SEMINAR 2019 BACTERIO-RHODOPSIN 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.

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 colour 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 Halo bacterium 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.

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MEMORY RESERCH AND DEVELOPMENT

Forthat era but this technology is already showing its age. As the millennium nears, research
into memorytechnologies is expanding into new previously unexplored areas for digital stor
age solutions. Thesenew fields promise to fulfill the data processing and computational nee
ds of the 21st century. Theprimary 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 con
struction of smaller and smaller chips is becoming increasingly difficult. Manufacturers are
working with dies inthe .18 .25 micron range. This will decrease even more but there is a fin
ite limit to how far you canreduce the die sizes. The restrictions are twofold. One restriction
is simply economic. The cost of producing smaller chips is skyrocketing. More importantly th
ough 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 monthsand this has held true ever since he made his prediction in the 1960s. Semicondu
ctor chips aremanufactured using a process known as photolithography where the desired ci
rcuit features aremapped onto the silicon via a mask and a light source. The problem arises t
hough that your lightsource must be at least as small as the features you're trying to fashion
. This becomes increasinglydifficult as the wavelengths of the spectrum are fixed and will no
t change. KryptonFluoride ultravioletlaser light is currently being used as the light source for
.25 micron mask operations and although themasks can still be smaller, the task becomes in
creasingly complex. One developmental system whichseeks to overcome these limitations is
optical computing. Optical computing relies on photons ratherthan electrons for data transf
er. Electrons although fast have mass and are limited in velocity. Photonson the other hand
are based on light waves are as such have no mass are travel at the speed of light.The proce
ss of using light to store data is known as holography.

Holographic data storage reads and writes entire blocks in a single operation making it extre
mely fastas a storage medium. The parallel nature of the data access means that speeds of u
p to 1 Gbps can beachieved and storage densities of 10 GB per cubic centimetre are capable.
Polymer memory cubesexist which allow data to be stored and accessed in three dimension
s making it very fast for opticalstorage. Another advantage is that the photons in the optical

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computer are not subject to electrical ormagnetic interference as are their electronic counte
rparts.

Building a system around photonics isn't as easy as it sounds though and many years of rese
arch anddevelopment will be needed before a successful system can be built. Several groups
are working onsuch a system though. Researchers from TRW Space Technology Group, the
University of CaliforniaBerkley, the National Institute of Standards and Technology, Hewlett-
Package Research Division andStanford University are all working together in order to devel
op a digital computer system based onphotonics. One of the difficulties which arise in buildi
ng such a machine is that it is much more difficult to construct hardware which can control
the photons. A second alternative to traditional difficult to construct hardware which can
control the photons . A second alternative to traditional storage mediums is molecular
memory.Atfirst this approach might seem somewhat odd and possiblyinsane. However som
e of the greatest scientific minds in history were considered insane at the time. Professor
Robert Birge has developed a system to represent binary data using a protein known as
bacterio rhodops in one might question
why proteins would be used to store data. Size in generalallows proteins to be a good candi
date for data storage and the bacteriorhodopsin was chosen becauseits sensitivity to light al
lows it to change structurally and would be a good representation of a logicgate, the primar
y building block of our m11emory cell. A series of lasers is then used to excite the proteinmo
lecules and read or set their states.Currently speeds of 10 Mbps can be achieved however Pr
ofessor Birge is convinced that 80 Mbps canbe reached. So currently molecular memory isn't
very fast in comparison to semiconductor memoriesbut its advantages lie is the cost of deve
lopments, 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
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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. Currently, a 64MB DIMM costs over$400.
All Dimms are 12cm by 3cm by 1cm or about 36 cubic centimetres. Whereas a 5
cubiccentimeter block of bacteriorhodopsin studded polymer could theoretically store 512
gigabytes of information. When this comparison is made, the advantage becomes quite
clear. Also, these bacteriorhodopsin 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 approaches include memory storage using holography, polymer-based memory.

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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

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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.

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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 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.

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

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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.

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INTRINSIC WORTH

However, the merits of molecular storage have garnered sufficient interest that three of
NASA's Space Shuttle missions explored methods to improve the manufacture of the data
cubes by using microgravity. The resulting material was more homogeneous and provided
an enhanced storage density. 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 competes with traditional semiconductor memory? 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 bacteriorhodopsin
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.

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 important feature of bacteriorhodopsin is that these two states have widely
different absorption spectra. This makes 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, it’s safer the using a small hard
drive a cartridge for this task.

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RECENT TRENDS

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

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

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

Typical computer memory circuits are manufactured using metal arranged on silicon. Since
the manufacturing process requires extremely high temperatures it is usually impossible for
thin materials like 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 will therefore 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
improves the technology is further developed. Along with fairly rapid information recording,
memory devices based on protein will likely be unaffected by magnetic interference and will
remain relatively stable at temperatures lower than the typical computer.

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

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

Last year another Japanese research team at the naro institute of science and technology
developed a protein-based computer memory component based on the protein ferritin, an
iron-storing protein common to mammals and also to certain forms of bacteria. NAIST has
not yet published definitive results although they expect to be at the product development
stage with the next few years.

The applications of protein based storage are intended primary for a commercial market ,
but Majima also hopes to develop applications that will ameliorate the function of various
medical devices and test procedures. 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 memory devices do seem to hold a lot of potential in
that area. As the fields of biology and computer science converge, it will be interesting to
discover what other biological molecules have potential computing applications. Perhaps we
will succeed in creating an intelligent machine that is a fusion of living and artificial
components. If current research efforts are any indication of the future of computer
developed ,”resistance is futile”.

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CONCLUTION

Birge’s system which he categorise as a level-I prototype (i.e., a proof of concept), sits on a
lab bench. moved 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 and operate within a desktop personal computer. "We're a year or two away from doing
internal testing on a level-II prototype," says Birge. "Within three to five years, we could
have a level-III beta-test prototype ready, which would be commercial products.

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BIBILIOGRAPHY

[1] https://www.scribd.com/doc/49347044/Computer-Memory-Based-on-Protein-Bacterio-

Rhodopsin-Full-Report

[2]https://www.seminarsonly.com/Bio-Medical-Engineering/Bacterio-Rhodopsin

Memory.php

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