PROTEIN MEMORY
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While magnetic and semiconductor 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 is the protein-based optical memory storage. This paper focuses mainly on protein-based optical memory storage using the photosensitive protein bacteriorhodopsin with the two-photon method of exciting the molecules. Bacteriorhodopsin is a light-harvesting protein from bacteria that live in salt marshes that has shown some promise as a feasible optical data storage. The use of this hybrid technology in which the molecules and semiconductors combine and share the duty will appreciably improve the speed and reduce the size of the computers.
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#2
submitted by:-
ANJALI SINGH

Protein memory for computer
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INTRODUCTION
Molecular electronics is an emerging field that lies at the interface of chemical physics, electrical engineering and solid state science.
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.
the limits of the current 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.
Why do we need this technology
The design and construction of smaller and smaller chips is becoming increasingly difficult.
Manufacturers are working with dies in the .18 - .25 micron range. This will decrease even more but there is a finite limit to how far you can reduce the die sizes.
The restrictions are twofold.
One restriction is simply economic.
More importantly though the laws of physics will eventually halt this progression of decreasing dies. Moore's law states that the number of transistors on a chip will double approximately even 18 months and this has held true ever
Semiconductor chips are manufactured using a process known as photolithography.
The problem arises though that the light source must be at least as small as the features we are trying to fashion.
This becomes increasingly difficult as the wavelengths of the spectrum are fixed and will not change.
Professor Robert Birge has developed a system to represent binary data using a protein known as bacteriorhodopsin.
why proteins would be used to store data?
Size in general allows proteins to be a good candidate for data storage
The bacteriorhodopsin was chosen because its sensitivity to light allows it to change structurally and would be a good representation of a logic gate, the primary building block of our memory cell.
Currently speeds of 10 Mbps can be obtained and speed of 80 mbps is beieved to be achieved.
advantages lie is the cost of developments, storage density, and its non-volatility.
BIOMOLECULAR COMPUTERS
Is a computer based on the dynamics of bio molecular activities rather than on electronic switching.
Since 1960’s the computer industry has been compelled to make the individual components on semiconductor chips smaller and smaller inorder to manufacture large memories and more powerful processors economically.
These chips consists of array of switches, usually of the kind known as logical gates that flip between two states-0 or 1 in response to electric current passing through them.
The size of single logic gate will approach the size of molecules in the year 2030.
the use of biological molecules as the active components in computer circuitry may offer an alternative approach that is more economical.
Molecules can potentially serve as computers switches because their atoms are mobile and change position in a predictable way.
A biomolecular computer in principle is one-fifth of the size of the present day semiconductor computer.
This theoretically makes it thousand times modern computers. Researchers have introduced parallel processing architecture which allows multiple rows of data to be manipulated simultaneously.  
In order to expand memory capacities, they are devising hardware that stores data in 3D instead of usual ways.
The ability of creating proteins to change their properties in response to light should simplify the hardware required for its implementations.
Although no computer components made from proteins are in the market yet, ongoing international research efforts are making enticing headway.
Several molecules are under consideration for the use in computers. Bacteriorhodopsin has generated the most interest.
BACTERIORHODOPSIN
Bacteriorhodopsin is a light harvesting protein found in the purple membranes of several species of bacteria, most notably Halobacterium halobium and is the key protein in Halobacterial photosynthesis.
Bacteriorhodopsin is a protein found in the purple membranes of several species of bacteria, most notably Halobacterium halobium.
This bacteria live in salt marshes. Salt marshes have very high salinity and temperatures can reach 140 degrees Fahrenheit.
bacteriorhodopsin does not break down at these high temperatures.
It functions like a light –driven photo pump.
Upon absorption of light it generates a chemical and osmotic potential that serves as energy source.
It has the ability to form thin films that exhibit excellent optical characteristics and offer long term stability .
Among the most serious of the problems was the instability and unreliable nature of proteins, which are subject to thermal and photochemical degradation.
Process of protein extraction….
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.
The data is assigned as either a 0 or 1.
PHOTOCYCLE
Bacteriorhodopsin comprises a light absorbing component known as CHROMOPHORE , that absorbs light energy and triggers a series of complex internal structural changes to alter the protein’s optical and electrical characteristics. This phenomenon is known as photocycle.
Green light Changes the initial resting state known as Br to the intermediate K.
Next K relaxes, forming M and then O. If the O intermediate is exposed to red light, a so called branching section occurs.
O converts to the P state and quickly relaxes to the Q state-a form that remains stable indefinitely.
Blue light will convert Q back to bR .
Any two long lasting states can be assigned the binary value 0 or 1,making it possible to store information as a series of bacteriorhodopsin molecules in one state or another.
The intermediates absorb light in different regions of the spectrum.
we read the data by shining laser beams on molecules and noting the wavelengths that don’t pass through the detector. Since we can alter the structure of bacteriorhodops in with one laser and another laser, we have the needed basis for writing and then reading from memory.
INTERCONNECTION FACE BIMOLECULAR COMPUTING
VLSI circuit technology cause serious interconnection problems in chip area, power consumption and noise.
Biomolecular computers based on specifity of enzymes in their choice of reactants and substrates.
Foundation of this computing system is SLV(set valued logic).
Large number of enzymes used in this concept.
Has low data rates,but advantage lies in natural and massive parallelism.
PARALLEL PROCESSING
Certain intermediates produced after bacteriorhodopsin initially exposed to light will change to unusual structures when they absorb energy from second laser beam, in a process known as sequential 1-photon architecture.
data writing process:
Cube of bacteriorhodopes is surrounded by two arrays of laser beams placed 90 degree from each other.
green laser ,called pagging beams, activates the photocycle of proteins in any selected square plane or page within the cube.
when the number of 0 intermediates reaches near maximum, the other laser array of red beams is fired.
Second array illuminates the activated square where the data bits are to be written, switching the molecules to the P structure . The P intermediate then relaxes.
data reading process:
green paging beam fire at the square of the protein to be read .
After 2 ms, the entire laser assay is turned on at a very low intensity of red light .
Molecules in the binary 1 state do not absorbe these, red molecules in the binary 0 state (bR) do absorbe the beams.
Detector reads 0 and 1 in terms of binary code.
The process completes in about 10 ms, a rate of 10 megabytes per second for each page of memory.
For data erasing:
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.
can bulk-erase by exposing to an incandescent light with ultraviolet output.
Data refreshing:
read/write operations use 2 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 via a new write operation.
3-D MEMORY
3-d cubes of bacteriorhodopes provides much more space than 2-d optical memories.
Major impact on area of volumetric memory and its speed.
If we illuminate a square measuring 1,024 bits by 1,024 bits within a larger tube of protein, we can write 105 KB into memory in a 10 mS cycle.
Thus, overall write speed of 10 million characters per second comparable to slow semiconductor memory.
ADVANTAGES:
based on a protein that's inexpensive to produce in quantity.
operates over a wider range of temperatures than semiconductor memory.
the data is non volatile.
Data recorded on a bacteriorhodopsin storage device would be stable for approximately five years.
the two binary states have widely different absorption spectra.
can remove the small data cubes and ship gigabytes of data around for storage or backups.
CONCLUSION
The hyhrid computer we envision would be highly flexible by taking advantage of particular combinations of the memory card described above
Large pools of data carry out complex scientific simulations or serve as a unique platform for investigation of artificial intelligence
With above a tetra byte of memory in cubes of bacteriorhodopsin , this machine would handle large data bases with alacrity.
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