dna computing pradeep chawla

DNA Computing-based

Cryptography

Seminar Report

Submitted By-

Pradeep Chawla

10clmxx677 MCA 5th sem

Department of Computer Science & Engineering

Lachoo Memorial College Of Science & Technology, Jodhpur

Decmber - 2012

DNA Computing-based Cryptography 1

Table of Contents

Abstract 3

1. Introduction 4

2. What is DNA? 5

2.1 DNA Structure 5

3. What is DNA Computing? 7

3.1 Adleman’s Experiment 8

4. DNA Computing in Security Field 9

4.1 DNA Cryptography 9

4.2 DNA Steganography 12

4.3 DNA Authentication 14

5. Advantages of DNA Computing 15

6. Conclusion 15

7. References 16


Abstract— DNA computing has a great deal of advantage over conventional silicon-based

computing. DNA computers can store billions of times more data than personal computer. DNA

computers have the ability to work in a massively parallel fashion, performing many calculations

simultaneously. DNA molecules that provide the input can also provide all the necessary

operational energy.

DNA cryptography is new field of cryptography arising with DNA computing research in

recent years. DNA computing theories can be applied in cryptography and it is a very emerging

field. Though still in primitive level, it applies in many areas and solved some hard problems

successfully. It can realize several security technologies such as Encryption, Steganography,

Signature and Authentication by using DNA molecular as information medium. The art of

cryptography security is to make sure that anybody cannot get the message, by encoding plain

text. This paper use a new way to show how cryptography works with DNA computing, it can

transmit message securely and effectively. The RSA algorithm belongs to asymmetric key

cryptography, it is used in this paper connecting with DNA computing technique to encrypt

message.

In this report first I introduced the basic idea of DNA computing, and then discuss the

information security technology (DNA-based Cryptography) in DNA computing.


1. Introduction

DNA was proposed for computation by Adleman in 1994. After that many approaches

have been investigated. Theoretical consideration that it may simulate Turing machines and

cryptography. It has been shown that DNA computing was suitable for some problems currently

hard to resolve (intractable) and could work faster than electronic computer. A good background

between the DNA molecule and computer engineering are required to develop the efficient

algorithms of DNA computing.After Adleman solved the Hamilton Path Problem using a

combinatorial molecular method, many hard computational problems were calculated by DNA

computer.

The world of encryption appears to be ever shrinking. Several years ago the thought of a

56-bit encryption technology seemed forever safe, but as mankind's’ collective computing power

and knowledge increases, the safety of the world’s encryption methods seems to disappear

equally as fast. Mathematicians and physicists attempt to improve on encryption methods while

staying within the confines of the technologies available to us. Existing encryption algorithms

such as RSA have not yet been compromised but many fears the day may come when even this

bastion of encryption will fall. There is hope for new encryption algorithms on the horizon

utilizing mathematical principles such as Quantum Theory however the science of our very

genetic makeup is also showing promise for the information security world.

The concepts of utilizing DNA computing in the field of data encryption and DNA

authentication methods for thwarting the counterfeiting industry are subjects that have been

surfacing in the media of late. How realistic are these concepts and is it feasible to see these

technologies changing the security marketplace of today?


2. What is DNA?

Before delving into the principles of DNA computing, we must have a basic

understanding of what DNA actually is. All organisms on this planet are made of the same type

of genetic blueprint which bind us together. The way in which that blueprint is coded is the

deciding factor as to whether you will be bald, have a bulbous nose, male, female or even

whether you will be a human or an oak tree.

Within the cells of any organism is a substance called Deoxyribonucleic Acid (DNA)

which is a double-stranded helix of nucleotides which carries the genetic information of a cell.

This information is the code used within cells to form proteins and is the building block upon

which life is formed.

2.1 Structure of DNA

James D. Watson and Francis H. C. Crick deduced double-helix structure of DNA in 1953

and got Nobel Prize in 1962.

Strands of DNA are long polymers of millions of linked nucleotides. These nucleotides

consist of one of four nitrogen bases, a five carbon sugar and a phosphate group. The

nucleotides that make up these polymers are named after the nitrogen base that it consists of;

Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). These nucleotides will only

combine in such a way that C always pairs with G and T always pairs with A.


The two strands of a DNA molecule are antiparallel where each strand runs in an

opposite direction. Figure 1 illustrates two strands of DNA and the bonding principles of the 4

types of nucleotides and the Figure 2 illustrates the double helix shape of DNA.

Fig 1 – Graphical representation of inherent bonding properties

ofDNA.

Fig 2 – Illustration of double helix shape of DNA.

The combination of these 4 nucleotides in the estimated million long polymer strands can

result in billions of combinations within a single DNA double-helix. These massive amount of

combinations allows for the multitude of differences between every living thing on the planet

from the large scale (mammal vs. plant), to the small (blue eyes vs. green eyes).

With the advances in DNA research in projects such as the Human Genome project (a

research effort to characterize the genomes of human and selected model organisms through

complete mapping and sequencing of their DNA) and a host of others, the mystery of DNA and

its construction is slowly being unraveled through mathematical means. Distinct formulae and

patterns have emerged that may have implications well beyond those found in the fields of

genetics.

You must be thinking, what does all this chemistry and biology have to do with security

and cryptography? To answer that question we must first look at how biological science can be

applied to mathematical computation in a field known as DNA computing.


3. What is DNA Computing?

DNA computing is a form of computing which uses DNA, biochemistry and molecular

biology, instead of the traditional silicon-based computer technologies. DNA computing, or,

more generally, bimolecular computing, is a fast developing interdisciplinary area. Research and

development in this area concerns theory, experiments, and applications of DNA computing.

A DNA computer, as the name implies, uses DNA strands to store information and taps

therecombinative properties of DNA to perform operations. A small test tube of DNA strands

suspended in asolution could yield millions to billions of simultaneous interactions at speeds —

in theory— faster than today's fastest supercomputers.

DNA computer uses the recombinative property of DNA to perform operations.Themain

benefit of using DNA computers to solve complex problems is that different possiblesolutions

are created all at once. This is known as parallel processing. Humans and mostelectronic

computers attempt to solve the problem one process at a time (linear processing).

DNA itself provides the added benefits of being a cheap, energy-efficient resource.In a

different perspective, more than 10 trillion DNA molecules can fit into an area no larger than 1

Cubic centimeter. With this, a DNA computer could hold 10 terabytes of data and perform 10

trillioncalculations at a time.

In a traditional computer, data are represented by and stored as strings of zeros and ones.

With a DNAcomputer, a sequence of its four basic nucleotides — adenine, cytosine, guanine,

and thymine — is used torepresent and store data on a strand of DNA. Calculations in a

traditional computer are performed by movingdata into a processing unit where binary operations

are performed. Essentially, the operations turnminiaturized circuits off or on corresponding to the

zeros and ones that represent the string of data.


3.1 Adleman’s Experiment

In order to introduce the principles of DNA computing we briefly review the model which

Prof. Adleman hadused to solve a directed Hamiltonian path problem. The Hamiltonian path

problem is to find a path that begins at vin,ends at voutand enters every other vertex exactly once

on a directed graph. For each vertex i in the graph, a random 20-mer oligonucleotide DNA

sequence was generated. The process to solve the directed Hamiltonian path problem is list

asfollows:

(1) Generate random paths through the graph.

(2) Keep only those paths which begin with vinand end with vout.

(3) If the graph has n vertices, then keep only those paths which enter exactly n vertices.

(4) Keep only those paths which enter all of the vertices of the graph at least once.

(5) If any paths remain, say “yes”, otherwise say “no”.

Generally speaking, Adleman used the DNA sequence encoding of all possible answers to

the problems, removingthe solutions that do not meet the requirements through a series of

restrictive conditions. Finally, Adleman found thesolution. From the algorithm solving the

directed Hamiltonian path problem, we can see the difference between DNAcomputing and

traditional computing that DNA computing has massive parallelism and high density information

of biomolecules.

DNA computing pioneer Adleman reviewed DNA computing as follows:

“For thousands of years, humans have tried to enhance their inherent computational abilities

using manufactureddevices. Mechanical devices such as the abacus, the adding machine, and the

tabulating machine were importantadvances. But it was only with the advent of electronic

devices and, in particular, the electronic computer some 60 yearsago that a qualitative threshold

seems to have been passed and problems of considerable difficulty could be solved. Itappears

that a molecular device has now been used to pass this qualitative threshold for a second time.”

The development of DNA cryptography benefits from the progress of DNA computing. On

the one hand,cryptography always has some relationship with the corresponding computing

model more or less. On the other hand,some biological technologies used in DNA computation

are also used in DNA cryptography.


4. DNA Computing in Security

4.1 DNA Cryptography

The DNA computing gives a new way to cryptography. The powerful parallelism capability

in DNA computation takes new challenges for modern cryptography. We could realize new

cryptographic about DNA cryptograph, it base on two fields. The cryptography is critical aspects

of traditional computing and it is also important to DNA database applications. This paper

provides basic technology used cryptography with DNA computing. Assume a sender sends a

message to a receiver, no one could read the message in the sending process. The message is

initially written in plaintext with a list of alphabet. Encryption is the step of confusing the

plaintext message and transforming it into an encrypted message as cipher.

Simulation the asymmetric key cryptography of RSA algorithm with DNA computing

technology, and show how to encrypt a message and how the processing of algorithm works

Figure.2 could be demonstrating the algorithm.

Figure.2. Algorithm


Setup Plaintext

Recovery plaintext

Matching with nucleotides

Nucleotides to numbers

Encrypted message

Simulation

It has a requirement to set up a list for corresponding plaintext. It is shown as Table 1.

Table.1. Encode Plaintext

TABLE.2 Mapping Process from base nucleotides to numbers

The experimentation encrypts a message for security consideration, which aims at not being

read by others. For instance, assume the plaintext as one word: ‘boy’ andthe modulus is: n,

encrypt exponential is: e.

Step 1. Set positive integer to n and e, n =852167, e = 11. We can get the prime number of n

through the function of Matlab, it is a random number.

Step 2. To get the base nucleotides, use the Table.1.to turn plaintext into corresponding

nucleotides, The result of plaintext 'boy' is 'GTTCGGAAA'.

Step 3. Turn the base nucleotides chain into numbers with Table.2, and the result is:

72020030707010101.

Core code is:

for k=l :sl

for j=O: (s2-1),


Ind = s2-j;

y (k) =y(k) + yvec(k , ind) * 100j;

end;

end;

Step 4 Compute eth power of n, the result is: 501700.

Core code is: a (j, k) = invmodn (a (j, k), n);

Compute the decipher exponential d=232409. It need compute mathematics method about

Euclidean algorithm (gcd (a, b) = gcd (b, a mod b)) to get the result of

d: (D* E) mod(P -1) * (Q-1) = 1

Step 5. Separate the number 72020030707010101 into three parts: {720200, 307070, 10101}

Make sure every part of number is less than 852167.

Step 6. Through calculate of the three parts numbers, we getthe cipher text: 512537,

365324,615863. In the calculationprocess, it needs to compute Euler's theorem with

CT = PTK modN

Core code is:

while (mod (zl,2) ==0) ,

zl = (z1/2);

a1 =mod ((a1 *a1),n );

x=x*a1;

x=mod(x, n);

Step 7.For decryption, calculate the plaintext from thecipher text as this: PT = CTD mod N,

then get the number is:72020030707010101, it is corresponding with the numbersinto which

plaintext changed. Therefore, we can get theconclusion that the combination of DNA computing

withcryptography is feasible on theory.


4.2 DNA Steganography

Experiments in DNA Steganography have been conducted by Carter Bancroft and his

team at the Mt. Sinai School of Medicine to encrypt hidden messages within microdots. Bancroft

using the microdot methodology utilized in message hiding during World War II data

transmission has done something similar this time using DNA encoded microdots.

The principles used in this experiment used a simple code to convert the letters of the

alphabet into combinations of the four bases which make up DNA and create a strand of DNA

based on that code. A piece of DNA spelling out the message to be hidden is synthetically

created which contains the secret encrypted message in the middle plus short marker sequences

at the ends of the message. The encoded piece of DNA is then placed into a normal piece of

human DNA which is then mixed with DNA strands of similar length. The mixture is then dried

on to paper that can be cutup into microdots with each dot containing billions of strands of DNA.

Not only is the microdot difficult to detect on the plain message medium but only one strand of

those billions within the microdot contains the message.

The key to decrypting the message lies in knowing which markers on each end of the

DNA are the correct ones which mean there must be some sort of shared secret that is

transmitted previously for this type of transmission to work successfully. Once the strand is

determined via identifying the markers, the recipient uses polymerase chain reaction to multiply

only the DNA which contains the message and applies the simple code to finally decode the true

message. Utilizing these methods, Bancroft and his team were successfully able to encode and

decode the famous message ‘June 6 Invasion: Normandy’ within a microdot placed in the full

stops on a posted typed letter.


Figure 6.DNA Steganography.

a, Structure of secret message DNA strand illustrating marker sequences.

b, key used to encode message in DNA.

c, Gel analysis of DNA strand.

d, Sequence of cloned product of PCR amplification and resulting encoded message.

Perhaps this all appears a bit farfetched at first and the skeptics state that the same problems

with the DNA cryptography are evident in DNA steganography as well. The ‘test tube’

environment used in this type of steganography is far from practical for everyday use. The DNA

microdot team does see this technology having applications in another field however – that of

authentication. With the amount of plant and animal genetic engineering that is taking place

today and will continue to do so in the future, this methodology would allow engineers to place

DNA authentication stamps within organisms they are working with to easily detect counterfeits

or copyright infringements.


4.3 DNA Certification

Strictly speaking, DNA certification doesn’t deal with much DNA computing techniques, but

mainly employ the biological characteristics of DNA. Currently, the DNA certification is broadly

applied in the field of justice, finance, and so on, which will certificate biological individuals

accurately.

Celland apply their methods to the purpose of certification and security. In 2000, DNA

Technology Company of Canada also using the DNA sequence to the product certification of the

Sydney Olympic game in those years. Nearly 50,000,000 keepsakes were all marked with a

special ink from Olympic T-shirts to coffee cups. This kind of DNA segment in the inky mark

was randomly extracted an athlete’ genome from nearly a hundred, then it was rather difficult to

fabricate. This kind of way to utilize a portable scanner to scan the information in the ink

marking would distinguish whether the keepsakes were authentic which were much cheap than

the whole interest trademarks but the increasing cost was only one nickel.

If we make use of the basic principle of DNA steganography to the appraisal of DNA, we can

carry on much wider certification. At present, there have been masses of biological genetic

engineering are under way. The above technologies will make the researchers add the DNA

certification information to the organ tissue, and by identifying the information of DNA

certification to validate the customer identity and the copyright information.

Currently, in these kinds of DNA techniques, the development of DNA certification

technique is most mature and the application is most wide. However, we introduce the DNA

computing into the DNA steganography and certification techniques will improve the

complication of algorithm and the level of security.


5. Advantages of DNA Computing

Speed – Conventional computers can perform approximately 100 MIPS (millions of

instruction per second). Combining DNA strands as demonstrated by Adleman, made

computations equivalent to 109or better, arguably over 100 times faster than the fastest

computer. The inherent parallelism of DNA computing was staggering.

Minimal Storage Requirements – DNA stores memory at a density of about 1 bit per cubic

nanometer where conventional storage media requires 1012cubic nanometers to store 1 bit. In

essence, mankind’s collective knowledge could theoretically be stored in a small bucket of DNA

solution.

Minimal Power Requirements - There is no power required for DNA computing while the

computation is taking place. The chemical bonds that are the building blocks of DNA happen

without any outside power source. There is no comparison to the power requirements of

conventional computers.

6. Conclusion

Although DNA computing creates a molecular computing precedent and broadens the

understanding of people to natural computing phenomena, it still stayed in a theoretical stage.

There are some problems unresolved successfully about DNA computing:

A. Itscomputing model is mostly just using moleculartechnique to resolve a certain

problem; the varieties ofproblems result in the discrepancy of computing schemes,

there still haven’t a uniform computing and coding model currently.

B. DNA computing onlyconverts the time complexity into space complexity.

C. There are also error codes in DNA computing, theygenerate randomly according to

probability and cangradually amplified with the increase of the experiment step.


D. DNA liquid is very easy todeteriorate in the process of reaction and evenadsorption

of the test tube wall may result in fatal error.

E. Most of these proposals implementedcomputing processes by performing a series

ofbiochemical reactions on a set of DNA molecules,which require human

intervention at each step.

Thus,the difficulties of such methods for DNA computingare that the large numbers of

laboratory proceduresand the time consuming, which grow with the size ofthe problem.

Therefore, DNA computing is not verygood in resolving real problem according to

theavailable pattern in recent year.Therefore, in terms of existing DNA computingmode, it is

not able to construct real intimidation tothe security of cryptography. At the same time,

allkinds of encryption scheme pouring out unceasinglybased on DNA computing, providing

escorting to the DNA molecules’ bank and DNA molecules’ information. But, because the

security, general,validity and key management of the encryptmechanism have not been

carried out systematictheory analysis. So, DNA cryptography still needsstudying exclusively

and discussion broadly, itsprospect is still uncertain before DNA computingbecome really

mature. But DNA cipher is thebeneficial supplement to the existing mathematical cipher; it is

a prior choice especially to the lowerdemand real-time encryption system.

Relativelyspeaking, DNA computing has a brighter developmentpotential in steganography

and authentication, whichhave a more layer protection than a single encryption.With the

rapid development of modern biotechnology,the costly biological experiment has become a

normalone. If the molecular word can be controlled at will, itmay be possible to achieve

vastly better performancefor information storage and information security.


References

[1] Xing Wang, Qiang Zhang ― “DNA computing-based cryptography”http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5338153&tag=1

[2] GuangzhaoCui ,Limin Qin ― “Information Security Technology Based on DNA Computing”http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04244832

[3] Haobin Li, Xiaoguang Li ― “DNA Computing and Its Application to Information Security Field”

http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5364229

[4] http://www.howstuffworks.com/dna-computer.htm

[5] http://en.wikipedia.org/wiki/DNA_computing


http://en.wikipedia.org/wiki/DNA_computing

http://www.howstuffworks.com/dna-computer.htm

http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5364229

http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04244832

http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5338153&tag=1

dna computing pradeep chawla

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