Protein Memory

Protein Memory

TECHNICAL RESEARCH PAPER

Submitted in partial fulfillment of the requirements

For the award of the degree of

Bachelor of Computer Application (BCA)

To
Guru Gobind Singh Indraprastha University, Delhi

Submitted by:
Sahil Saluja
(07021102011)

Institute of Information Technology & Management,

New Delhi – 1100 58
Batch (2011-2014)

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TABLE OF CONTENT
S NO. TITLE P NO.
1 Introduction 3

1.1 History 3
1.2 Why Do We Need To More Storage Space 4
2 PROTEIN-BASED MEMORY 5
3 8
THE STRUCTURE OF
BACTERIORHODOPSIN

3.1 BACTERIORHODOPSIN PHOTOCYCLE 8

4 DATA WRITING TECHNIQUE 12
5 DATA READING TECHNIQUE 20
6 24
DATA ERASING TECHNIQUE
Conclusion 29
REFRENCES AND BIBLOGRAPHY 31

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Abstract
A digital signature scheme allows one to sign an electronic message and later
the produced signature can be validated by the owner of the message or by
any verifier. Most of the existing digital signature schemes were developed
based on the use of hash function and massage redundancy to resist against
forgery attack. In this paper we propose a signature scheme with message
recovery and without using one way hash function which is secure and
practical. The proposed scheme is shown to be secure against the parameter
reduction attack and forgery attack. Security of the scheme is based on the
complexity of solving the discrete logarithm problem and integer
factorization. The proposed scheme does not use message redundancy and is
suitable to provide signature on long messages.

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CHAPTER 1

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.
These record can be seen on the wall of caves in many parts of the world. Pictures gave
way to letters which represented spoken sounds. Then came people who invented spoken
languages and the need arose to record what one was saying without hearing it firsthand.
Therefore, years later, earlier scholars invented writing to convey what was being said.
Eventually clay tablets gave way to parchment, which gave way to paper. Paper was, and
still is, the main way people convey information. With the time our need of expression has
increased and so our need to store information. The cost of saving information has widely
decreased with latest development in technologies like circuits which saves cost and space
required to store as compared to paper. But the need for storage space is ever increasing,
new technologies are being invented which further reduce cost and provide more storage
space to store more of our documents, selfies, music etc. One such technology is protien
memory based storage techniques these techniques can be used to create more compact,
and more affordable memory storage devices

1.1 HISTORY:
Since the start of human history humans have tried to create and store various types
of data form hunting pictures on the wall of caves to early tattoo arts. We have always tried
to store some data in one way or another and pass it to others.

With the time and increase in volume of information soon pictures gave way to
letters which represented spoken sounds. Then came people who invented spoken
languages and the need arose to record what one was saying without hearing it firsthand.
Therefore, years later, earlier scholars invented writing to convey what was being said.
Eventually clay tablets gave way to parchment, which gave way to paper. Paper was, and
still is, the main way people convey information but soon after introduction of non paper
technologies like early circuits and computers slowly paper is losing its hold as the main
source of distribution of information. In the mid twentieth century computers began to
come into general use. Computers have gone through their own evolution in storage media.
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In the forties, fifties, and sixties, everyone who took a computer course used punched cards
to give the computer information and store data. 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. The fastest and most expensive storage technology today is based
on electronic storage in a circuit such as a solid state "disk drive" or flashRAM. This
technology is getting faster and is able to store more information thanks to improved circuit
manufacturing techniques that shrink the sizes of the chip features. New digital circuits
have made a lot of contribution is our recent paperless transactions. Now we create digital
data store it digitally and share it digitally.

With the time our need of expression has increased and so our need to store information.
The cost of saving information has widely decreased with latest development in
technologies like digital circuits which saves cost and space required to store as compared
to paper and other old storage devices like cd-roms . But the need for storage space is ever
increasing, new technologies are being invented which further reduce cost and provide
more storage space to store more of our documents, selfies, music etc. One such technology
is protein memory based storage techniques these are more compact and more affordable
memory storage devices, several alternatives have appeared in recent years. Among the
most promising approaches include memory storage using protein-based memory.

1.2 When do you need more storage space?

With the time our need of expression has increased and so our need to store information.
Paper has lost its efficiency as a medium to store information as the cost of managing and
storing the information on paper is more as compared to new storage mediums like pen
drives and cd roms.
The cost of saving information has widely decreased with latest development in
technologies like electronic storage in a circuit such as a solid state "disk drive" or
flashRAM which saves cost and space required to store information as compared to paper.
But with increased automation in almost every field the need to store has increased
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manifolds also information generated by each and every one of us also require increased
storage space

But our need for storage is ever increasing, each person daily creates gb’s of information
which require additional space to store. Also our daily interaction with our computerized
devices like pc’s and cellphones create allot of information, all the picture that we take all
the messages and calender events we create need some space to be stored. The space on our
devices and memory card are limited which fills after the available space if completely
filled. Some of us store the oyr data on the cloud i.e cloud services like My Drive, BOX
etc. But this is not the solution for our problem as the data on the cloud is not magically
stored in the cloud itself, it is actually stored on the servers of the service provider which
are nothing but memory devices which store and retrieve the data. The need for storage
space is ever increasing, our current generation storage devices are falling short to the
demand. New technologies are being invented which further reduce cost and provide more
storage space to store more of our documents, selfies, music etc. Many new technologies
are being implemented to reduce physical space needed to store information. One such
technology is protein memory based storage techniques these are more compact, and more
affordable memory storage devices, several alternatives have appeared in recent years.
Among the most promising approaches include memory storage using protein-based
memory.

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CHAPTER 2
PROTEIN-BASED MEMORY

There have been many methods and proteins researched for use in computer
applications in recent years. However, among the most promising approaches, the
main one is 3-Dimensional 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. This particular bacterium
lives in salt marshes. Salt marshes have very high salinity and temperatures can reach
140 degrees Fahrenheit. 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. Largely through trial and error, and thanks in part to
nature's own natural selection process, scientists stumbled upon a light-harvesting
protein that has certain properties which make it a prime candidate for computer
applications. While bacteriorhodopsin can be used in any number of schemes to store
memory, we will focus our attention on the use of bacteriorhodopsin in 3-Dimensional
Optical Memories.

Many organic molecules can exist in two distinct stable states that differ in some
measurable property and are interconvertable.These could be switches of molecular
electronics. For example, bacteriorhodopsin, a bacterial pigment, exists in two optical
states: one state absorbs green light, the other orange. Shinning green light on the
green-absorbing state converts it into the orange state and vice versa. Birge and his
coworkers have developed high density memory drives using bacteriorhodopsin.

"Electron transport in photosynthesis one of the most important energy generating

systems in nature, is a real-world example of what we're trying to do," said Phil Seiden,
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manager of molecular science, IBM, Yorkstown Heights, N.Y. Birge, who heads the
Center for Molecular Electronics at Carnegie-Mellon, said two factors are driving this
developing revolution, more speed and less space.

CHAPTER 3

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THE STRUCTURE OF BACTERIORHODOPSIN

Bacteriorhodopsin - as all retinal proteins from Halo bacterium - folds into a seven-Tran
membrane helix topology with short interconnecting loops. The helices (named A-G) are
arranged in an arc-like structure and tightly surround a retinal molecule that is
covalently bound via a Schiff base to a conserved lysine (Lys-216) on helix G. The
cross-section of BR with residues important for proton transfer and the probable path of
the proton are shown in Fig.1. The 3D structure is also available. Retinal separates a
cytoplasmic from an extra cellular half channel that is lined by amino acids crucial for
efficient proton transport by BR . The Schiff base between retinal and Lys-216 is located
at the center of this channel. To allow vectorial proton transport, de- and reprotonation
of the Schiff base must occur from different sides of the membrane. Thus, the
accessibility of the Schiff base for Asp-96 and Asp-85 must be switched during the
catalytic cycle. The geometry of the retinal, the protonation state of the Schiff base, and
its precise electrostatic interaction with the surrounding charges and dipoles tune the
absorption maximum to fit its biological function.

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Fig. 1: The 3D structure of Bacteriorhodopsin

3.1 BACTERIORHODOPSIN PHOTOCYCLE

Fig 2:Bacteriorhopsin Photocycle

Bacteriorhodopsin comprises of 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 photocycle. In response to light Bacteriorhodopsin “pumps”
proton across the membrane, transporting charged ions in and out of the cell.
Bacteriorhodopsin goes through different intermediates during the proton pumping
cycle. These stages have been labelled K, L, M, N and O, each one easily identifiable
because Bacteriorhodopsin changes colour during each stage of the process. The
native photo cycle has several spectroscopically unique steps, bR --> K <--> L <--> M1
-->M2 <--> N <-->O, which occur in a roughly linear order The photo cycle of
bacteriorhodopsin or its cycle of molecular states depend on the luminous radiation that
it absorbs. The initial state known as bR evolves into state K under the effect of green
light. From there it spontaneously passes to state M then to state O (relaxation
transitions).
Exposure to red light from O state will make the structure of the bacterium
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evolve to state P then spontaneously to state Q, which is a very stable state.

Some of the intermediates are stable at about 80K and some are stable at room
temperature, lending themselves to different types of RAM. Nevertheless, radiation from
blue light can take the molecule from state Q back to the initial state 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.
Genetic engineering has been used to create bacteriorhodopsin mutants with enhanced
materials properties.

Three-dimensional optical memory storage offers significant promise for the

development of a new generation of ultra-high density RAMs. One of the keys to this
process lies in the ability of the protein to occupy and form cubic matrices in a polymer
gel, allowing for truly three-dimensional memory storage. The other major component in
the process lies in the use of photons to read and write data. As discussed earlier,
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. The memory storage scheme which we will focus on, proposed by Robert
Birge in Computer (Nov. 1992), is designed to store up to 18 gigabytes within a data
storage system with dimensions of 1.6 cm * 1.6 cm * 2 cm. Bear in mind, this memory
capacity is well below the theoretical maximum limit of 512 gigabytes for the same
volume (5-cm3).

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CHAPTER 4
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.

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Fig 3. Data Writing Technique

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 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 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
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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.

CHAPTER 5
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.

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Fig 4.Data Reading Technique

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 milliseconds, a rate of 10 megabytes per
second for each page of memory.

CHAPTER 6

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DATA ERASING TECHNIQUE

To erase data; a brief pulse from a blue laser returns molecules in the Q state back to
the rest state. The blue light doesn't necessarily have to be a laser; you can bulk-
erase the cuvette by exposing it to an incandescent light with ultraviolet output.

CHAPTER 7

WHY BACTERIORHODOPSIN?

Bacteriorhodopsin (BR), a photon-driven proton pump, is a transmebrane protein found in

the purple membrane of the archaeon, Halobacterium halobium. The BR is organized with
polyprenoid lipid chains in the hydrophobic moiety on a highly ordered two-dimensional
lattice in the membrane. Enormous interest has been generated by application of the
structural and dynamic properties of the BR protein in bioelectronics devices. Embedding
bacteriorhodopsin in membrane films is essential to achieve functionality of such devices.
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Although some prototype devices have been fabricated, instability of the membranes is
acknowledged as a major impediment to the development of BR-based devices. Whereas
there has been much biotechnological experimentation on the properties and functionalities
of the BR protein, comparatively little attention has been paid to the critically important
supporting lipid matrices in which BR functions. Archaeal membranes consist
predominantly of isoprenoid chains ether-linked to an alcohol such as glycerol. These
isoprene structures are unique and are not prone to decomposition at high temperatures.
That isoprene molecular fossils have been found in geologic Miocene deposits attests to the
extreme durability and stability of these structures. In viable organisms BR functions in
high efficiency at temperatures as high as 140˚C, in near-saturating concentrations of salt,
and in highly acidic environments. Specific lipids of the purple membrane are required for
normal bacteriorhodopsin structure, function, and photo cycle kinetics.At ambient
temperatures,the membranes are in a liquid crystalline state that provides optimal
functioning of the BR..Adaptations of the membrane lipids allow maintenance of the liquid
crystalline state even as the indigenous conditions change. Nevertheless, as a consequence
of light absorption, BR initiates a photo cycle through structurally distinctive
conformations, causing tractable optical and electronic properties of the protein. The
characteristics of the lipids in the membrane dictate the large-amplitude motions of BR,and
by consequence the broad utility of bR in bioelectronic devices.The research to be
developed under this topic would have military and civilian importance. Some of the
bionanotechnological applications that are anticipated include: ultra rapid optical data
acquisition with parallel processing capabilities and extreme high density holographic 3-
dimensional data and image storage.

CHAPTER 7

BACTERIORHODOPSIN OPTICAL MEMORY

Following are the features of Bacteriorhodopsin Optical Memory:-

1. Purple membrane from Halobacterium Halobium

2. Bistable red/green switch

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3. In protein coat at 77K, 107-108 cycles

4.10,000 molecules/bit

5. Switching time, 500 femtoseconds

6. Monolayer fabricated by self-assembly

7. Speed currently limited by laser addressing

Using the purple membrane from the bacterium Halobacterium Halobium, Prof.
Robert Birge and his group at Syracuse University have made a working optical bistable
switch, fabricated in a monolayer by self-assembly, that reliably stores data with 10,000
molecules per bit. The molecule switches in 500 femtoseconds--that's 1/2000 of a
nanosecond, and the actual speed of the memory is currently limited by how fast you
can steer a laser beam to the correct spot on the memory.

CHAPTER 8
MERITS

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Fig 5.Birge’s Memory cell

● This is based on a protein that is inexpensive to produce in quantity.

● .The system has the ability to operate over a wider range of temperatures than the
semiconductor memory.

● The data is stable, i.e. the memory system’s power is turned off, the molecules retain their
information.

● This is portable, i.e. we can remove small data cubes and ship GBs of data around for
storage or backups

● Data can be stored for years without any refreshment.

CHAPTER 8

APPLICATIONS

Most successful applications of bacteriorhodopsin have been in the

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development of holographic and volumetric three- dimensional memories. Other

applications of Bacteriorhodopsin are:-

When nutrients get scarce, this Bacteriorhodopsin becomes a light-converting

enzyme. It's a protein powerhouse that in times of famine flips back and forth
between purple and yellow colours. If controllable, this could be valuable
in building battery conserving and long lasting computer display panels.

Protein’s photoelectric properties could be used to manufacture photo detectors.

Bacteriorhodopsin could be used as light sensitive element in artificial retinas.

German scientists have used holographic thin films of bacteriorhodopsin to

make pattern-recognition systems with high sensitivity and diffraction-limited
performance.

Nano biotechnology based medical diagnostics may use this proteins in imaging
devices.

Molecules can potentially serve as computers switches because their atoms

are mobile and change position in a predictable way. By directing the atomic
motion two discrete states can be generated in a molecule, which can be used to
represent either 0 or 1. This results in reduction of size, that is, a bimolecular
computer in principle is one-twentieth of the size of the present day
computer.

bR has all desired properties for usage in associative memory applications.

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Conclusion

In this paper we introduced the concept of digital watermarking used to protect intellectual
property rights, copyrights and rightful ownership. We presented required criteria for a
watermarking scheme to be successful. We also identified areas (types of digital media)
where watermarking can be applied as well as other areas (such as raw text) where no
current watermarking scheme exists. We finally addressed the issue of whether the
presence of a watermark can prove ownership and concluded that this is only possible
through the use of a higher, controlling governing body where all original media can be
registered.

A final conclusion: Digital watermarking can successfully be employed if the value of the
digital media warrants the added expense. If not, it is an exercise in futility.

Digital signature relies on the protection afforded a private signature key by the signer, and
the procedures implemented by a Certification Authority.

Digital signatures must be applied by a computer commanded by the signer.

Forgery of digital signatures, in the absence of compromise of the private signature key, or
hijacking of the signature mechanism, is virtually impossible.

Due to the cryptographic nature of digital signatures, attempted forgeries are immediately
obvious to any verifier, except in the case where a private signature key has been
compromised, or control of the signing mechanism has been seized. In these cases,
distinguishing between a valid and invalid digital signature may be impossible, even for a
computer forensics specialist.

Digital signatures are fiendishly complex, involving arcane number theory, the workings
of computer operating systems, communications protocols, certificate chain processing,
certificate policies, and so on. There are very few people on this planet (if any) who
completely understand every process involved in generating and verifying a digital
signature. The potential for confused lawyers, judges and juries is extreme.

Digital signatures have the potential to have the greatest impact on commerce since the
invention of money. Digital signatures allow us to identify ourselves and make
commitments in cyberspace in much the same way as we do in actual space. Nonetheless,
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digital signature has important limitations, the most significant being their temporary
nature:

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REFRENCES:

➢ www.cem.msu.edu
➢ www.ieee.org
➢ www.wikipedia.com
➢ Samuel Styne Protein-Based Three-Dimensional
➢ Memory, American Scientist, pp.328-355, July-August 2002.

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