DNA COMPUTERS

Swathi Manjunath – 108

Theagarajan – 111
Varsha Kumar – 112
Varun Aggarwal – 113
Vedashree S Gowda - 114

1
 Introduction

 Biocomputers use systems of biologically derived

molecules such as DNA and proteins, to perform
computational calculations involving storing, retrieving, and
processing data
 DNA computing is a form of computing which
uses DNA, biochemistry and molecular biology instead of
the traditional silicon-based computer technologies
 Introduction – contd.

 This field was initially developed by Leonard Adleman of

the University of Southern California, in 1994.Adleman
demonstrated a proof-of-concept use of DNA as a form of
computation which solved the seven-point Hamiltonian path
problem.

 In 2002 - A programmable molecular computing machine

was developed which was composed of enzymes and DNA
molecules instead of silicon microchips.
 Introduction – contd.

 In 2004 – DNA computer coupled with an input and

output module was developed which would theoretically
be capable of diagnosing cancerous activity within a cell,
and releasing an anti-cancer drug upon diagnosis.

 In 2009 – Bio computing systems were coupled with

standard silicon based chips for the first time.
 DNA- a unique data structure
 DNA – Deoxyribonucleic Acid

Genetic information “memory”

Nucleotides strung into

polymer chains (DNA Strands)

Four classes of nucleotides:

Adenine, Guanine, Cytosine, Thymine (A,C,G,T)
 DNA- a unique data structure –
contd.
DNA Density - The bases (also known as nucleotides) are
spaced every 0.35 nanometers along the DNA molecule,
giving DNA an remarkable data density of nearly 18 Mbits
per inch.

Double stranded - The bases A and T, and C and G, can

bind together, forming base pairs. Therefore every DNA
sequence has a natural complement.

Operations in parallel - many copies of the enzyme can

work on many DNA molecules simultaneously.
 DNA vs Silicon

• DNA is easily available and hence it is a cheap

resource.

• DNA biochips can be made cleanly, unlike the toxic

materials used to make traditional microprocessors.

• DNA computers can be made many times smaller

than today's computers.

• DNA has the ability to perform many parallel

operations. Each operation on a test tube of DNA is
carried out on all strands in the tube in parallel !
 DNA vs Silicon

• Dense information storage -1 gram of DNA can

hold about 1x1014 MB of data.

• Extraordinary energy efficiency. Adleman

figured his computer was running 2 x 1019
operations per joule.

• The uniqueness of the DNA helps in error

correction.
 Applications of DNA
computing
• Storage and Associative Memory - large content
addressable memory using DNA

• Massively Parallel Processing - handle millions of

operations in parallel

• Hamiltonian’s problem

• Cryptography
 Applications- contd.
• Recoding natural DNA –
• DNA sequencing;
• DNA fingerprinting;
• DNA mutation detection
 Cryptography

Inverse initial
Initial
Input Computation permutation
permutation Output
IP -1
IP

Plain-text
Cipher-text

Key
 Travelling Salesman problem
• Aldeman chose a task that represents a whole class of
hard-to-solve problems.

• PROBLEM: A hypothetical salesman tries to find a

route through a set of cities so that he visits each
city only once.

• Eg: I live in LA and need to visit four cities: Dallas,

Chicago, Miami, and NY, with NY being my final
destination. The airline I’m taking has a specific set of
connecting flights that restrict which routes I can take.
 Hamiltonian problem –
contd.
• Part 1: Encode city names in short DNA
sequences. Encode itineraries by connecting
the city sequences for which routes exist.
Los Angeles GCTACG

Chicago CTAGTA

Dallas TCGTAC

Miami CTACGG

New York ATGCCG

 Hamiltonian problem -
contd.
• You can encode the routes between cities by encoding
the compliment of the second half (last three letters) of
the departure city and the first half (first three letters) of
the arrival city.

• For example the route between Miami (CTACGG) and

NY (ATGCCG) can be made by taking the second half
of the coding for Miami (CGG) and the first half of the
coding for NY (ATG). This gives CGGATG. The
complement of this is GCCTAC.
 Hamiltonian problem
- contd.
• You can encode the routes between cities by encoding
the compliment of the second half (last three letters) of
the departure city and the first half (first three letters) of
the arrival city.
•
• For example the route between Miami (CTACGG) and
NY (ATGCCG) can be made by taking the second half
of the coding for Miami (CGG) and the first half of the
coding for NY (ATG). This gives CGGATG. The
complement of this is GCCTAC.

16
 Hamiltonian problem –
contd.

• Part 2:
- Select itineraries that start and end
with the correct cities
- Select itineraries that contain the
correct number of cities.
- Select itineraries that have a
complete set of cities 17
 Future Outlook
DNA over Conventional
• When problems are able to be divided into separate, non
sequential tasks,
• Due to the fact that they can hold much more memory and
perform more operations at once

Conventional over DNA

• Problems that require many sequential operations are likely
to remain much more efficient on a conventional computer
 Future outlook - Relation with
other sciences

• High levels of collaboration between academic

disciplines is extremely important

• Collaborations toward the development of a DNA

computer may lead to:
1. Increased understanding of the DNA and other
biological mechanisms
2. Need for precision demands progress in biomolecular
techniques that might not otherwise be considered
 The Future?

With advancements in DNA computing

• Enhance understanding of both the natural and computer
sciences
• Help explore medium for use of evolutionary programming
and understand the limits of computing

Even if a practical DNA computer cannot be built;

• DNA based computation methods as a means of simulating
and predicting the emergent behaviour of complex systems
e.g. fields pertaining to weather forecasting, economics.
• medium for use of evolutionary programming