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Dna Computing: A Presentation by Anirban Mitra Anjali Singh Neha Mazumder Sikha Choubey Suman Majumder

DNA computing uses DNA molecules to store and process information in a massively parallel manner. Leonard Adleman demonstrated the potential of DNA computing in 1994 by using DNA strands to solve an instance of the Hamiltonian Path Problem (HHP) involving 7 vertices. While DNA computing shows promise for extremely dense information storage and efficient energy usage, it currently has limitations such as high error rates, small problem sizes, and lengthy laboratory procedures that prevent it from competing with electronic computers for most tasks. Further research is still needed but DNA computing may be applicable in specialized domains like encryption or genetic programming in the future.

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73 views28 pages

Dna Computing: A Presentation by Anirban Mitra Anjali Singh Neha Mazumder Sikha Choubey Suman Majumder

DNA computing uses DNA molecules to store and process information in a massively parallel manner. Leonard Adleman demonstrated the potential of DNA computing in 1994 by using DNA strands to solve an instance of the Hamiltonian Path Problem (HHP) involving 7 vertices. While DNA computing shows promise for extremely dense information storage and efficient energy usage, it currently has limitations such as high error rates, small problem sizes, and lengthy laboratory procedures that prevent it from competing with electronic computers for most tasks. Further research is still needed but DNA computing may be applicable in specialized domains like encryption or genetic programming in the future.

Uploaded by

Anirban Mitra
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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DNA presentation by A COMPUTING

Anirban Mitra Anjali Singh Neha Mazumder Sikha Choubey Suman Majumder

Introduction
The search is on for the next generation of microprocessors. And its within us. Computation using not computation on DNA. DNA but

Initiated in 1994 by an article written Adleman on solving HDPP using DNA.

by

What is DNA ?
Nucleic acid that contains coded genetic information in the form of base pair sequence. Double helix structure proposed by Watson & Crick. Length of strand measured in number of base pairs.

DNA Structure
There are two antiparallel strands made up of 2deoxyribose, a pentose sugar, connected by phosphodiester bonds. The two strands are connected by AdenineThymine or GuanineCytosine base pairs. These base pairs are connected internally by Hbonds.

Why DNA ?
DNA is a unique computational element Extremely dense information storage. Massive parallelism. Extraordinary energy efficiency.

Dense Information Storage


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

How Dense is the Information 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.

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.

How extraordinary is the energy efficiency?


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

Extraction of DNA

Formation strands.

of

DNA Precipitation of more DNA strands in alcohol

Spooling the DNA with a metal hook or similar device

Adlemans solution of the Hamiltonian Directed Path Problem

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

The Problem
A directed graph G=(V,E) |V|=n, |E|=m and two distinguished vertices Vin = s and Vout= t Verify whether there is a path (s,v1,v2,.,t)
Which is a sequence of one-way edges that begins in Vin and Vout Whose length (in number of edges) is n-1 (i.e. enters all vertices) Whose vertices are all distinct (i.e. enters every vertex exactly once)

This problem is NP Complete

Example
2 A directed graph A Hamiltonian path is (S,2,4,6,3,5,T) Here Vin = S and Vout = T S 4 T 6

Why not brute force algorithm?


Brute force algorithm is to Generate all possible paths with exactly n-1 edges. Verify whether one of them obeys the problem constraints. Problem: nCr i.e. (n-2)! number of paths need to be examined. So, what did Adleman use? Generate and test strategy where a number of random paths were generated and tested.

Adlemans Experiment
DNA molecules are used to solve HDPP. Random path generation allows each path to be generated independent of all others thus allowing parallelism. No. of Lab procedures grows linearly with the no. of vertices in the graph. Linear no. of lab procedures is due to the fact that an exponential no. of operations is done in parallel. At the heart, it is a brute force algorithm executing an exponential number of operations.

Algorithm (non-deterministic)
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.

Discover magazine published an article in comic strip format about Leonard Adleman's discovery of DNA computation.

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. Only that which happens within the boundaries of 3 dimensional world are counted which involves a lot of probability. Errors take place during the manipulation of DNA strands. Most dangerous operations: The operation of Extraction. Undesired annealings.

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, since for n vertices, we require 2n molecules. Time consuming laboratory procedures. Good computer programs that can solve Travelling Salesman Problem for 100 vertices in a matter of minutes. No universal method of data representation.

Size restrictions
Adlemans process to solve the traveling salesman problem for 200 cities would require an amount of DNA that weighed more than the Earth. The computation time required to solve problems with a DNA computer does not grow exponentially, but amount of DNA required does.

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.

Hidden factors affecting complexity


There may be hidden factors that affect the time and space complexity of DNA algorithms with underestimating complexity by as much as a polynomial factor because: They allow arbitrary number of test tubes to be poured together in a single operation. Unrealistic assessment of how reactant concentrations scale with problem size.

The Future of DNA Computing


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 chipbased DNA computers.

The Future of DNA Computing contd


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.

Related Technologies
Biocomputers - Uses a developing field called nanobiotechnology and has further given rise to the following
Biochemical Computers Biomechanical Computers Bioelectronic Computers

Moletronics - Involves the study and application of molecular building blocks for the fabrication of electronic components.

Related Technologies contd


Peptide Computing - A form of computing which uses peptides and molecular biology, instead of traditional silicon-based computer technologies. Wetware Computer - An organic computer (also known as an artificial organic brain or a neurocomputer) built from living neurons.

Conclusion
Popularity and ever decreasing costs of silicon based computer technology. Much more research is required before a commercial DNA Computer is feasible. Once it can be built, the savings in time and power will be phenomenal. DNA Computers have the potential of powering the computationally hungry future, affected by scarcity of power and raw materials that we now face.

Thank You

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