Manu Nair Semester: 7: "Fact Is Always Stranger Than Fiction"

“FACT IS ALWAYS STRANGER THAN FICTION”
MANU NAIR
COMPUTER SCIENCE &ENGINEERING
SEMESTER: 7
INTRODUCTION
• Growing needs of mankind-Rapid Development.

• Rapid advancement in computer technology will
lose its momentum when silicon chip reaches its full
capacity & miniaturization
• Solving complex problems which today's
supercomputers are unable to perform in stipulated
period of time.
WHAT COULD BE A REMEDY TO THIS CONCERN?????
What is Biological Computer?
• Biological Computers are computers which
use synthesized biological components to
store and manipulate data analogous to
processes in the human body.
• The result is small yet faster computer that
operates with great accuracy.
• Main biological component used in a
Biological Computer is :
What is DNA?
• DNA Stands for DeOxyRiboNucleic Acid.
• A hereditary material found in almost all living
organisms.
• Located inside the nucleus of a cell.
• Helps in long term storage of information.
• Information in DNA is stored as a code made
of four chemical bases (A,T,G & C).
• Order & sequence of these bases determine
the kind of information stored.
Structure of DNA
• The two strands of DNA
molecule are anti parallel
where each strand runs in
opposite direction
• Complementary base pairs
Adenine(A) & Thymine(T)
Guanine(G) &
Cytosine(C).
• Two strands are held
together by weak
hydrogen bonds between
the base pairs.
Graphical Representation of Inherent Bonding Properties
of
DNA
What is a DNA Computer?
DNA Computers are small, fast and highly
efficient computers which includes the
following properties:-
• Dense data storage.

• Massively parallel computation.
• Extraordinary energy efficiency.
How Dense is the Data Storage?
• with bases spaced at 0.35 nm along DNA, data
density is over a million Gbits/inch compared
to 7 Gbits/inch in typical high performance
HDD.
• Check this out………..
Some Facts…
 This image shows 1 gram of DNA
on a CD. The CD can hold 800
MB of data.
 The 1 gram of DNA can hold

about 1x1014 MB of data.
 The number of CDs required to

hold this amount of information,
lined up edge to edge, would
circle the Earth 375 times, and
would take 1630 centuries to
listen to.
How Enormous is the Parallelism?
• A 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 !
• Check this out……. We Typically use
How Extraordinary is the Energy
Efficiency?
• Modern supercomputers only operate at

109 operations per joule.
• Adleman figured his computer was running
2 x 1019 operations per joule.
Adleman-
Inventor of Biological Computers
• His article released in 1994,described how to use

DNA to solve a well-known mathematical problem,
called the directed Hamilton Path problem.
• Goal of the problem is to find the shortest route
between a number of cities, going through each city
only once. As you add more cities to the problem,
the problem becomes more difficult.
Steps in Adleman’s Experiment
 Strands of DNA represent the seven cities. In genes, genetic
coding is represented by the letters A, T, C and G. Some
sequence of these four letters represented each city and
possible flight path.
 These molecules are then mixed in a test tube, with some of
these DNA strands sticking together. A chain of these strands
represents a possible answer.
 Within a few seconds, all of the possible combinations of DNA
strands, which represent answers, are created in the test
tube.
 Adleman eliminates the wrong molecules through chemical
reactions, which leaves behind only the flight paths that
connect all seven cities.
Extraction
Spooling the DNA with a metal

hook or similar device
Precipitation of more DNA

strands in alcohol
Formation of DNA strands.

Hamilton Path Problem
(also known as the travelling salesperson problem)
Darwin
Perth Alice Spring Brisbane
Sydney
Melbourne
Is there any Hamiltonian path from Darwin to Alice Spring?

Adleman’s Experiment (continued…)
• Encode each city with complementary base - vertex
molecules
Sydney - TTAAGG
Perth - AAAGGG
Melbourne - GATACT
Brisbane - CGGTGC
Alice Spring - CGTCCA
Darwin - CCGATG
• Encode all possible paths using the

complementary base – edge molecules
Sydney  Melbourne – AGGGAT
Melbourne  Sydney – ACTTTA
Melbourne  Perth – ACTGGG
etc…
• Merge vertex molecules and edge molecules.

All complementary base will adhere to each
other to form a long chains of DNA molecules
Solution with Merge Solution with
vertex DNA & edge DNA
molecules Anneal molecules
Long chains of DNA molecules (All

possible paths exist in the graph)
• Select a path that starts with proper city and

ends with final city.
• Select paths with correct number of cities.
• Select path which contains each city only

once.
• The solution is a double helix molecule:
Darwin Brisbane Sydney Melbourne Perth Alice Spring
CCGATG – CGGTGC – TTAAGG – GATACT – AAAGGG – CGTCCA
TACGCC – ACGAAT – TCCCTA – TGATTT – CCCGCA
Darwin Brisbane Sydney Melbourne Perth

Brisbane Sydney Melbourne Perth Alice Spring
Hence Adleman proved DNA can be used to solve complex problems……….

Conventional vs. Biological Computers
Conventional Biological
Component Inorganic, e.g. silicon Biological, e.g.

materials DNA
Processing scheme Sequential and limited Massively parallel
massively parallel
Current max. 1012 Op.s per sec. 1014 Op.s per sec.
operations
Quantum effects a Yes No
problem?
Toxic components? Yes No
Energy efficient? No Yes
Applications
• Can be a general purpose tool for a variety of
problems
• Many possible applications:
Pattern recognition
Cryptography
Evaluating gene sequence
• Medical Application: ‘developing disease’ treatments
such as cancer
• Taiwan introduced the world's first DNA
authentication chip & was used for national
identification cards in order to crack down on
frauds using fake ID cards.
Advantages of Biological Computers
Parallel Computing- Biological computers are massively

parallel.
Incredibly light weight- With only 1 LB of DNA you have

more computing power than all the computers ever made.
Low power- The only power needed is to keep DNA from

denaturing.
Solves Complex Problems quickly- A DNA computer can

solve hardest of problems in a matter of weeks.
Advantages (Continued…)
•Perform millions of operations simultaneously.
•Generate a complete set of potential solutions.
• Efficiently handle massive amounts of working memory.
•cheap, clean, readily available materials.
•amazing ability to store information .

Limitations
•Error: Molecular operations are not perfect.
•Efficiency: How many molecules contribute?
•Encoding problem in molecules is difficult
•DNA computing involves a relatively large amount of error.
•As size of problem grows, probability of receiving incorrect answer

eventually becomes greater than probability of receiving correct
answer
•Reliability- There is sometime errors in the pairing of DNA strands
•DNA in vitro decays through time, so lab procedures should not

take too long.
The Future
Algorithm used by Adleman for the traveling salesman problem
was simple. As technology becomes more refined, more efficient
algorithms may be discovered.
DNA Manipulation technology has rapidly improved in recent

years, and future advances may make DNA computers more
efficient.
The University of Wisconsin is experimenting with chip-based

DNA computers.
THANK YOU!!!
It will take years to develop a practical, workable

Biological Computer.
But…Let’s all hope that this DREAM comes

true!!!
MANU NAIR
I have taken reference from all sources in
internet….& thank all those sources

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“FACT IS ALWAYS STRANGER THAN FICTION”

• Growing needs of mankind-Rapid Development.

• Dense data storage.

 The 1 gram of DNA can hold

 The number of CDs required to

• A test tube of DNA can contain trillions of

• Modern supercomputers only operate at

• His article released in 1994,described how to use

Spooling the DNA with a metal

Precipitation of more DNA

Formation of DNA strands.

Perth Alice Spring Brisbane

Is there any Hamiltonian path from Darwin to Alice Spring?

• Encode all possible paths using the

• Merge vertex molecules and edge molecules.

Long chains of DNA molecules (All

• Select a path that starts with proper city and

• Select paths with correct number of cities.

• Select path which contains each city only

• The solution is a double helix molecule:

Darwin Brisbane Sydney Melbourne Perth Alice Spring

CCGATG – CGGTGC – TTAAGG – GATACT – AAAGGG – CGTCCA

TACGCC – ACGAAT – TCCCTA – TGATTT – CCCGCA

Darwin Brisbane Sydney Melbourne Perth

Hence Adleman proved DNA can be used to solve complex problems……….

Component Inorganic, e.g. silicon Biological, e.g.

Parallel Computing- Biological computers are massively

Incredibly light weight- With only 1 LB of DNA you have

Low power- The only power needed is to keep DNA from

Solves Complex Problems quickly- A DNA computer can

•Perform millions of operations simultaneously.

•Generate a complete set of potential solutions.

• Efficiently handle massive amounts of working memory.

•cheap, clean, readily available materials.

•amazing ability to store information .

•Efficiency: How many molecules contribute?

•Encoding problem in molecules is difficult

•DNA computing involves a relatively large amount of error.

•As size of problem grows, probability of receiving incorrect answer

•Reliability- There is sometime errors in the pairing of DNA strands

•DNA in vitro decays through time, so lab procedures should not

DNA Manipulation technology has rapidly improved in recent

The University of Wisconsin is experimenting with chip-based

It will take years to develop a practical, workable

But…Let’s all hope that this DREAM comes

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