Protein memory

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

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Protein memory

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, year’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.

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Protein memory

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).

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Protein memory

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

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Protein memory

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.

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Protein memory

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

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Protein memory

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

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Protein memory

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

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Protein memory

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 protein’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.

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RELAXES

bR

K

M

O

P

Q

RED LIGHTSOURCE

BLUE LIGHT

SOURCE

GREEN LIGHT

SOURCE

CONVERTS CONVERTS

CONVERTSRELAXES

RELAXES

Protein memory

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

Photo cycle of bacteriorhodopsin

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Protein memory

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.

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Protein memory

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.

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Protein memory

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

doesn’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 matrix’s strip conductors are made of

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Protein memory

(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 opticom’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

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Protein memory

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).

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bRMEMORY CUBE

DETECTOR

LASER ARRAY 1

LASER ARRAY 2

Fig: Arrangement for data storage into bR cube

Protein memory

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.

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Protein memory

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

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bR CUBE

Arrangement for retrieval of data

DETECTOR

LASER ARRAY 1

LASER ARRAY 2

RED LASER

Protein memory

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.

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Protein memory

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.

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Protein memory

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!!!

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Protein memory

References

www.cem.msu.edu

www.ieee.org

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

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Protein memory

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

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Fig: Arrangement for data storage into bR cube

Protein memory

13. DATA ERASING TECHNIQUE

14. LATEST DEVELOPMENTS

15. CONCLUSION

16. REFERENCE

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