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, 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.
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 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.

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

GREEN
LIGHT
SOURCE

b BLUE
LIGHT
R
CONVERTS CONVERTS SOURCE

K Q

RELAXES RELAXES

M P

RELAXES CONVERTS

RED LIGHT
SOURCE

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 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 (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

Data Writing Technique

Fig: Arrangement for data storage into bR cube

Laser Array 1

Laser Array 2 Detector

bR
MEMORY CUBE

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.

Laser Array 1

Laser Array 2 Detector

RED
LASER
bR CUBE

Arrangement for retrieval of data

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

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
 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
Fig: Arrangement for data storage into bRWRITING
cube TECHNIQUE

11. DATA READING TECHNIQUE

12. DATA ERASING TECHNIQUE

13. DATA ERASING TECHNIQUE

14. LATEST DEVELOPMENTS

15. CONCLUSION

16. REFERENCES