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					DNA COMPUTING

                           BY



Satish kumar.O           K.N.K.Teja              A. Ajay,
III B.Tech (IT),         III B.Tech (IT),        III B.Tech (CSE),
GITAM,                   GITAM,                  ANITS,
Visakhapatnam.           Visakhapatnam.          Visakhapatnam.




              E-mail id: sattu_0826@yahoo.com
                         tejaknk@gmail.com
                         ajayakunuri@gmail.com




       Contact no: 9885054346, 9885559232 and 9885129827
Abstract
               Silicon microprocessors      information processing tools such as
have been the heart of computing world      enzymes, copying tools, proofreading
for more than forty years. Computer chip    mechanisms and so on, that evolution
manufacturers are furiously racing to       has spent millions of years refining.
make the next microprocessor that will      Now we are taking those tools in large
topple speed records and in the process     numbers molecules and using them as
are cramming more and more electronic       biological computer processors.
devices onto the microprocessor. Sooner                DNA computing has a great
or later the physical speed and             deal of advantage over conventional
miniaturization     limits   of   silicon   silicon-based       computing.      DNA
microprocessors is bound to hit a wall.     computers can store billions of times
              Chipmakers need a new         more data than your personal computer.
material to produce faster computing        DNA computers have the ability to work
speed with fewer complexities. You          in a massively parallel fashion,
won‟t believe where scientists have         performing         many      calculations
found this new material. DNA, the           simultaneously. DNA molecules that
material our genes are made of, is being    provide the input can also provide all the
used to build the next generation of        necessary operational energy.
microprocessors. Scientists are using                  DNA computing has made a
this genetic material to create nano-       remarkable progress in almost every
computers that might take the place of      field. It has found application in fields
silicon computers in the next decade.       like      biomedical,    pharmaceutical,
               A nascent technology that    information security, cracking secret
uses DNA molecules to build computers       codes, etc.
that are faster than the world‟s most                   Scientists and researchers
powerful human-built computers is           believe that in the foreseeable future
called DNA computing. Molecular             DNA computing could scale up to great
biologists are beginning to unravel the     heights!
Introduction
             Man‟s thirst for knowledge        binary data is encoded with ones and
has driven the information revolution.         zeros, a strand of DNA is encoded with
Human brain, a master processor,               four bases, represented by letters A
processes the information about the            (Adenine), T (Thymine), C (Cytosine)
internal and external environment and          and G (Guanine).
sends signals to take appropriate actions.
In nature, such controls exist at every
level. Even the smallest of the cells has a
nucleus, which controls the cell. Where
does this power actually come from? It
lies in the DNA. The ability to harness
this computational power shall
determine the fate of next generation of
computing.
             DNA computing is a novel
technology that seeks to capitalize on the     Graphical representation of   Illustration of
                                               inherent bonding properties   double helix
enormous informational capacity of             of DNA                        shape of DNA.
DNA, biological molecules that can
store huge amounts of information and
are able to perform operations similar to                    The bases (nucleotides)
that of a computer, through the                are spaced every 0.35 nanometers along
deployment of enzymes, biological              the DNA molecule, giving it a
catalysts that act like software to execute    remarkable data density of nearly
desired operations. The appeal of DNA          18Mbits per inch. These nucleotides will
computing lies in the fact that DNA            only combine in such a way that C
molecules can store far more                   always pairs with G and T always pairs
information       than      any     existing   with A. This complementarity makes
conventional computer chip. Also,              DNA a unique data structure for
utilizing DNA for complex computation          computation and can be exploited in
can be much faster than utilizing a            many ways.
conventional computer, for which
massive parallelism would require large        Computer in a test tube
amounts of hardware, not simply more                            The idea of using DNA to
DNA.                                           store and process information took off in
                                               the year 1994 when Leonard Adleman, a
Structure of DNA                               computer scientist at the University of
           All organisms on this planet        Southern California, came to the
are made of the same type of genetic           conclusion that DNA had computational
blueprint, which bind us together.             potential. Adleman caused an avalanche
Within the cells of any organism is a          in the fields of biology; mathematics and
substance called Deoxyribonucleic Acid         computers by solving a problem called
(DNA), which is a double-stranded helix        the Directed Hamiltonian Path problem
of nucleotides, which carries the genetic      or sometimes referred to as the Traveling
information of a cell. The data density of     Salesman Problem. The „salesman‟ in
DNA is impressive. Just like a string of       this problem has a map of several cities
that he must visit to sell his wares where     bonding tendencies of nucleotides to
these cities have only one-way streets         DNA strands representing pathways
between some but not all of them. The          between the cities.
crux of the problem is that the salesman                    By placing a few grams of
must find a route to travel that passes        every DNA city and street in a test tube
through each city (A through G) exactly        and allowing the natural bonding
once, with a designated beginning and end.     tendencies of the DNA building blocks
The salesman does not want to backtrack        to occur, the DNA bonding created over
or go more than once through any of the        10^9 answers in less than one second.
paths. This is a non-deterministic             Out of the answers that came about the
polynomial time problem.                       correct answers were determined
                                               considering that the correct path must
                                               start at A and end at G, it must pass
                                               through all cities at least once and must
                                               contain each city in turn.
                                                            The correct answer was
                                               determined by filtering the strands of
                                               DNA according to their end-bases to
                                               determine which strands began from A
                                               and end in city G. The remaining strands
                                               were      then      measured      through
                                               electrophoreic techniques to determine if
 Basic outline of Traveling Salesman Problem   the path they represent has passed
                                               through all seven cities. Finally the
                                               resulting sets of DNA were examined
Adleman used a basic seven city,
                                               individually to determine if they contain
thirteen street model for Traveling
                                               each city in turn. That strand(s) that
Salesman Problem and created randomly
                                               remained was then determined to be the
sequenced DNA strands 20 bases long to
                                               answer(s). This process took Adleman
chemically represent each city and a
                                               about a week. A conventional computer
complementary 20 base strand that
                                               is better suited for deterministic
overlaps each city‟s strand half way to
                                               computation permitting at most one next
represent each street. This representation
                                               move at any step in computation. The
allowed each multi-city tour to become a
                                               inherent parallel computing ability of
piece of double stranded DNA with the
                                               DNA, however, is perfectly suited for
cities linked in some order by the streets.
                                               solving such non-deterministic type of
                                               problems.

                                               A      Successor to
                                               Silocon
                                                           Silicon     microprocessors
                                               have been the heart of computing world
                                               for more than forty years.Computer chip
                                               manufacturers are furiously racing to
                                               make the next microprocessor that will
   Representation of 20 bases DNA              topple speed records and in the process
strand representing a city showing the
are cramming more and more electronic          would take one DNA computer only 1
devices onto the microprocessor. Many          year to polish off!
have predicted that Moore‟s law (which
states that the microprocessors would           Scope and recent updates
double in complexity every two years)                          Scientists have taken
will soon reach its end, because of the        DNA from the free-floating world of the
physical speed and miniaturization limits      test tube and anchored it securely to a
of silicon microprocessors.                    surface of glass and gold. University of
              DNA computers have the           Wiscosnin-Madison researchers have
potential to take computing to new             developed a thin, gold-coated plate of
levels, picking up where Moore‟s law           glass about an inch square. They believe
leave off. DNA computers could surpass         it is the optimum working surface on
their silicon-based predecessors. The          which they can attach trillions of strands
several advantages of DNA over silicon         of DNA. Putting DNA computing on a
are:As long as there are cellular              solid surface greatly simplifies the
organisms, there will be a supply of           complex and repetitive steps previously
DNA. The large supply of DNA makes it          used in rudimentary DNA computers.
a cheap resource. Unlike the toxic             Importantly it takes DNA out of the test
materials used to make traditional             tube and puts it on a solid surface,
microprocessors, DNA biochips can be           making the technology simpler, more
made cleanly. DNA computers are many           accessible and more amenable to the
times smaller than today‟s computers.          development of large DNA computers
             DNA molecules have a              capable of tackling the kind of complex
potential to store extensively large           problems that conventional computers
amount of information. It has been             now handle routinely. Researchers
estimated that a gram of dried DNA can         believe that by the year 2010 the first
hold as much information as a trillion         DNA chip will be commercially
CD‟s. More than 10 trillion DNA                available.
molecules can fit into an area of 1 cubic
centimeter. With this small amount if
DNA a computer would be able to hold           Applications
10 terabytes of data, and perform 10                           DNA logic gates are the
trillion calculations at a time.               first step towards creating a computer
          In a biochemical reaction-taking     that has a structure similar to that of an
place in a tiny surface area, a very large     electronic PC. Instead of using electrical
number of DNA molecules can operate            signals to perform logical operations,
in concert, creating a parallel processing     these DNA logic gates rely on DNA
system that mimics the ability of the          code. They detect fragments of genetic
most powerful supercomputer. DNA               material as input, splice together these
computers have the ability to perform          fragments and form a single output.
many       calculations      simultaneously;   Recent works have shown how these
specifically, on the order of 10^9             gates can be employed to carry out
calculations per ml of DNA per second!         fundamental computational operations,
A calculation that would take 10^22            addition of two numbers expressed in
modern computers working in parallel to        binary. This invention of DNA logic
complete in the span of one human‟s life
gates and their uses are a breakthrough      algorithms in the world of information
in DNA computing.                            security.
              A group of researchers at      Advantages
Princeton University in early 2000            The advantage of DNA approach is
demonstrated an RNA computer similar            that it works in parallel, processing
to Adleman‟s, which had the ability to          all possible answers simultaneously.
solve a chess problem involving how           DNA computing is an example of
many ways there are to place knights on         computing at a molecular level,
a chessboard so that none can take the          potential a size limit that may never
others.While a desktop PC is designed to        be reached by the semiconductor
perform one calculation very fast, DNA          industry.
strands produce billions of potential          It can be used to solve a class of
answers simultaneously. This makes the          problems that are difficult or
DNA computer suitable for solving               impossible to solve using traditional
"fuzzy logic" problems that have many           computing methods.
possible solutions rather than the             There is no power required for DNA
either/or logic of binary computers. In         computing while the computation is
the future, some speculate, there may be        taking place. The chemical bonds
hybrid machines that use traditional            that are the building blocks of DNA
silicon for normal processing tasks but         happen without any outside power
have DNA co-processors that can take            source. Its energy-efficiency is more
over specific tasks they would be more          than a million times that of a PC.
suitable for.                                  DNA computing is a cost-effective
            DNA computing is in its             method for solving complex
infancy, and its implications are only          computational problems.
beginning to be explored. But DNA
computing devices could revolutionize        Disadvantages
the pharmaceutical and biomedical
fields. Some scientists predict a future      DNA computers require human
where our bodies are patrolled by tiny         assistance.
DNA computers that monitor our well-          Technological challenges remain
being and release the right drugs to           before DNA computing. Researchers
repair damaged or unhealthy tissue.            need to develop techniques to reduce
They could act as „Doctors in a cell‟.         number of computational errors
DNA computing research is going so             produced by unwanted chemical
fast that its potential is still emerging.     reactions with the DNA strands.
                                               They need to eliminate, combine, or
DNA computing can be used by national          accelerate the steps in processing the
governments for cracking secret codes,         DNA.
or by airlines wanting to map more            The extrapolation and practical
efficient routes. The concept of using         computational environment required
DNA computing in the fields of                 are daunting. The „test tube‟
cryptography,     steganography     and        environment      used     for    DNA
authentication has been identified as a        computing is far from practical for
possible technology that may bring             everyday use.
forward a new hope for unbreakable
 To the naked eye, DNA computer looks
  like clear water solution in a test tube.
  There is no mechanical device. Hence
  to make the output visible, human
  manipulation is needed.

 Conclusion
              The beauty of DNA
 research is found in the possibility of
 mankind‟s utilization of its very life
 building blocks to solve its most difficult
 problems. DNA computing research is
 going so fast that its potential is still
 emerging. Scientists and mathematicians
 around the world are now looking at the
 application of DNA computers to a
 whole range of “intractable” computing
 problems. In any case, we will not be
 tossing out those PCs for test tubes of
 DNA anytime soon and the use of DNA
 computing in every walk of life is a long
 way off!

 References

 Websites:
 computer.howstuffworks.com
 users.aol.com/ibrandt/dna_computer.htm
 l
 arstechnica.com/reviews/2q00/dna/dna-
 1.html
 nationalgeographic.com
 cis.udel.edu
 hypography.com
 house.gov/science/landweber
 whyfiles.org/shorties/dna_computer.html
 www4.tpgi.com.au/users/aoaug/dna_co
 mp.html
 newsscientist.com
 iturls.com/English/TechHotspot
 theindianprogrammer.com
 news.bbc.co.uk/hi/english/ sci/tech
 chronicle.com/data/articles.dir
 olympus.co.jp/en/magazine/ TecZone

				
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