DNA computingBY ARUNITA BANERJI

What is DNA? Deoxyribo-neuclic-acid

Double stranded helix of nucleotides

Long polymers of millions of linked nucleotides

DNA is encoded with four bases :

A = Adenine

T = Thymine

G = Guanine

C = Cytosine

These bases are like 0’s and 1’s used in Silicon Computers.

Complements

Complement of AGGCT :

TCCGA

Complement of TAGGA :

ATCCT

Complement of GATTACCA :

CTAATGGT

Interesting facts

• DNA MOLECULE IS 1.7 METERS LONG

• STRETCH OUT ALL THE DNA IN YOUR CELLS AND YOU CAN REACH THE MOON 6000 TIMES!

Conception

Moore’s Law states that silicon microprocessors double in complexity roughly every two years.

Miniaturisation is reaching its limits

Intel scientists say it will happen in about the year 2018.

Require a successor to silicon.

DNA Computing

Around 1950 first idea (Precursor Feynman)

First important experiment 1994: Leonard Adleman

In only 5 grams of DNA we get around 1021 bases !

Each DNA strand represents a processor

Why DNA Computing?

To overcome the following conventional computing problem:

Limit of miniaturization

Particular range of speed

Why DNA computing?

High information density

1 bit can be stored in approximately one cubic nanometer. Others storage media, such as videotapes, can store 1 bit in 1,000,000,000,000 cubic nanometer.

Operations on DNA are massively parallel:

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.

DNA : Parallelism

Enzymes do not function sequentially over DNA.

Many copies of Enzymes can work on many DNA molecules simultaneously.

What is parallel computing? 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

Storage density

One gram of DNA can hold 1x1014 MB of data

Specifications

One pound of DNA can store more information

One cm3 of DNA can hold approx 10TB of data

DNA computer the size of a teardrop more powerful than supercomputer

Evolution of the DNA computer

First practical DNA computer unveiled in 2002. Used in gene analysis.MAYA-II ( Molecular Array of YES

and AND logic gate )

MAYA–Il has more than loo DNA circuits

Evolution of the DNA computer

• Self-powered DNA computer unveiled in 2003 by Ehud Shapiro

• First programmable autonomous computing machine in which the input, output, software and hardware were all made of DNA molecules

o Can perform 330 trillion operation/sec

o Can perform a billion operations per second with 99.8% accuracy.

“This re-designed device uses its DNA input as its source of fuel," said Ehud Shapiro, who led the Israeli research team

Evolution of the DNA computer

• Biological computer developed that could be used to fight cancers.

o ‘Designer DNA’ identifies abnormal and is attracted to it.

o The Designer molecule then releases chemicals to inhibit its growth or even kill the malignant cells.

o Successfully tested on animals.

Advantages of DNA computers

• There is always a plentiful supply of it.

• It is a cheap resource.

• DNA biochips can be made cleanly

• “Doctors in Cells”

• DNA computers are massively parallel in their computation.

o Solutions that would otherwise take months to compute could be found in hours.

o Excellent for NP problems such as the Travelling Salesman problem.

Doctors in cells

Travelling salesman problem

Each city is treated as a node

Encode city names in short DNA sequences. Encode path by connecting the city sequence for which routes exist which routes exist.

Chicago

New York

MiamiDallas

Los Angeles

Los Angeles

GCTACG

Chicago CTAGTA

Dallas TCGTAC

Miami CTACGG

New York ATGCCG

MiamiCTAGG

New YorkATGCCG

Miami To New YorkGCCTAC

MiamiCTAGG

New YorkATGCCG

Miami to New YorkGCCTAC

Los Angeles GCTACG

Chicago CTAGTA

Dallas TCGTAC

Miami CTACGG

New York ATGCCG

City Encoding

Route encoding

Hybridised encoding

DNA computer v/s conventional computer

DNA BASED COMPUTING SILICON BASED COMPUTING

Slow at individual operations Fast at individual operations

Can do billion operations simultaneously

Can do fewer operations simultaneously

Can provide huge memory in small space

Smaller memory

Setting up a problem may involve considerable preparations

Setting up of a requires keyword input

DNA is sensitive to chemical deterioration

Electronic data are vulnerable but can be backed up easily

Current problems with the DNA computer

• Not completely accurate at this moment in time• During an operation, there is a 95% chance a particular

DNA molecule will ‘compute’ correctly

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

found.

Conclusion

DNA computers showing enormous potential, especially for medical purposes as well as data processing applications.

Still a lot of work and resources required to develop it into a fully fledged product.

THANKS