dna computing final part

8/13/2019 Dna Computing final part

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10.Applications

Massively Parallel Processing-Basically any problem that can be turned into aHamiltonian problem and other complex problems can be solved.

Storage and Associative Memory-A truly content addressable memory occurs when adata entry can be directly retrieved from storage by entering an input that most closely

resembles it over other entries in memory. This contrasts with a conventional

computer memory, where the specific address of a word must be known to retrieve it.

DNA computers could fight cancer-New computers made of biological moleculesthat react to DNA hold the promise to diagnose and treat diseases such as cancer by

operating like doctors inside the body, Israeli scientists said.[8]

DNA2DNA Applications-Another area of DNA computation exists whereconventional computers clearly have no current capacity to compete. This is the

concept of DNA2DNA computations such as DNA sequencing; DNA fingerprinting;

DNA mutation detection or population screening; and Other fundamental operations

on DNA.

Implications to Biology, Chemistry, and Medicine-A particular area within the naturaland applied sciences that may benefit from advances in DNA computation is

combinatorial chemistry.

DNA's Role in Computer Science- DNA based computers may postpone certainexpected thermodynamic obstacles to computation as well as questioning theories of

computation based on electronic and mechanical models.

This can be quite useful in figuring out how to route telephone calls, plane trips. It is also been claimed that DNA can be used to solve optimization problems

involving business management.

It is even said that DNA can be used in devising the wiring schematics for circuits. DNA computers can be used to control chemical and biological systems in a way

thats analogous to the way we use electronic computers to control electrical and

mechanical systems.


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Another application being mentioned nowadays is that DNA computing can docryptography. [2,5] It is used in various security applications

10.1 DNA Cryptography

The DNA cryptography is a new and very promising direction in cryptography research.

DNA can be used in cryptography for storing and transmitting the information, as well as for

computation. Here we try to utilize the power of DNA to hide message.

Ashish Gehani, Thomas LA Bean and John Reif of Duke University have published a paper

entitled DNA-based Cryptography [5] which puts an argument forward that the high level

computational ability and incredibly compact information storage media of DNA computing

has the possibility of DNA based cryptography based on one time pads. They argue that

current practical applications of cryptographic systems based on one-time pads is limited to

the confines of conventional electronic media whereas as small amount of DNA can suffice

for a huge one time pad for use in public key infrastructure (PKI). To put this into terms of

the common Alice and Bob description of secure data transmission and reception, they are

basing their argument of DNA cryptography on Bob providing Alice his public key, and

Alice will use it to send an encrypted message to him. The potential eavesdropper, Eve, will

have an incredible amount of work to perform to attempt decryption of their transmission

than either Alice or Bob.

Public key encryption splits the key up into a public key for encryption and a secret key for

decryption. It's not possible to determine the secret key from the public key. Bob generates a

pair of keys and tells everyone his public key, while only he knows his secret key. Anyone

can use Bob's public key to send him an encrypted message, but only Bob knows the secret

key to decrypt it. This scheme allows Alice and Bob to communicate in secret without havingto physically meet as in symmetric encryption methods.

Injecting DNA cryptography into the common PKI scenario, the researchers from Duke argue

that we have the ability to follow the same inherent pattern of PKI but using the inherent

massively parallel computing properties of DNA bonding to perform the encryption and

decryption of the public and private keys. In essence, the encryption algorithm used in the

transaction can now be much more complex than that in use by conventional encryption

methods. [10]


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Method to encrypt the plaintext using DNA, so that it could be send securely over a

network.

Encryption

Step1:The binary data, text or image, is used under the form of ASCII code (in decimal

format).

Step2:These numbers are then grouped in blocks and encrypted in using a traditional method

(eg. DES, will form a 2 level encryption).

Step3:This encoded message is then changed to binary format.

Step4: Then these digits are grouped into two and substituted as A for 00, T for 01, G for 10,

and C for 11.

Step5: We then fit the primers on either side of this message. Primers will act as stoppers and

detectors for the message. This has to be given to the receiver prior to the communication.

Step6: This message is followed by our own DNA sequence followed by another

stopper/primer.

Step7: This message is then flanked by many sequences of DNA or by confining it to a

microdot in the micro-array.

Step8: If considered as a pseudo method: this sequence is transferred to the receiver through

the Internet. Else the micro-array is sent physically (though time consuming).

Decryption

This message can then be recovered only by an intended recipient who both can find it, and

who knows the sequences of the PCR primers employed, and also the encryption key (2 level

encryption used). For this method:

Step1. The DNA sequence is searched for the primers (start primer and end primer). The

message in-between them is retrieved and the next DNA sequence before the next primer (our

DNA) is retrieved.

Step2. The ATGC characters are substituted accordingly (00,01,10,11 respectively). Step3.

They are then converted into ASCII code and then the message is retrieved.

10.2 DNA Steganography


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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.

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. [2] 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. [11]

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.

10.3 DNA Authentication

It is worth mentioning that DNA authentication is currently at work in the marketplace today

albeit not in the genetic engineering form envisioned by Bancroft and his team. Forms of


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DNA authentication have already been used for such items as the official clothing from the

Sydney Olympic Games, sports collectibles and limited edition art markets such as original

animation cells distributed by the Hanna Barbara group of artists.

In the case of the clothing used in the Sydney Olympic Games, a Canadian company named

DNA Technologieswas able to showcase its DNA-tagging abilities on the world stage in the

summer of 2000. All Olympic merchandise from shirts and hats to pins and coffee mugs

were tagged with special ink that contained DNA taken from an unnamed Australian athlete.

DNA was taken via saliva samples from the athlete and mixed into existing ink compounds

which was in turn used in the regular merchandise manufacturing process. A hand held

scanner is then used to scan the inked area of the clothing to determine if a piece of

merchandise is authentic or not. As it is estimated that the human genome is roughly 3

billion base pairs in size, and the samples taken were from a random athlete from a Olympic

team of hundreds, the possibility of counterfeiting this merchandise is difficult to say the

least. For the Sydney games, DNA inks were applied too nearly 50 million items at a cost

of about five cents each, including licensing, databasing , and back-end support.

There are possibilities of this type of technology to be used in the arenas of currency and

other such brandable items where existing authentication methods such as holograms are

proving ineffective and costly. DNA-tagging is much cheaper in comparison and ultimately

more difficult to thwart.

11.Future Scope


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Its different way of thinking about computing. Its different way of thinking about

chemistry, says Dr. Corn, a chemistry professor at the University of Wisconsin at Madison

who is collaborating on a DNA-computer project with three other Madison faculty members:

Lloyd M. Smith, a chemistry professor, Max G. Lagally, a materials-science professor, and

Anne E. Condon, a computer science professor.

The Wisconsin approach would use the gold-plated square of glass as something akin (related

blood) to a conventional memory chip. As many as a trillion individual strands of DNA

would be anchored (fixed firmly) to the glass, each strand containing information being

stored in the DNA computer.

A rival approach, pioneered by Leonard M. Adleman allows the bits of DNA to float freely in

a test-tube. Dr. Adleman, in 1994 solved the traveling salesman problem using his test-tube

approach. The TSP on a large scale is effectively unsolvable by conventional computer

systems (its theoretically possible, but wouldtake an extremely long time).

His work was picked up by Dr. Donald Beaver, among others, who analyzed the approach

and organized it into a highly accessible web page which includes concise annotated

bibliography. One major contributor to this page is the research group of Dr. Richard Lipton,

Dan Bonech and Christopher Dunworth-a professor of computer science and two graduate

students at Princeton University. They are currently using a DNA computer to break the

governments DES.

In Liptons article speeding upcomputation via molecular biology he shows how DNA can

be used to construct a Turing machine, a universal computer capable of performing any

calculation. While it currently exists only in theory, its possible that in years to come

computers based on work of Adleman, Lipton, and others will come to replace traditional

silicon-based machines.

In other words of Dr. Goodman its clearly theoretically possible, the question is whether

the chemical operations can actually be done with a low-enough error frequency.

dna computing final part

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