COLLEGE OF ENGINEERING AND TECHNOLOGY

COLLEGE OF ENGINEERING
AND TECHNOLOGY

DNA
COMPUTING
Presented by:
Debabrata panda
REG NO:0801106191
3 rd yr CSE
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INTRODUCTION

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qEver wondered where we would find the

new material needed to build the next
generation of microprocessors????
qHUMAN BODY (including yours!)
…….DNA computing
q“Computation using DNA” but not
“computation on DNA”
qInitiated in 1994 by an article written by
Dr. Adleman on solving HDPP using DNA

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Uniqueness
of DNA
Why is DNA a Unique Computational


Element???
qExtremely dense information storage.
qEnormous parallelism.
qExtraordinary energy efficiency.

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Advantages
of dna
q1 CD = 800 MB
q1 gram DNA = 1X10^14 MB
q1 gram DNA = 145 trillion CDs
qHDD Data Density = 7 Gbits/inch
qDNA Storage = Over Million Gbits/inch
qA test tube of DNA can contain trillions
of strands. Each operation on a test tube of DNA is carried

out on all strands in the tube in parallel !

q

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A little more…
qBasic suite of operations: AND,OR,NOT & NOR in
CPU while cutting, linking, pasting, amplifying
and many others in DNA.
qComplementarity makes DNA unique.
qEx: in Error correction.

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BIOCHEMISTRY
BASICS

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Extaction

Annealing

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Polymerase Chain Reaction

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GEL ELECTROPHORESIS

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HAMILTONIAN DIRECTED
PATH PROBLEM

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Adleman’s solution of the
Hamiltonian Directed Path
Problem(HDPP). 2 6
qWhy not brute force algorithm???
qSo, what did Dr. Adleman use? s 4 t
q‘Generate and test’ strategy where number
 of random paths were generated and tested.
3 5
qgood thing about random path generation-each path can
be generated independent of all others bringing into
picture-- “Parallelism” . On the other hand adding
“Probability” too.
qNo. of Lab procedures grows linearly with the no. of
vertices in the graph.
q

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Algorithm
(non-deterministic)
qStep1: Generate Random paths[Annealing and
Ligation]
qStep2: From all paths created in step 1, keep only
those that start at s and end at t.[PCR with selected
primers]
qStep3: From all remaining paths, keep only those
that visit exactly n vertices.[Gel purification]
qStep4: From all remaining paths, keep only those
that visit each vertex at least once.[Magnetic bead
purification]
qStep5: If any path remains, return “yes”;otherwise,
return “no”.[PCR]
q

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DANGERS OF
ERROR

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Errors possible
qAssuming that the operations used by Adleman model are
perfect is not true.
qBiological Operations performed during the algorithm are
susceptible to error
qOnly that which happens within the boundaries of 3
dimensional world are counted…lot of probability
involved
qErrors take place during the manipulation of DNA strands.
Most dangerous operations:
qThe operation of Extraction
qUndesired annealings

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The operation of
Extraction
qWhat would happen if a ‘good’ path were lost during one of
the extraction operations in step4?
qFALSE NEGATIVE!
qAdleman’s suggestion: to amplify the content of the test
tube.
qWhat if a ‘bad’ path is taken as if it were ‘good’?
qFALSE POSITIVE!!
qLess dangerous,because the solution could be verified at
the end of the computation

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Undesired Annealings
qTypes of Undesired annealings:
qPartial Matches:A strand u could anneal with one that’s
similar to ū, but it is not the right one.
qUndesired matches between two shifted strands: Ex:A
strand vu could partially anneal with ūw.
qFinally,a strand could anneal with itself, losing its linear
structure.
qHow can the probability of all these undesired annealings
be decreased??
qwith an opportune choice of strands used to encode the
data of the problem.


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LIMITATIONS

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DNS vs electronic
computers
qAt Present,NOT competitive with the state-of-the-
art algorithms on electronic computers
qOnly small instances of HDPP can be
solved.Reason?..for n vertices, we require
2^n molecules.
qTime consuming laboratory procedures.
qGood computer programs that can solve TSP
for 100 vertices in a matter of minutes.
qNo universal method of data representation.


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The future
qAlgorithm used by Adleman for the traveling salesman problem
was simple. As technology becomes more refined, more efficient
algorithms may be discovered.
qDNA Manipulation technology has rapidly improved in recent
years, and future advances may make DNA computers more
efficient.
qThe University of Wisconsin is experimenting with chip-based
DNA computers.
qDNA computers are unlikely to feature word processing, emailing
and solitaire programs.
qInstead, their powerful computing power will be used for areas of
encryption, genetic programming, language systems, and
algorithms or by airlines wanting to map more efficient routes.
Hence better applicable in only some promising areas.
q

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References
vhttp://en.wikipedia.org/wiki/DNA_computing
vhttp://dope.caltech.edu/winfree/DNA.html
vhttp://www.cs.virginia.edu/~robins/Computing_with_DNA.p
df
vhttp://ezinearticles.com/?DNA-Computing&id=4133566
v


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ANY QUESTIONS
???

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THANK
YOU
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