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Sandeep M

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Contents
 Traditional Computers
 Introduction to DNA
 Structure of DNA
 DNA Computers
 Advantages & Disadvantages
 Develoments in DNA Computing
 References
Traditional Computation
 Traditional computers started with vacuum
tubes, mechanical switches.
 Now we have IC’s and processors with
VLSI, ULSI technologies.
 These computers are examples of Von
Neumann architecture.
Traditional Computation
(continued)
 Silicon is the life for today's computers.
 Moore’s Law states that silicon
microprocessors double in complexity
roughly every two years.
 One day this will no longer hold true when
miniaturisation limits are reached.
 Require a successor to silicon.
What is DNA ?
 Deoxyribonucleic acid (DNA) is a nucleic
acid that contains the genetic instructions
used in the development and functioning of
all known living organisms.
 DNA is nothing but blueprint or a code,
since it contains the instructions needed to
construct other components of cells, such
as proteins and RNA molecules.
Structure of DNA
Structure of DNA
(continued)
 Chemically, DNA consists of two
long polymers of simple units
called nucleotides, with backbones made of
sugars and phosphate groups joined
by ester bonds.
 These two strands run in opposite directions to
each other and are therefore anti-parallel.
 There are 4 nucleotides in DNA
A – Adenine T –Thymine
C – Cytosine G – Guanine
DNA Computing
 DNA computing is a form
of computing which
uses DNA, biochemistry and molec
ular biology, instead of the
traditional silicon-based computer
technologies.
 This field was initially developed
by Leonard Adleman of
the University of Southern
California, in 1994.
DNA
Computing(continued)
 Adleman demonstrated a proof-of-
concept use of DNA as a form of
computation which solved the seven-
point Hamiltonian path problem.
 DNA computers are faster and smaller than
any other computer built so far. But DNA
computing does not provide any new
capabilities from the standpoint
of computability theory .
Computation Algorithm
 STEP1:Encode the city names in short DNA
sequences . Encode the Itineraries by
connecting the city sequences for which the
routes exist .
CITY DNA SEQUENCE
MUMBAI GCTACG
DELHI CTAGTA
BANGALORE TCGTAC
CHENNAI CTACGG
KOLKATA ATGCCG

 The DNA molecules are generated by a


machine called DNA synthesizer
•Polymerase chain reaction is used to produce many
copies of the DNA
•PCR is iterative and uses an enzyme called
polymerase
•Polymerase copies a section of single stranded DNA
starting at the position of the primer, which is DNA
complimentary to one end of the Interested section.
Step 2: Sort the DNA by length and select
the DNA whose length Corresponds to 5 cities.

• Gel electrophoresis force


the DNA through a gel matrix
by using an electric field.
• DNA forces its way through the
gel which slows down the
DNA at different rates.
STEP 3:Successively filter the DNA molecules
by city, one city at a Time.
•Finally, use affinity separation procedure to
weed out paths without all the cities
•Iterative procedure (for each vertex/city)
•Probe molecules attached on iron balls attract
the correct strands; the rest is poured out

•If any DNA is left in the tube, it is the


Hamiltonian Path.
Advantages
The power of DNA in view of computation
capability:
 vast parallelism: 10 trillion ligation reaction
could be done simultaneously in a marble-
sized space.
 exceptional energy efficiency:
2×1019 operations/J,
theoretical bound 3×1019 operations/J,
existing computer: 109 operations/J.
 extraordinary information density:
1gram = 4×1021 bits = 1 trillion CDs.
Disadvantages
 DNA computing involves a relatively large
amount of error.
 Requires human assistance!
 Time consuming laboratory procedures.
 No universal method of data
representation.
 DNA has a half-life.
Solutions could dissolve away before the end
result is found
DNA V/s Conventional
Computer
Developments in DNA
computation
 Began in 1994 when Dr. Leonard Adleman
wrote the paper “Molecular computation of
solutions to combinatorial problems” &
succeeded in using it.
 First practical DNA computer unveiled in 2002
by Olympus Optical Co., Ltd . Used in gene
analysis. DNA computer for gene
analysis (development
prototype).

High-speed fully-
automated process
from sample injection to
reaction enables
quantitative gene
expression profiling.
Developments in DNA
computation(continued)
Self-powered DNA computer unveiled in
2003.
>First programmable autonomous computing
machine in which the input, output, software and
hardware were all made of DNA molecules.
>Can perform a billion operations per second with
99.8% accuracy
• In 2004 an autonomous DNA computer that is
capable of diagnosing cancerous activity within a
cell, and then releasing an anti-cancer drug upon
diagnosis is constructed by Prof. Shapiro & team.
They claim in the journal Nature that they were
successful.
Developments in DNA
computation(continued)
 A DNA Sequence Design for Direct-Proportional
Length-Based DNA Computing using
DNASequenceGenerator is developed in
Universiti Teknologi Malaysia in 2008.
 A Method to Encrypt Information with DNA
Computing has been suggested by Zheng
Zhang, Xiaolong Shi, Jie Liu of Department of
Control Science and Engineering, Huazhong
Univ of Sci&Tech,China in 2008.
Conclusion
 DNA computers showing enormous
potential, especially for medical purposes
as well as data processing applications.

 Many issues to be overcome to produce a


useful DNA computer.
References
 www.news.nationalgeographic.com/news/2003/
02/0224_030224_DNAcomputer.html -
 www.cnn.com
 www.sciam.com/article.cfm?articleID=000A4F2
E-781B-1E5A-A98A809EC5880105
 http://unisci.com/stories/20021/0315023.htm
 www.howstuffworks.com
 www.bbcworld.com
 www.wikipedia.com
 IEEE papers on DNA computing
Thank you…