DNA COMPUTING

Shashwat Shriparv
dwivedishashwat@gmail.com
InfinitySoft
 Introduction

 Ever wondered where we would find the new

material needed to build the next generation of
microprocessors????
HUMAN BODY (including yours!)…….DNA
computing.
 “Computation using DNA” but not “computation
on DNA”
 Dr. Leonard Adleman is often called “The inventor
of DNA Computers”.
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 What is a DNA?

A nucleic acid that carries the genetic information in

the cells.
DNA is composed of A (Adenine), C (Cytosine),
G (Guanine) and T (Thymine)

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 DNA MEMORY
A DNA string can be viewed as a memory resource to
save info:
 4 types of units (A,C,G,T)
 Complementary units: A-T,C-G

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 Uniqueness of DNA

Why is DNA a Unique Computational Element???

 Extremely dense information storage.

 Enormous parallelism.

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 Dense Information Storage
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.

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 DNA Computing

It can be defined as the use of biological molecules,

primarily DNA , to solve computational problems

that are adapted to this new biological format

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 Computers Vs DNA computing

DNA based Computers Microchip based Computers

 Slow at Single Operations  Fast at Single Operations

(Fast CPUs)
 Able to simultaneously perform  Can do substantially fewer
Millions of operations operations simultaneously

 Huge storage capacity  Smaller capacity

 Require considerable  Immediate setup

preparations before

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 Why do we investigate about “other”
computers?
 Certain types of problems (learning, pattern
recognition, fault-tolerant system, large set searches,
cost optimization) are intrinsically very difficult to
solve with current computers and algorithms

 NP problems: We do not know any algorithm that

solves them in a polynomial time  all of the current
solutions run in a amount of time proportional to an
exponential function of the size of the problem

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Adleman’s solution of the Hamiltonian
Directed Path Problem(HDPP).

I believe things like DNA computing will eventually

lead the way to a “molecular revolution,” which
ultimately will have a very dramatic effect on the
world. – L. Adleman
 An example of NP-problem: the Traveling
Salesman Problem

 TSP: A salesman must go from the city A to the city

Z, visiting other cities in the meantime. Some of the
cities are linked by plane. Is it any path from A to Z
only visiting each city once?

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 An example of NP-problem: the
Traveling Salesman Problem
1. Code each city (node) as an 8 unit DNA string

2. Code each permitted link with 8 unit DNA strings

3. Generate random paths between N cities (exponential)

4. Identify the paths starting at A and ending at Z

5. Keep only the correct paths (size, hamiltonian)

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 Coding the paths
(Hybridization and ligation between city molecules and intercity link molecules )

1, Atlanta – Boston:
ACTTGCAGTCGGACTG
|||||||| Solution A+B+C+D:
CGTCAGCC
R:(GCAGTCGG)
2,(A+B)+Chicago: ACTTGCAGTCGGACTGGGCTATGTCCGAGCAA
ACTTGCAGTCGGACTGGGCTATGT
||||||||
TGACCCGA R:(ACTGGGCT) 13
 Filter the correct solutions

1.Identify the paths starting at A and ending at Z

 PCR for identifying sequences starting with the last nucleotides of A and
ending at the first nucleotides of Z
2. Keep only the paths with N cities (N=number of cities)
 Gel electrophoresis
3. Keep only those paths with all of the cities (once)
 Antibody bead separation with each vertex (city)

The sequences passing all of the steps are the solutions

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 Algorithm

1.Generate Random paths

2.From all paths created in step 1, keep only those that
start at s and end at t.
3.From all remaining paths, keep only those that visit
exactly n vertices.
4.From all remaining paths, keep only those that visit
each vertex at least once.
5.if any path remains, return “yes”;otherwise, return
“no”.
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 DNA Vs Electronic computers

 At Present,NOT competitive with the state-of-

the-art algorithms on electronic computers
 Only small instances of HDPP can be
solved.Reason?..for n vertices, we require 2^n
molecules.
 Time consuming laboratory procedures.
 No universal method of data representation.

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 Advantages

 Ample supply of raw materials.

 No toxic by-products.

 Smaller compared to silicon chips.

 Efficiency in parallel computation.

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 Disadvantages

 Time consuming.

 Occasionally slower.

 Reliability.

 Human Assistance.
 Danger of Errors possible

 Assuming that the operations used by Adleman

model are perfect is not true.
 Biological Operations performed during the

algorithm are susceptible to error

 Errors take place during the manipulation of

DNA strands. Most dangerous operations:
 The operation of Extraction

 Undesired annealings.

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 Error Restrictions

 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

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 Applications

 Satisfiability and Boolean Operations

 Finite State Machines
 Road Coloring
 DNA Chip
 Solving NP-hard problems
 Turing Machine
 Boolean Circuits
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 Conclusion

 DNA Computing uses DNA molecules to

computing methods
 DNA Computing is a Massive Parallel
Computing because of DNA molecules
 Someday, DNA Computer will replace the
silicon-based electrical computer

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 Future!

It will take years to develop a practical,

workable DNA computer.

But…Let’s all hope that this DREAM comes

true!!!

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THANK YOU

Shashwat Shriparv
dwivedishashwat@gmail.com
InfinitySoft
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