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DNA Computing

DNA computing uses DNA molecules to store and process information in a massively parallel manner. Leonard Adleman demonstrated the first DNA computing experiment in 1994 by solving a Hamiltonian path problem. DNA computing encodes information using the complementarity of DNA base pairs and massive parallelism to evaluate all possibilities simultaneously. However, DNA computing faces significant engineering challenges and has not yet found applications that could drive development of DNA-based computers for real-world use.

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238 views18 pages

DNA Computing

DNA computing uses DNA molecules to store and process information in a massively parallel manner. Leonard Adleman demonstrated the first DNA computing experiment in 1994 by solving a Hamiltonian path problem. DNA computing encodes information using the complementarity of DNA base pairs and massive parallelism to evaluate all possibilities simultaneously. However, DNA computing faces significant engineering challenges and has not yet found applications that could drive development of DNA-based computers for real-world use.

Uploaded by

arpit_7228
Copyright
© Attribution Non-Commercial (BY-NC)
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DNA Computing

By Thierry Metais
Email: [email protected]
Introduction to DNA:
 The life’s molecule:
Introduction:
 What is DNA computing ?
 Around 1950 first idea (precursor Feynman)
 First important experiment 1994: Leonard Adleman

 Molecular level (just greater than 10-9 meter)


 Massive parallelism.
 In a liter of water, with only 5 grams of DNA we get
around 1021 bases !
 Each DNA strand represents a processor !
A bit of biology
 The DNA is a double stranded molecule.
 Each strand is based on 4 bases:
 Adenine (A)
 Thymine (T)
 Cytosine (C)
 Guanine (G)
 Those bases are linked through a sugar
(desoxyribose)
 IMPORTANT:
 The linkage between bases has a direction.
 There are complementarities between bases (Watson-
Crick).
(A) (T)
(C)(G)
DNA manipulations:
 If we want to use DNA as an information bulk, we must
be able to manipulate it .
 However we are talking of handling molecules…
 ENZYMES = Natural CATALYSERS.
 So instead of using physical processes, we would have
to use natural ones, more effective:
 for lengthening: polymerases…
 for cutting: nucleases (exo/endo-nucleases)…
 for linking: ligases…
 Serialization: 1985: Kary Mullis  PCR
Thank this reaction we get millions of identical strands, and we are
allowed to think of massive parallel computing.
And what now ?
 Situation:
 Molecular level.
 Lots of “agents”. (strands)

 Tools provided by nature. (enzymes)

 How can we use all this? If there is a


utility …
Coding the information:
 1994: THE Adleman’s experiment.
 Given a directed graph can we find an
hamiltonian path (more complex than the
TSP).
 In this experiment there are 2 keywords:
massive parallelism (all possibilities are generated)
complementarity (to encode the information)
 This experiment proved that DNA computing wasn’t just a theoretical
study but could be applied to real problems like cryptanalysis
(breaking DES ).
Adleman experiment:
 Each node is coded randomly with 20 bases.
 Let Si be a code, h be the complementarity mapping.
h(ATCG) = TAGC.
 Each Si is decomposed into 2 sub strands of length 10:
Si = Si’ Si’’
 Edge(i,j) will be encode as h(Si’’Sj’)( preserve edge
orientation).
 Code:
 Input(N) //All vertices and edges are mixed, Nature is working
 NB(N,S0) //S0 was chosen as input vertice.
 NE(N,S4) //S4 was chosen as output vertice.
 NE(N,<=140) // due to the size of the coding.
 For i=1 to 5 do N+N(N, Si) //Testing if hamiltonian path
 Detect(N) //conclusion …
Exampl
e: 0
1

5 2

3
4

S0 S2 S5 S3 S1 S4 S6
E0-2 E2-5 E5-3 E3-1 E1-4 E4-6
New generation of
computers?
 In the second part of [1], it is proven
through language theory that DNA
computing “guarantees universal
computations”.
 Many architectures have been invented for
DNA computations.
 The Adleman experiment is not the single
application case of DNA computing…
Stickers model:
 Memory complex = Strand of DNA (single or
semi-double).
 Stickers are segments of DNA, that are
composed of a certain number of DNA
bases.
 To use correctly the stickers model, each
sticker must be able to anneal only at a
specific place in the memory complex.
To visualize:

0 0 0 1 0 1 0 0 1 0
Memory complex:
Semi-double

Soup of stickers:

=
A G C A T G A T

Zoom
About a stickers machine?

 Simple operations: merge, select, detect, clean.


  Tubes are considered (cylinders with two entries)
 However for a mere computation (DES):
 Great number of tubes is needed (1000).
 Huge amount of DNA needed as well.

 Practically no such machine has been created….


 Too much engineering issues.
Why don’t we see DNA
computers everywhere?
 DNA computing has wonderful
possibilities:
 Reducing the time of computations*
(parallelism)
 Dynamic programming !

 However one important issue is to


find “the killer application”.
 Great hurdles to overcome…
Some hurdles:

 Operations done manually in the


lab.
 Natural tools are what they are…
Formation of a library (statistic way)
Operations problems
Conclusion:
 The paradigm of DNA computing has lead
to a very important theoretical research.
 However DNA computers won’t flourish
soon in our daily environment due to the
technologic issues.
 Adleman renouncement toward electronic
computing.
 Is all this work lost ?
 NO !  “Wet computing”
Bibliography:
 DNA Computing, New Computing
Paradigms. Gheorghe Paun,Grzegorz
Rozenberg, Arto Salomaa
 DIMACS: DNA based computers
 Reducing Errors in DNA Computing
by Appropriate Word Design.
wdesign.pdf
Links:
 http://www.cs.wayne.edu/~kjz/KPZ/Natur
http://www.cs.wayne.edu/~kjz/KPZ/Natu
 http://dna2z.com/dnacpu/dna.html
 http://www.intermonde.net/adn/liens.htm

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