.

ABSTRACT

The bacterio-rhodopsin protein is one of the most promising organic memory materials.
Seven helix-shaped polymers form a membrane structure, which contains a molecule known as the
retinal chromophor. The chromophor 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

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 particular

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 particular web page, is
3-Dimensional Optical RAM storage using the light sensitive protein bacterio-rhodopsin. Bacterio-
rhodopsin is a protein found in the purple membranes of several species of bacteria, most notably
Halobacterium halobium. This particular bacteria lives in salt marshes. Salt marshes have very high
salinity and temperatures can reach 140 degrees Fahrenheit. Unlike most proteins, bacterio-
rhodopsin does not break down at these high temperatures
 INDTRODUCTION

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.

The bacterio-rhodopsin protein is one of the most promising organic memory materials. Seven helix-
shaped polymers form a membrane structure, which contains a molecule known as the retinal
chromophor. The chromophor 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.

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 particular web page, is
3-Dimensional Optical RAM storage using the light sensitive protein bacterio-rhodopsin. Bacterio-
rhodopsin is a protein found in the purple membranes of several species of bacteria, most notably
Halobacterium halobium. This particular bacteria lives in salt marshes. Salt marshes have very high
salinity and temperatures can reach 140 degrees Fahrenheit. Unlike most proteins, bacterio-
rhodopsin does not break down at these high temperatures
 WORKING

In a prototype memory system, bacterio-rhodopsin stores data in a 3-D matrix. The matrix can be
build by placing the protein into a curvette (a transparent vessel) filled with a polyacrylamide gel.
The protein, which is in the bR state , gets fixed in by the polymerization of the gel. A battery of
Krypton lasers and a charge-injection device (CID) array surround the curvette and are used to write
and read data.

While a molecule changes states within microseconds, the combined steps to read or write
operation take about 10 milliseconds. However like the holographic storage, this device obtains data
pages in parallel, so a 10 Mbps is possible. This speed is similar to to that of slow semiconductor
memory.

Data Writing Technique

Bacterio-rhodopsin, 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 bacterio-rhodopsin
to carry out these operations at room-temperature.

Data Writing Technique

Bacterio-rhodopsin, 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 bacterio-rhodopsin
to carry out these operations at room-temperature.

The process breaks down like this

Upon initially being struck with light (a laser beam), the bacterio-rhodopsin alters it's 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 photocycle 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.

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
 STRUCTURE OF BACTERIO-RHODOPSIN

PHOTO CYCLE OF BACTERIO-RHODOPSIN

Bacterio-rhodopsin 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 photo cycle.

The initial resting state of the molecule is known as ‘bR’. Green light transforms the initial ‘bR’ state
to the intermediate state ‘K’. Next ‘K’ relaxes, forms another intermediate state ‘M’ and then ‘O’
converts to another intermediate state ’P’, which then relaxes to a more stable state ‘Q’. Blue light
converts ‘Q’ black to the initial state ‘bR’. Here the idea is to assign any two long-lasting states to the
binary values of ‘0’ and ‘1’, to store the required information.

Many of the erstwhile memory devices based on Bacterio-rhodopsin could operate only at extreme
cold temperatures of liquid nitrogen, where light-induced switching between ‘bR’ and the
intermediate state ‘K’ could be controlled. These devices were much faster than conventional
semiconductor-based devices, as these exhibited the speed of a few trillionths of a second. Today,
most Bacterio-rhodopsin based devices function even at room temperature, switching between ‘bR’
and another intermediate stable state ‘M

If a number of Bacterio-rhodopsin molecules are arranged in a three-dimensional fashion, high-

speed, high-density, low-cost memories with vast capacities that can handle large volumes of data
can be realized. Such memories offer over 300-fold improvement in storage capacity over their two-
dimensional counterparts. Read/Write operations on these can be performed with the help of
colored lasers that are fixed at such points as to direct the beams through the required points in the
plane of the cube.

Such memory cubes must be extremely uniform in their composition and must be homogeneous to
ensure good results, since excess of defect of molecules in one particular region tends to distort the
stored information and render the memory cube useless. The entire process of data storage or
retrieval can be carried out in few milliseconds. The speed of these memories depends on the
number of cubes operating in parallel.

Retrieval of stored data is carried out in a manner similar to storing the information, except that a
detector images the light passing through the memory cube and senses 1’s and 0’s. Here the
property of selective absorption of red light by the intermediate state ‘O’ is relied upon. The
detector senses the luminescent power falling upon it and converts the variations of optical power
into a correspondingly varying electric current. An associative memory device that builds on
holographic properties of thin films of Bacterio-rhodopsin has been developed.

Associative memories take images of data blocks as input, scan the entire memory independently of
a central processor for data block that matches the input, and return the closest match. Such
holographic thin films allow multiple images to be stored in the same segment of memory, thereby
permitting simultaneous analysis of large sets of data. However, holograms based on Bacterio-
rhodopsin are erasable.
 MEMORY RESERCH AND DEVELOPMENT

forthat era but this technology is already showing its age. As the millennium nears, research into mem
orytechnologies is expanding into new previously unexplored areas for digital storage solutions. These
new fields promise to fulfill the data processing and computational needs of the 21st century. Thepri
mary forms of memory which are currently being explored are optical memory and molecularmemory

One of the reasons why the need for new technologies has arisen is that the design and construction
of smaller and smaller chips is becoming increasingly difficult. Manufacturers are working with dies int
he .18 - .25 micron range. This will decrease even more but there is a finite limit to how far you canre
duce the die sizes. The restrictions are twofold. One restriction is simply economic. The cost of produc
ing smaller chips is skyrocketing. More importantly though the laws of physics will eventuallyhalt this
progression of decreasing dies.

Moore's law states that the number of transistors on a chip will double approximately even 18 month
sand this has held true ever since he made his prediction in the 1960s. Semiconductor chips aremanuf
actured using a process known as photolithography where the desired circuit features aremapped ont
o the silicon via a mask and a light source. The problem arises though that your lightsource must be at
least as small as the features you're trying to fashion. This becomes increasinglydifficult as the wavele
ngths of the spectrum are fixed and will not change. KryptonFluoride ultravioletlaser light is currently
being used as the light source for .25 micron mask operations and although themasks can still be smal
ler, the task becomes increasingly complex. One developmental system whichseeks to overcome thes
e limitations is optical computing. Optical computing relies on photons ratherthan electrons for data t
ransfer. Electrons although fast have mass and are limited in velocity. Photonson the other hand are b
ased on light waves are as such have no mass are travel at the speed of light.The process of using light
to store data is known as holography.

Holographic data storage reads and writes entire blocks in a single operation making it extremely fast
as a storage medium. The parallel nature of the data access means that speeds of up to 1 Gbps can be
achieved and storage densities of 10 GB per cubic centimetre are capable. Polymer memory cubesexis
t which allow data to be stored and accessed in three dimensions making it very fast for opticalstorag
e. Another advantage is that the photons in the optical computer are not subject to electrical ormagn
etic interference as are their electronic counterparts.

Building a system around photonics isn't as easy as it sounds though and many years of research andd
evelopment will be needed before a successful system can be built. Several groups are working onsuc
h a system though. Researchers from TRW Space Technology Group, the University of California-
Berkley, the National Institute of Standards and Technology, Hewlett-
Package Research Division andStanford University are all working together in order to develop a digita
l computer system based onphotonics. One of the difficulties which arise in building such a machine is
that it is much more difficult to construct hardware which can controll the photons . A secend
alternative to traditional difficult to contruct hardware which can controll the photones . A secend
alternative to traditional storage mediums is molecular memory . At
first this approach might seem somewhat odd and possiblyinsane. However some of the Greatest
scientific minds in history were considerd insane at the time .

Proffeser robert Birge has developed a system to represent binary data using a protein known as
bacterio rhodopsin one might
queststion why proteins would be used to store data. Size in generalallows proteins to be a good cand
idate for data storage and the bacteriorhodopsin was chosen becauseits sensitivity to light allows it to
change structurally and would be a good representation of a logicgate, the primary building block of
our m11emory cell. A series of lasers is then used to excite the proteinmolecules and read or set their
states.Currently speeds of 10 Mbps can be achieved however Professor Birge is convinced that 80 Mb
ps canbe reached. So currently molecular memory isn't very fast in comparison to semiconductor me
moriesbut its advantages lie is the cost of developments, storage density, and its non-volatility.

Semiconductor Memory Developments

The demands made upon computers and computing devices are increasing each year.
Processor speedsare 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 increasethe 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 invarious capacities from a few hundred kilobytes of RAM to
about 64 megabytes. Anything more isboth expensive and rare. These modules are generally
70ns; however 60ns and 100ns modules areavailable.The lower the nanosecond rating, the
more the module will cost. Currently, a 64MB DIMM costs over$400. All Dimms are 12cm
by 3cm by 1cm or about 36 cubic centimeters. Whereas a 5 cubiccentimeter block of
bacteriorhodopsin studded polymer could theoretically store 512 gigabytes of information.
When this comparision is made, the advantage becomes quite clear. Also,
thesebacteriorhodopsin modules could also theoretically run 1000 times

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
approachesinclude memory storage using holography, polymer-based memory
 Intrinsic Worth

However, the merits of molecular storage have garnered sufficient interest that three of NASA's
SpaceShuttle missions explored methods to improve the manufacture of the data cubes by
usingmicrogravity. The resulting material was more homogeneous and provided an enhanced
storagedensity. It remains to be seen, however, whether microgravity manufacturing will be
sufficiently cost-effective to justify the observed factor-of-four improvement

.Can molecular storage compete with traditional semiconductor memory? The design certainly has
itsmerits. First, it's based on a protein that's inexpensive to produce in quantity. In fact,
geneticengineering is being used to boost the output of the protein by the bacterium. Second, the
system hasthe 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 bacteriorhodopsin
moleculesretain their information. This makes for an energy-efficient computer that can be powered
down yetstill be ready to work with immediately because the contents of its memory are preserved.

Data recorded on a bacteriorhodopsin storage device would be stable for approximately five
years."We have lab samples that have held information reliably for two years," he says. Another
importantfeature of bacteriorhodopsin is that these two states have widely different absorption
spectra. Thismakes it easy to determine a molecule's current state using a laser tuned to the proper
frequency.

Finally, you can remove the small data cubes and ship gigabytes of data around for storage or
backups.Because the cubes contain no moving part,its safer tha using a small hard drive a cartridge
for this task
 Recent Trends

In recent news that seems more science fiction than applied science, Japanese researchers
haveunveiled exciting new research that could change the way we create and use computers in years
tocome. Japanese professor Tetsuro Majima of Osaka University has demonstrated that proteins --
oncethe concern of chemists and biologists -- could now have impressive potential in the world of
computerscience.

Majima's research has indicated that proteins isolated from select bacteria species are able to
storecomputer data, and that this type of storage could exceed the capabilities of current magnetic
andoptical storage components.

The fluorescent bacterial protein is etched onto glass, and read using precise combinations of light
andchemicals. The data can be read, manipulated, and erased in a manner almost identical to
currentcomputer memory devices.

Typical computer memory circuits are manufactured using metal arranged on silicon. Since
themanufacturing process requires extremely high temperatures it is usually impossible for thin
materialslike plastic or glass to be used as circuits since they cannot withstand the necessary high
temperatures.

Protein-based memory devices will not require the use of high-temperature manufacturing, and
willtherefore be able to incorporate much thinner materials than traditional optical and magnetic-
based memory systems

proteins can be "fixed" (etched with information) in about one minute, a speed that will improveas
the technology is further developed. Along with fairly rapid information recording, memory
devicesbased on protein will likely be unaffected by magnetic interference and will remain relatively
stable attemperatures lower than the typical computer.

Protein-based memory promises users a faster, more efficient and more reliable form of data relay
thancurrent technologies, and one that will likely come in a much smaller package. The use of
thinnermaterials will allow developers to create much smaller devices that will greatly expand the
range of applications possible for protein technology

With so many desirable qualities, it's no surprise that Majima's team is not the first to think of
usingproteins as a computer storage device. Researchers have been exploring the applications of
variousproteins for use in computer memory since 1995

Last year another japanese reasearch tean at the naro institude of science and technology developed
a protein-based computer memory component based on the protein ferritin, an iron-storingprotein
common to mammals and also to certain forms of bacteria. NAIST has not yet publisheddefinitive
results although they expect to be at the product devolopment stage with the next few years.
The applications of protien based storage are intended primary for a commercial market , but
Majimaalso hopes to develop applications that will ameliorate the function of various medical devices
and testprocedures. Majima hopes to have a commercially viable product developed within the next
five years.A thinner, faster computer is definitely appealing to most consumers, and protein-based
memorydevices do seem to hold a lot of potential in that area. As the fields of biology and computer
scienceconverge, it will be interesting to discover what other biological molecules have potential
computingapplications. Perhaps we will succeed in creating an intelligent machine that is a fusion of
living andartificial components. If current research efforts are any indication of the future of
computer developed ,”resistance is futile”
 ADVANTAGE


 CONCLUTION

Birge’s sysytem which he catogorise as a level-I prototype (i.e., a proof of concept), sits on a labbench.
meived additional funding from the U.S. Air Force, Syracuse University (Syracuse,NY), and the W. M.
Keck Foundation to develop a level-II prototype. Such a prototype would fit andoperate within a
desktop personal computer. "We're a year or two away from doing internal testing ona level-II
prototype," says Birge. "Within three to five years, we could have a level-III beta-testprototype ready,
which would be a commercial products
BIBILIOGRAPHY