store large amount of data. By using lasers, the protein can be changed depending upon various wavelengths, allowing them to store and recall data. As a result protein can be used to store enormous amount of data using laser to read and write binary code. This article focuses mainly on protein-based optical memory storage using the photosensitive protein bacterio-rhodopsin with the two-photon method of exciting the molecules. Bacterio-rhodopsin is a light-harvesting protein from bacteria that live in salt marshes that has shown some promise as feasible optical data storage.
Keywords- Bacterio-rhodopsin, Three-dimensional data storage system, Photo cycle, Laser, P state, Q state, O state.
INTRODUCTION
Since the dawn of time, man has tried to record important events and techniques for everyday life. 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. 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. So currently protein memory isn't very fast in comparison to semiconductor memories but its advantages lie is the cost of developments, storage density, and its non-volatility.
The demands made upon computers and computing devices are increasing each year. Processor speeds are increasing at an extremely fast clip. However, the RAM used in most computers is the same type of memory used several years ago. The limits of making RAM denser are being reached. Surprisingly, these limits may be economical rather than physical. A decrease by a factor of two in size will increase the cost of manufacturing of semiconductor pieces by a factor of 5.
Currently, RAM is available in modules called SIMMs or DIMMS. These modules can be bought in various capacities from a few hundred kilobytes of RAM to about 64 megabytes. Anything more is both expensive and rare. These modules are generally 70ns; however 60ns and 100ns modules are available. The lower the nanosecond rating, the more the module will cost. All Dimms are 12cm by 3cm by 1cm or about 36 cubic centimeters. Whereas a 5 cubic centimeter block of bacterio-rhodopsin studded polymer could theoretically store 512 gigabytes of information. When this comparison is made, the advantage becomes quite clear. Also, these bacterio-rhodopsin modules could also theoretically run 1000 times faster.
In response to the demand for faster, more compact, and more affordable memory storage devices, several viable alternatives have appeared in recent years. Among the most promising approaches include memory storage using holography, polymer-based memory, and our focus, protein-based memory.
3-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-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 108bits 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.

PROCESS OF PROTEIN EXTRACTION
The chemical is bacterio-rhodopsin, a purple protein essential to the cell wall of Halobacterium halobium, a mysterious resident of salt-marshes and lakes. When nutrients get scarce, this bacterio-rhodopsin becomes a light-converting enzyme that keeps the organism's life cycle going. The process of making the protein cube has many different steps. First the bacterial DNA is splice and mutated to make the protein more efficient for use as a volumetric memory. Then, the bacteria must be grown in large batches and the protein extracted. Finally, the purified protein is put into the cube and used as a volumetric storage medium. The cube is read by two lasers as binary code. One laser is used to activate the protein in a section of the cube. The other laser is used to write or read binary information in the same section.
BACTERIO-RHODOPSIN PHOTOCYCLE
Bacterio-rhodopsin is a photo chemically 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. Photo chemically active means that it reacts to light. It has a photochemical reaction cycle, or photo cycle. This cycle basically transports protons from inside the cell to outside the cell in the bacteria Halobacterium halobium. The native photo cycle 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.

Figure 1 Structure of a Chromophore
At around the temperature of 80 K, the native protein undergoes this photo cycle 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 meta-stable configurations. The main event follows these steps:
1. A change in the shape of the conformational potential energy surface resulting from electron excitation
2. A conformational change
3. A non-radiative decay to the ground state

Figure 2 Photo cycle for Computer Memory
DATA WRITING TECHNIQUE
Bacteriorhodopsin, after being initially exposed to light (in our case a laser beam); will change to between photoisomers during the main photochemical event when it absorbs energy from a second laser beam. This process is known as sequential one-photon architecture, or two-photon absorption. Upon initially being struck with light, the bacterio-rhodopsin 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 bacterio-rhodopsin 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 bacterio-rhodopsin reaches near maximum. Now the other set, or array, of lasers - this time of red beams - is fired.

Figure 3 The write process
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 bacterio-rhodopsin. 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.

Figure 4 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.
DATA ERASING
To erase data, a brief pulse from a blue laser returns molecules in the Q state back to the rest state. The blue light doesn't necessarily have to be a laser; you can bulk-erase the cuvette by exposing it to an incandescent light with ultraviolet output.

Figure 5 Actual implementation
CONCLUSION
Molecular storage can compete with traditional semiconductor memory. The merits of molecular storage have garnered sufficient interest. The design certainly has its merits. First, it's based on a protein that's inexpensive to produce in quantity. In fact, genetic engineering is being used to boost the output of the protein by the bacterium. Second, the system has the ability to operate over a wider range of temperatures than semiconductor memory. Third, the data is stable. If you turn off the memory system's power, the bacterio-rhodopsin molecules retain their information. This makes for an energy-efficient computer that can be powered down yet still be ready to work with immediately because the contents of its memory are preserved.

REFERENCES

[1] [2] http://www.seminarsonly.com/computer%20science/Computer%20memory%20based%20on%20the%20protein%20bacterio%20rhodopsin.php [3] http://www.slideshare.net/lijomatthew/protein-memoryseminar-report [4] http://wiki.answers.com/Q/Computer_memory_based_on_the_protein_bacterio-rhodopsin [5] http://abdulla-ck.blogspot.in/2005/08/computer-memory-based-on-protein.html [6] http://www.scribd.com/doc/49347044/Computer-Memory-Based-on-Protein-Bacterio-Rhodopsin-Full-Report [7] http://www.authorstream.com/Presentation/adinater-1331441-protein-memory [8] http://www.infopackets.com/news/humor/2008/20080228_protein_adds_muscle_to_computer_memory.htm [9] http://www.buzzle.com/editorials/5-2-2004-53655.asp [10] http://pinktentacle.com/2007/09/ferritin-proteins-yield-ultrathin-computer-memory/