DNA COMPUTING

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DNA COMPUTING

Introduction

The DNA is a Double_Stranded molecule. Each Strand is based on 4 Bases:

Adenine (A) Thymine (T) Cytosine (C) Guanine (G)

These bases are linked through a sugar (deoxyribose). IMPORTANT:

The linkage between bases has a direction. There are complementarities between bases (Watson-Crick).

(A) (T) (C)(G)

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DNA COMPUTING

DNA STRUCTURE

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DNA COMPUTING

Extraction

given a test tube T and a strand s, it is possible to extract all the strands in T that contain s as a subsequence, and to separate them from those that do not contain it.

Formation of DNA strands.

Precipitation of more DNA strands in alcohol

Spooling the DNA with a metal hook or similar device

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DNA COMPUTING

Uniqueness of DNA

DNA is a Unique Computational Element because of:

Extremely dense information storage. Enormous parallelism. Extraordinary energy efficiency.

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DNA COMPUTING

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.

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 163,000 centuries to listen to.04/11/2023

DNA COMPUTING

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

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DNA COMPUTING

How extraordinary is the energy efficiency?

Adleman figured his computer was running

2 x 1019 operations per joule.

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DNA COMPUTING

Coding the information:

1994: The Adleman’s experiment.

Given directed graph can we find an hamiltonian path.In this experiment there are 2 keywords:

massive parallelism (all possibilities are generated)complementarity (to encode the information)

This proved that DNA computing wasn’t just a theoretical study but could be applied to real problems.

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DNA COMPUTING

Model of DNA computer

Test tube is a set of molecules of DNA (multi-set of finite strings over the alphabet {A,C,G,T})

Operations on the tube:1. Separate (extract)

2. Merge

3. Detect

4. Amplify

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DNA COMPUTING

Separate

Tube T, string S {A,C,G,T} +(T,S)

all the molecules in T containing S

-(T,S) All the molecules in T not containing S

Done using a magnetic bead

system or affinity column

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DNA COMPUTING

Merge

Tubes T1, T2

U(T1, T2) = T1 U T2

Done by pouring T1 and T2 into one test tube

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DNA COMPUTING

Detect

Given a tube T, say yes if T contains at least one DNA molecule, and say no if it contains none.

Done using PCR with appropriate primers, followed by gel electrophoresis

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DNA COMPUTING

Amplify

Given a tube T, produce two tubes T’(T) and T’’(T), such that T = T’(T) = T’’(T)

Complex process, prone to error May be preferable to avoid it

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DNA COMPUTING

Polymerase Chain Reaction

PCR: One way to amplify DNA.

PCR alternates between two phases: separate DNA into single strands using heat; convert into double strands using primer and polymerase reaction.

PCR rapidly amplifies a single DNA molecule into billions of molecules

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EVOLUTION OF DNA COMPUTERS

DNA COMPUTING

Evolution of the DNA computers

Began in 1994 when Dr. Leonard Adleman wrote the paper “Molecular computation of solutions to combinatorial problems”.

He then carried out this experiment successfully – although it took him days to do so!

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DNA COMPUTING

Evolution of the DNA computers

DNA computers moved from test tubes onto gold plates.

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DNA COMPUTING

Evolution of the DNA computers

First practical DNA computer unveiled in 2002. Used in gene analysis.

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DNA COMPUTING

Evolution of the DNA computers

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.

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DNA COMPUTING

Evolution of the DNA computers

Biological computer developed that could be used to fight cancers. ‘Designer DNA’ identifies abnormal and is

attracted to it. The Designer molecule then releases chemicals to

inhibit its growth or even kill the malignant cells. Successfully tested on animals.

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DNA COMPUTING

ENVIRONMENTAL CAPABILITY

DNA computer must aim to be compatible with seven environments to succeed.

Intrapsychic – Already complies since it has been conceptualised!

Construction/manufacture – This will be answered in time.

Adoption – Should inherit customer base of silicon computers.

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DNA COMPUTING

ENVIRONMENTAL CAPABILITY

Use – Already seen the potential for this.Failure – Inherits this from silicon

microprocessors.Scrapping – Cleaner to dispose of than

current microprocessors.Political/ecological – Could face opposition

from technophobes.

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DNA COMPUTING

Advantages of DNA Computers

DNA Computing guarantees UNIVERSAL COMPUTATIONS.

There is a plenty supply and hence, it is a cheap resource.

DNA computers can be made many times smaller than today's computers

DNA computers are massively parallel in their computation.

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LIMITATIONS

DNA COMPUTING

LIMITATIONS

DNA computers are not completely accurate at this moment in time. During an operation, there is a 95% chance a particular

DNA molecule will ‘compute’ correctly. Would cause a problem with a large amount of operations.

DNA has a half-life. Solutions could dissolve away before the end result is

found.

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DNA COMPUTING

THE FUTURE!

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.

DNA computers are unlikely to feature word processing, emailing and solitaire programs.

Instead, 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.

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DNA COMPUTING

THANK YOU!

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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