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    DNA Computing (19-04-2010)

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    lukochens
    This document provides an overview of DNA computing. It begins by explaining the basic structure and properties of DNA. It then discusses the origins of DNA computing, which began in 1994 when Leonard Adleman proposed using DNA's properties for massively parallel computation. The document describes how DNA computing works by using DNA strands and enzymes to represent and process information similarly to a traditional computer. It highlights benefits like DNA's high data density and potential for massive parallelism. Finally, it discusses some applications of DNA computing and limitations that still need to be addressed.

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    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd

    DNA Computing (19-04-2010)

    Uploaded by

    lukochens
    59 views24 pages
    This document provides an overview of DNA computing. It begins by explaining the basic structure and properties of DNA. It then discusses the origins of DNA computing, which began in 1994 when Leonard Adleman proposed using DNA's properties for massively parallel computation. The document describes how DNA computing works by using DNA strands and enzymes to represent and process information similarly to a traditional computer. It highlights benefits like DNA's high data density and potential for massive parallelism. Finally, it discusses some applications of DNA computing and limitations that still need to be addressed.

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    DNA Computing(19-04-2010)

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    This document provides an overview of DNA computing. It begins by explaining the basic structure and properties of DNA. It then discusses the origins of DNA computing, which began in 1994 when Leonard Adleman proposed using DNA's properties for massively parallel computation. The document describes how DNA computing works by using DNA strands and enzymes to represent and process information similarly to a traditional computer. It highlights benefits like DNA's high data density and potential for massive parallelism. Finally, it discusses some applications of DNA computing and limitations that still need to be addressed.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    59 views24 pages

    DNA Computing (19-04-2010)

    Uploaded by

    lukochens
    This document provides an overview of DNA computing. It begins by explaining the basic structure and properties of DNA. It then discusses the origins of DNA computing, which began in 1994 when Leonard Adleman proposed using DNA's properties for massively parallel computation. The document describes how DNA computing works by using DNA strands and enzymes to represent and process information similarly to a traditional computer. It highlights benefits like DNA's high data density and potential for massive parallelism. Finally, it discusses some applications of DNA computing and limitations that still need to be addressed.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 24

    DNA Computing

    By: Libin Lukose Emmanuel


    1NH05IS020
    Fundamentals about
    DNA Structure
    ØDNA is Deoxyribo Nucleic Acid and is the building
    block of all living beings
    Ø
    ØIt is a polynucleotide and has a double helical structure
    Ø
    ØIt is made of nucleotides
    Adenine(A),Guanine(G),Thiamine(T) and Cytosine( C)
    Ø
    ØAdenine bonds only with Thiamine and Guanine bonds
    only with Cytosine
    Ø
    ØThe two helix are complimentary of each other
    Basics and Origin of DNA
    Computing
    Ø In 1994, Leonard Adleman, scientist at the university of
     California, introduced the idea of using DNA to solve
     complex mathematical problems
    Ø
    Ø Leonard Adleman proposed that the makeup of DNA
     and its multitude of possible combining nucleotides
     could have application in computational research techniques
    Ø
    Ø DNA computing is utilizing the property of DNA for massively parallel computation
    Ø
    Ø With an appropriate setup and enough DNA, one can potentially solve huge problems
    by parallel search
    Ø
    Ø Utilizing DNA for this type of computation can be much faster than utilizing a
    conventional computer

    What is DNA Computing
    Ø The field of DNA computing is concerned with the possibility of
    performing computations using biological molecules.

    Ø It is also concerned with understanding how complex biological


    molecules process information here an attempt to gain insight
    into new models of computation.
    Ø
    Ø So, DNA computer can be defined as a computer that
    “computes” using enzymes that react with DNA strands,
    causing reactions. These reactions act as a kind of
    simultaneous computing or parallel processing.
    How does it work?
    Ø Use specially coded DNA as initial conditions for biological
    reaction
    Ø
    Ø DNA is taken as software and enzymes as hardware.

    Ø Natural enzymes duplicate DNA


    Ø Matching DNA base pairs attach to each other


    Ø Find answer in resulting soup of DNA strands



    Why is it interesting?
    Ø Cross-discipline (CS meets Molecular Biology)

    Ø High data density


    Ø Massively parallel

    Ø Energy efficient

    Ø Potential to perform computation inside the body


    Dense Information
    Storage
    ØThis image shows 1 gram of DNA on a
    CD.The CD can hold 800 MB of data.
    Ø
    ØThe 1 gram of DNA can hold about 1x1014
    MB of data.
    Ø
    ØThe 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.
    Ø
    ØWith 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
    Ø
    How enormous is the
    parallelism?
    Ø 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 !
    Ø Enzymes work over many DNA molecules simultaneously
    providing DNA Parallelism.
    Ø Each DNA strand represents a processor !
    Ø
    Ø Desktop PC : 109 ops/sec
    Ø Supercomputer : 1012 ops/sec
    Ø 1 µmol of DNA : 1026 reactions…(isn’t amazing)



    How extraordinary is the
    energy efficiency?
    ØAdleman figured out that his computer was running 2 x
    1019 operations per joule.

    Inventor Of DNA
    Computing:
    Leonard Adleman
    Ø Adleman is often called the inventor of DNA computers. His
    article in a 1994 issue of the journal Science outlined how to
    use DNA to solve a well-known mathematical problem, called
    the directed Hamilton Path problem, also known as the
    "traveling salesman" problem.
    Ø
    Ø The 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. Adleman chose to find the shortest route between
    seven cities using a brute force approach.

    RAVELLING SALESMAN ALGORITHM

    A hypothetical salesman tries to find a route through a set of cities so that he


    visits each city only once

    Chicago
    Source Destination
    Los Angeles New York

    Dallas Miami

    Adleman’s Experiment
    Steps in Adleman’s
    experiment would be
    as follows:
    1)Generate all possible routes
    2)
    3)Select itineraries that start and end with the correct cities
    4)
    5)Select itineraries that contain the correct number of cities
    6)
    7)Select itineraries that have a complete set of cities
    Generate all possible
    STEP I:
    routes
    STRATEGY: 1)Encode city names in short DNA sequences.
    2)Encode itineraries by connecting the city sequence for
     which routes exist

    City Encodings

    Los Angeles GCTACG


    Chicago CTAGTA
    Dallas TCGTAC
    Miami CTACGG
    New York ATGCCG

    Synthesizing short single stranded DNA by DNA SYNTHESIZER


    G e n e ra tio n o f d iffe re n t
    Itin e ra rie s
    Route Encoding

    Miami
    C T A C G G A T G C CG
    CTA CGG
    Miami New York Miami to New York
    GC CTAC
    CGG ATG
    New York
    G C C TA C
    ATG CCG
    Hybridized DNA
    Output of Step I

    C T A G T A

    Chicago
    G C T A C G A T G C C G
    Los Angeles New York
    Source Destinatio
    n

    Dallas Miami
    T C G T A C C T A C G G
    S T E P II: Select itineraries that
    start and end with the correct
    cities
    Technique used is: POLYMERASE CHAIN REACTION (PCR)
    Allows to produce many copies of a specific sequence of DNA
    ØPolymerase Chain Reaction is iterative and uses an enzyme called polymerase
    ØPolymerase copies a section of single stranded DNA starting at the position of
    the primer, which is DNA complimentary to one end of the interested section.

    START END
    PRIMER PRIMER
    CGATGC TACGGC

    GCTACG ATGCCG
    Los Angeles New York

    Source Destination
    STEP III : Select itineraries that
    contain the correct number of
    cities
    STRATEGY: Sort the DNA by length & select the DNA whose length equals to
    five cities
    Technique used is: GEL ELECTROPHORESIS
    Used to resolve size of DNA
    + VOLTAGE
    DNA Starts here ØGel Electrophoresis force the DNA through
    a gel matrix by using an electric field.
    Ø
    ØGenerally DNA is –vely charged molecule
    Gel Matrix

    but with constant charge density.


    Ø
    Long DNA ØGEL slows down the DNA passing through
    it at different rates depending on it’s length
    producing DNA bands.

    Short DNA
    - VOLTAGE
    Select itineraries that
    STEP IV :
    have a complete set of cities
    Technique used is: AFFINITY PURIFICATION
    Uses HYBRIDIZATION of DNA

    CGATGC GATCAT AGCATG GATGCC TACGGC

    GCTACG CTAGTA TCGTAC CTACGG ATGCCG

    LA to CHICAGO to DALLAS to MIAMI to


    CHICAGO DALLAS MIAMI NEW-YORK
    ØAffinity purification is done by attaching the compliment of the sequence in question to a
    substrate like magnetic bead.
    ØThe DNA which contains the sequence hybridizes with the complement sequence on the
    beads
    ØGraduated PCR can also be used if we already have the sequence of city encodings.
    First DNA computer
    :-MAYA II
    Ø Stand for (Molecular Array of YES and AND logic gate )
    Ø Replacing the normally silicon-based circuits, this chip has DNA
    strands to form the circuit
    Ø MAYA-II has more than 100 DNA circuits

    Applications

    Ø DNA sequencing
    Ø DNA fingerprinting
    Ø DNA mutation detection
    Ø The fabrication of nanoscale objects
    Ø The replacement of silicon devices
    Ø Design of expert systems
    Ø Medical diagnosis, drug discovery
    Ø To Solve NP-Complete Problems
    LIMITATIONS
    Ø The computation time required to solve problems with a DNA computer does
    not grow exponentially, but amount of DNA required DOES.
    Ø
    Ø DNA computing involves a relatively large amount of error
    Ø
    Ø High cost is time.
    Ø
    Ø Different problems need different approaches.
    Ø
    Ø Requires human assistance!
    Ø
    Ø No efficient implementation has been produced for testing, verification and
    general experimentation

    THE FUTURE!
    Ø Algorithm used by Adleman for the traveling salesman problem was simple.
    As technology becomes more refined, more efficient algorithms may be
    discovered.
    Ø
    Ø DNA Manipulation technology has rapidly improved in recent years, and
    future advances may make DNA computers more efficient.
    Ø
    Ø The University of Wisconsin is experimenting with chip-based DNA
    computers.
    Ø
    Ø DNA computers are unlikely to feature word processing, emailing and
    solitaire programs.
    Ø
    Ø 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.

    Conclusion
    ØThe paradigm of DNA computing has lead to a very important theoretical
    research.
    Ø
    ØThe beauty of DNA research trends is found in the possibility of mankind’s
    utilization of its very life building blocks to solve its most difficult problems.
    Ø
    Ø
    ØThe field of DNA computing is still in its infancy and the applications for this
    technology are still not fully understood.
    Ø
    ØIs DNA computing viable – perhaps, but the obstacles that face the field such as
    the extrapolation and practical computational environments required are daunting.

    Queries?

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