Biological Computers

“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).

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

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.

AdlemanInventor 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

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

Adleman’s Experiment (continued…) • Encode all possible paths using the complementary base – edge molecules Sydney  Melbourne – AGGGAT Melbourne  Sydney – ACTTTA Melbourne  Perth – ACTGGG etc…

Adleman’s Experiment (continued…) • Merge vertex molecules and edge molecules. All complementary base will adhere to each other to form a long chains of DNA molecules Solution with vertex DNA molecules

Merge & Anneal

Solution with edge DNA molecules

Long chains of DNA molecules (All possible paths exist in the graph)

Adleman’s Experiment (continued…) • 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.

Adleman’s Experiment (continued…) • 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

Brisbane Sydney

Sydney Melbourne

Melbourne Perth Alice Spring Perth

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

Conventional vs. Biological Computers Conventional

Biological

Component materials

Inorganic, e.g. silicon

Biological, e.g. DNA

Processing scheme

Sequential and limited massively parallel

Massively parallel

Current max. operations

1012 Op.s per sec.

1014 Op.s per sec.

Quantum effects a problem?

Yes

No

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