Dna Computing

DNA COMPUTING

DNA COMPUTINGSwati BandhewalCSE 2nd yrGS10UE0409

1OverviewIntroduction to DNAWhat is DNA computingAdlemans Hamiltonian path problem.Cutting Edge TechnologiesPros and ConsDNA Vs Electronic ComputersConclusionWhat is DNA?DNA stands for Deoxyribonucleic AcidDNA represents the genetic blueprint of living creaturesDNA contains instructions for assembling cellsEvery cell in human body has a complete set of DNADNA is unique for each individualDouble HelixSidesSugar-phosphate backbonesladderscomplementary base pairsAdenine & ThymineGuanine & CytosineTwo strands are held together by weak hydrogen bonds between the complementary base pairs

Uniqueness of DNAWhy is DNA a Unique Computational Element???

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

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.

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

Instructions in DNAInstructions are coded in a sequence of the DNA basesA segment of DNA is exposed, transcribed and translated to carry out instructionsSequence to indicate the start of an instructionInstruction that triggersHormone injectionInstruction for hair cellsA Little MoreBasic suite of operations: AND,OR,NOT & NOR in CPU while cutting, linking, pasting, amplifying and many others in DNA.

Complementarity makes DNA unique.

Can DNA compute?DNA itself does not carry out any computation. It rather acts as a massive memory.BUT, the way complementary bases react with each other can be used to compute things. Proposed by Adelman in 1994DNA COMPUTINGAcomputerthat uses DNA (deoxyribonucleic acids) to store information and perform complex calculations.The main benefit of using DNA computers to solve complex problems is that different possible solutions are created all at once. This is known asparallel processing.

Adlemans ExperimentHamilton Path Problem(also known as the travelling salesperson problem)PerthDarwinBrisbaneSydneyMelbourneAlice SpringIs there any Hamiltonian path from Darwin to Alice Spring?Adlemans Experiment Solution by inspection is:Darwin Brisbane Sydney Melbourne Perth Alice Spring BUT, there is no deterministic solution to this problem, i.e. we must check all possible combinations.PerthDarwinBrisbaneSydneyMelbourneAlice SpringAdlemans ExperimentEncode each city with complementary base - vertex moleculesSydney - TTAAGGPerth - AAAGGGMelbourne - GATACTBrisbane - CGGTGCAlice Spring CGTCCADarwin - CCGATGAdlemans Experiment (Contd)Encode all possible paths using the complementary base edge moleculesSydney Melbourne AGGGATMelbourne Sydney ACTTTAMelbourne Perth ACTGGGetcAdlemans Experiment (Contd)Merge vertex molecules and edge molecules. All complementary base will adhere to each other to form a long chains of DNA moleculesSolution with vertex DNA molecules Solution with edge DNA moleculesMerge& AnnealLong chains of DNA molecules (All possible paths exist in the graph)Adlemans Experiment (Contd)The solution is a double helix molecule:CCGATG CGGTGC TTAAGG GATACT AAAGGG CGTCCA

TACGCC ACGAAT TCCCTA TGATTT CCCGCA DarwinBrisbaneSydneyMelbournePerthAlice SpringDarwinBrisbaneBrisbaneSydneySydneyMelbourneMelbournePerthPerthAlice SpringOperations (Contd)Mergingmixing two test tubes with many DNA moleculesAmplificationDNA replication to make many copies of the original DNA moleculesSelectionelimination of errors (e.g. mutations) and selection of correct DNA moleculesTHE 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.

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.DNA Chip

Chemical IC

23The Smallest ComputerThe smallest programmable DNA computer was developed at Weizmann Institute in Israel by Prof. Ehud Shapiro last yearIt uses enzymes as a program that processes on 0n the input data (DNA molecules).

Pros and ConsMassively parallel processorDNA computers are very good to solve Non-deterministic Polynomial problems such as DNA analysis and code cracking.Small in size and power consumptionPros and Cons (Contd)Requires constant supply of proteins and enzymes which are expensiveErrors occur frequentlya complex selection mechanism is required and errors increase the amount of DNA solutions needed to computeApplication specificManual intervention by human is requiredDNA Vs Electronic computersAt Present, NOT competitive with the state-of-the-art algorithms on electronic computersOnly small instances of HDPP can be solved. Reason?..for n vertices, we require 2^n molecules.Time consuming laboratory procedures.Good computer programs that can solve HSP for 100 vertices in a matter of minutes.No universal method of data representation.

ConclusionMany issues to be overcome to produce a useful DNA computer.It will not replace the current computers because it is application specific, but has a potential to replace the high-end research oriented computers in future.

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