protein basic memory seminar report

7/29/2019 Protein Basic Memory Seminar Report

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BIOMOLECULAR COMPUTERS

Is a computer based on the dynamics of bio molecular

activities rather than on electronic switching. By exploiting some special

properties of biological molecules, particularly proteins, components that are

smaller, faster and more powerful than any electronic device can be made to

function.

Since 1960s 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. If the trends toward miniaturization continues, the size of single

logic gate will approach the size of molecules in the year 2030.

A serious roadblock to miniaturization is the increase in cost of

manufacturing a chip. At some point the search for even smaller electronic-2-


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devices may be limited by economics rather than physics. So the use of

biological molecules as the active components in computer circuitry may offer

an alternative approach that is more economical.

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BATCERIORHODOESIN

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Molecules can potentially serve as computers switches because their

atoms are mobile and change position in a predictable way. If we can direct the

atomic motion and thereby constantly generate two discrete states in a

molecule, we can use each state to represent either 0 or 1.This results in

reduction of size, that is, 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. So scientists have built nueral networks that mimic the

leasing by association capabilities of the brain. The ability of creating proteins

to change their properties in response to light should simplify the hardware

required for its implementations.

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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.

ORIGIN IN SALT MARSH

Bacteriorhodopsin is a light harvesting protein in the purple

membrane of a micro organism called Halobacterium halobium .Bacterior-

hodopsin , the bacterial protein , is the basic unit of protein memory and is

the key protein in Halobacterial photosynthesis .It functions like a light

driven photo pump. Under exposure to light it transports photons from the

halobacterial cell to another medium, changes its mode of operation from

photosynthesis to respiration, and converts light energy to chemical energy.

The response of this molecule to light energy can be utilised to frame prutein

memories.

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Bacteriorhodopsin grows in salt marshes ,where temperature can exceed

150 degree F for the extended time period and the salt concentration is

approximately six times that of sea water. Survival in such an environment

implies that this protein can resist thermal and photochemical damages.

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 .

Soviet scientists were the first to recognize and develop the

potential of the Bacteriorhodopsin sea for computing. Many aspect of this

ambitious project are still considered military secrets.

COMPUTER APPLICATION

At first interests were on the protein called rhodopsin ,but later

were focused on Bacteriorhodopsin because of the greater stability and better

optical properties It can be prepared in large quantities also. The application

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under study for computer processors and the memories on which they operate

exploit the photocycle of Bacteriorhopdopsin.

PHOTOCYCLE OF BACTERIORHODOPSIN

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 proteins optical and electrical

characteristics. This phenomenon is known as photocycle.

The sequence of structural changes induced by light as in figure allows for

the storage of data in memory. 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.

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O converts to the P state and quickly relaxes to the Q state-a form that remains

stable indefinitely. Blue light will however 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. As a

consequence, we can read the data by shining laser beams on molecules and

noting the wavelengths that dont pass through the detector. Since we can alter

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the structure of bacteriorhodops in with one laser and another laser, we have

the needed basis for writing and then reading from memory.

Most devices under study make use of resting state and one

intermediate. One state is designated as 0 and other as 1.Switching between the

states are controlled by means of laser beams. Most of the early memory

devices based on bacteriorhodopsin could operate only at extremely cold

temperatures of liquid nitrogen, at which the light induced switching between

the initial bR structure and intermediate known as the K could be controlled.

These devices were very fast compared with semiconductor switches. But the

need for low temperatures precluded general application.

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Today most bacteriorhodopsin devices functions at or near room

temperature, a condition under which another intermediate M is stable.

Although most bR based memory devices incorporate bR M switch, other

structures may actually prove more useful in protein - based computer systems.

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INTERCONNECTION FACE BIOMOLECULAR

COMPUTING

Over the past two decades VLSI circuit technology has developed

rapidly. Unfortunately in complex VLSI systems these increases cause serious

interconnection problems in chip area, power consumption and noise. One

promising candidate for breaking through these difficulties is the biomolecular

computer. The model is based on the specificity of enzymes in their choice of

reactants and substrates. They carry information by their presence or absence in

solution. At the specified destination, enzyme based biosensors selectively

detect the released substrates which automatically triggers a specific

biomolecular switch in solution.

The foundation of any computing system is its logic. To

support the systematic design of biomolecule computing systems, an algebraic

system called set valued logic (SLV),special class of multivalued logic is used.

In the SLV concept we use a large number of enzymes and their substrates in

our system and the varieties of substrate molecules represent SLV logic states.

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Electronic VLSI systems have very effective execution and fast

interactive capabilities. Though a biomolecular computer has low data rates,

their advantage in natural and massive parallelism. They offer a new parallel

processing architecture and bioprocessor executes operations in a data driven

manner that makes it possible to exploit the maximum parallelism of a given

algorithm.

Logic value 0 logic value 1------------------logic value r-1

Substrate 0 substrate 1---------------------substrate r-1

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MODEL OF BIOMOLECULAR SWITCHING DEVICE

Let L be the set of all the substrate that can be transmitted

simultaneously in solution. This simultaneous transmission is interpreted

algebraically as logic value multiplexing. An enzyme based biosensors can

exactly discriminate the molecular information.

In this the concept of MLV to design biodevice networks for

interconnection free computation is discussed.The use of more than two levels

of logic can reduce the complexity of intergrated circuit interconnection.

Practical MLV use continous electrical variables such as voltage,current and

change to convey information.

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AN ENZYME SUBRATE REACTION

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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. In the photocycle above, a branching section occurs from 0

intermediate to form P and Q. These are generated by two consecutive pulses

of laser light-first green and then red. Although P is fairly shortlived, it relaxes

to form Q which is stable for extended periods. Because of its extended

stability, the Q state has greater significance in search for long term, high

density memory.

The intermediate PandQ formedin the sequential 1- photon,

are particularly useful for parallel processing. For writing data in parallel our

approach incorporates another information-these dimensional data storage. A

cube of bacteriorhodops in is surrounded by two arrays of laser beams placed

90 degree from each other. One array of laser, all set to green and called

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pagging beams, activates the photocycle of proteins in any selected square

plane or page within the cube. After a few milliseconds, when the number of 0

intermediates reaches near maximum, the other laser array of red beams is

fired.

This second array is programmed to illuminate only the region of

activated square where data bits are to be written, switching the molecules to

the P structure. T he P intermediate then relaxes. Since the laser array can

activate molecules in various places throughout the chosen illuminated page,

multiple data locations, known as addressed can be written in parallel.

The system for reading stored memory during processing

or during the contraction of result relies on the selective absorption of red light

by the 0 intermediate. To read multiple bits of data in parallel ,we start just as

we do in the writing process First the green paging beam fire at the square of

the protein to be read , starting the normal photocycIe of molecules in bR state.

After two milli seconds, the entire laser assay is turned on at a very low

intensity of red light .Molecules that are in the binary 1 state do not absorbe

these, red molecules that started out in the binary 0 state (bR) do absorbe the-18-


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beams .The detector reads 0s and lsin terms of the binary code .The process is

complete in approximately 10 ms, a rate of 10 megabytes per second for each

page of memory

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THREE DIMENSIONAL MEMORY

In addition to facilitating parallel processing, 3D cubes of

bactrioshodcpsin provides much more space that two dimensional optical

memories. Three dimensional optical memories can theoratically approach

storage densities of one trillion bits per cubic centimeters .A 300 folds

improvement in storage capacity over 2-D devices should be possible .So a

major impact of bioelectronics on computer hardware will be in the area of

volumatric memory.

Speed is also an important benefit. of volumatric memories. The

complication of 3-D storage within the use of parallel architectures enhances

the speed of such memories , just a parallel processing in the human brain

overcomes relatively slow nueral processor and allows the brain, to be a

thinking machine with fast reflexces and rapid decision making capability .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. .So it means an

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overall write speed of 10 million characters per second comparable to slow

semiconductor memory.

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NUERAL NETWORKS

Associative memories operate rather differently from the memories that

dominate current computer architectures .This type of architecture takes a set

of data often in the form of an image and scans the entire memory bank until it

finds a data set that matches it .Since human brain operates in a nueral

associative mode , many computer scientists believe large - capacity

associative memories will be required if we are to achieve artificial

intelligence.

As associative memory device that relies in the holographic properties

of thin films of bacterioshodopsin, holograms allows multiple image to be

stored in the same segment of memory, permitting large data sets to be

analysed simultaneously. Associative memories have significant potential for

applications in optical computer architectures optically coupled nueral network

computers etc.

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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 plate form for investigation of artfical intelligence With above a tetra

byte of memory in cubes of bacteriorhodopsin , this machine would handle

large data bases with alacrity. Associative memory processing coupled with

volumetric memory would make databases searches. Many orders of

magnitude faster than is currently possible. Since this hybrid computer can be

designed to function as a nueral associative computer capable of learning and

analysing data like a human brain, the importance of hybrid computers to

studies in artificial intelligence cannot be under estimated.

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REFERENCES

BOOKS

1. SCIENTIFIC AMERICAN by ROBERT.R.BIRGE

2. THE LOCK KEY PARALDIGM by MICHAEL CONSAD

3. INTERCONNECTION FREE BIOMOLECULAR COMPUTING by

TAKAFUNI AOKI,MICHIKITA KAYEMA

4. A BIOLOGICAL MATERIAL FOR INFORMATION PROCESSING by

DIETER OESTHERHELT

WEBSITES

1. www.efy.com

2. www.protein memories.com

3. www.bacteriorhodopsin.com

4. www.ask.com

5. www.howstuffworks.com

6. www.astavista.com

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CONTENTS

INTRODUCTION

BIOMOLECULAR COMPUTERS

ORIGINS IN SALT MARSH

PHOTOCYCLE

INTERCONNECTION FACE BIOMOLECULAR

COMPUTING

MODEL OF A BIOMOLECULAR SWITCHING

DEVICE

PARALLEL PROCESSING

THREE DIMENSIONAL MEMORY

NUERAL NETWORKS

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CONCLUSION

REFERENCE

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ABSTRACT

The worlds most advanced super computer doesnt require a single

semiconductor chip.

The human brain consists of organic molecules that combines to form a

highly sophisticated network able to calculate, perceive, manipulate, self-

repair, think and feel. Digital computers can certainly perform calculations

much faster and more precisely than humans, but even simple organisms are

superior to computers in the other five domains. Computer designers may

never be able to make machines having all the facilities of natural brain,but we

can exploit some special properties of biological molecular-particularly

proteins-to build computer components that are faster ,smaller and more

powerful than any electronic devices .

Devices fabricated from biological molecules promise compact size and

faster data storage. They lead themselves to use in parallel processing

computers,3Dmemories and neural networks.

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As the trend towards miniaturization continues, the cost of manufacturing

a chip increases considerably. On the other hand ,the use of biological

molecules as the active components in a computer circuitry may offer an

alternative approach that is more economical.

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ACKNOWLEDGEMENT

I extend my sincere thanks to Prof. P.V.Abdul Hameed, Head of the

Department for providing me with the guidance and facilities for the Seminar.

I express my sincere gratitude to Seminar coordinator Mr. Manoj K,

Staff in charge, for his cooperation and guidance for preparing and presenting

this seminar.

I also extend my sincere thanks to all other faculty members of

Electronics and Communication Department and my friends for their support

and encouragement.

Priya. M

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protein basic memory seminar report

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