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Advantages of DNA Computing

This document discusses DNA computing models. It begins with an introduction and overview of biological preliminaries about DNA. It then explains several models of DNA computing including Adleman's model, splicing systems, insertion-deletion systems, and DNA-EC. Each model is summarized with examples. The document concludes by discussing advantages of DNA computing such as high speed, energy efficiency, and low error rates.

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Otty Naveen Rao
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22 views19 pages

Advantages of DNA Computing

This document discusses DNA computing models. It begins with an introduction and overview of biological preliminaries about DNA. It then explains several models of DNA computing including Adleman's model, splicing systems, insertion-deletion systems, and DNA-EC. Each model is summarized with examples. The document concludes by discussing advantages of DNA computing such as high speed, energy efficiency, and low error rates.

Uploaded by

Otty Naveen Rao
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPT, PDF, TXT or read online on Scribd

Jyoti prava Badajena

Roll:218L01
Computer Science & Engg.

1
TOPICS OF PRESENTATION
 Introduction.
 Biological preliminaries.
 Models of DNA computing.
 Adleman’s model.
 splicing systems.
 Insertion-Deletion systems.
 DNA-EC.
 Advantages.
 Conclusion.
 References.

2
Introduction
 DNAcomputer is a nanocomputer that
usesDNA (Deoxy ribo nucleic acids)to
store informations and to perform
complex calculations.

3
Biological preliminaries
 DNA is a basic substance where the genetic
informations of all the livingbeings are
recorded.
 A Double helix molecule of DNA is a double
sequence of units called nucleotides.
 Four types of nucleotides differ in their
chemical groups called base ( A,G,T,C ) .
 complementary : A bonds only with T and G
bonds only with C during annealing.

4
DNA:A UNIQUE DATA
STRUCTURE
 The bases are spaced every 0.35
nanometers along the DNA molecule,
giving DNA an remarkable data density
of nearly 18 Mbits per inch.
 In double stranded DNA ,data is
mirrored on two drives, allowing data to
be recovered from the second drive if
errors occur on the first.
5
 Models of DNA computing

 Adleman’s
. model.
 Insertion-Deletion systems.
 splicing systems.
 DNA-EC.

6
Adleman’s Model

 The first DNA computing model


sucessfully realized practically was
presented by Adleman in 1994.
 Gives solution to Hamiltonioan path
problem.

7
ALGORITHM
 Algorithm used by Adleman to solve the
problem:
 Given a graph G=(V,E)with n vertices and
two vertices Vin & Vout € V.
 Generate random paths through G.
 Keep only those paths that begins with Vin
and ends in Vout.
 Keep only those paths that only enters n
vertices.

8
ALGORITHM
 Keep only those paths that enter each
vertex atleast once .
 If any paths remain, the answer is “yes”
otherwise “no”.

9
SPLICING SYSTEMS
 In 1987 Head introduced the splicing systems
to analyze the generative capcity of the
recombinant behaviour of DNA.
 Splicing rule is a word in the form of
a#b$c#d.
where a,b,c,d €E*,
E*is generated by E consisting of all
sequences obtained by catenating the letters
of E.

10
 E is a finite nonempty set.
 Splicing->If we splice words X and Y
according to rule r both X and Y are cut
in the place determined by r,first part of
X will be merged with end parts of y
and similarly the other parts.

11
 Example:
(X,Y) ->(Z,W)
if X=X’abX’’ Z=X’adX’’
Y=Y’cdY’’ W=Y’cbY’’
for some X and y.

12
INS-DEL SYSTEM
 In 1996 Kari and Thierrin introduced the
insertion-deletion system as a model of DNA.
 Insertion:
u<-(x,y)v ={u1xvyu2|
u=u1xyu2,u1,u2€E*}

 Deletion:
u->(x,y)v ={u1xyu2|
u1,u2€E*,u1xvyu2}

13
DNA-EC
 This model was proposed by Yokomori and
kobyaschi.
 It is based on equality checking.

 It performs two test operations .

 Emptiness test(EM):return “yes” if T

contains a string and “no” otherwise.


 Equivalence test(EQ):return ”yes” if I(t)

contains a double stranded string else


“no”.

14
 Where T denotes a test tube containing
a set of strings fixed over alphabet and
I(T) be its containts.

15
 Set operations:
 Union: T’UT’’ I(T’) U I(T’’)
 Left cut: T=a\T’ I(T)={U|au€I(T’)}
 Left adding: T=aT’ I(T’)={a}I(T’)
 Right adding:T=T’a I(T’)=I(T’){a}

16
ADVANTAGES
 High speed.
 Energy efficiency.
 Economic information storing.
 Low rate of occurrence of error.

17
ADVANTAGES

18
ADVANTAGES

19

Common questions

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DNA provides remarkable data density, allowing for storage of nearly 18 Mbits per inch, and it mirrors data on two strands, enabling error recovery if one strand is compromised . Additionally, DNA computing benefits from high speed, energy efficiency, economic information storage, and a low rate of errors .

DNA computing offers superior energy efficiency and a lower error rate compared to traditional electronic computing. This efficiency arises from DNA’s natural propensity for vast and complex computations with minimal energy input, and its double-stranded nature allows for inherent error correction . These features contribute to its potential as a sustainable alternative for future computing applications .

Complementary base pairing ensures the integrity of DNA's structure by allowing A to bond only with T and G with C. This specificity locks the two strands together in a double helix, enabling reliable data mirroring and error correction capabilities inherent in DNA, thereby maintaining biological and computational data integrity .

Adleman's model solves the Hamiltonian path problem by generating random paths through a graph, retaining only those paths that start from a specific vertex and end at another, visiting each vertex once. The algorithm involves several filtering steps: retaining paths that start and end on defined vertices, ensuring paths enter exactly n vertices, and ensuring each vertex is visited .

Insertion-Deletion systems, introduced by Kari and Thierrin, manipulate sequences by adding or removing segments. In insertion, a particular segment is inserted between sequences in a word, while in deletion, specific segments are removed from sequences . For instance, inserting a segment (x,y) transforms u to u1xvyu2, while deleting (x,y) results in u1xyu2, altering the sequence structures .

The Insertion-Deletion model focuses on specifically inserting or removing segments in sequences, contrasting with splicing systems that recombine DNA segments based on pre-defined rules. While splicing relies on cutting at designated sites to recombine DNA, insertion-deletion directly alters sequence structures, allowing more granular manipulation of DNA .

Splicing systems, introduced by Head, are based on the recombination behavior of DNA. They use splicing rules in the form a#b$c#d to cut and recombine DNA sequences. The operation on words (X,Y) using such rules results in the formation of new words (Z,W) by merging cut segments as prescribed by the rule . For instance, using rule r, words X and Y are cut and recombined into Z and W, respectively .

Test tube operations such as union, left cut, left adding, and right adding facilitate complex data manipulations in DNA computing. These operations allow the combination and modification of DNA sequences in a controlled environment, enabling a versatile platform for various computational tasks like data processing and logical implementations . They extend DNA computing models' functionality by offering a set-oriented approach to handle DNA strings .

The DNA-EC model focuses on equivalence and emptiness testing of DNA strands. It performs an emptiness test (EM) to check if a test tube contains any strings, returning 'yes' if it does, and an equivalence test (EQ) to determine if the contents form a double-stranded string . These operations enhance DNA computing by establishing conditions and outcomes based on the structural integrity and organization of DNA contents .

While DNA computing offers multiple advantages, potential limitations include challenges in processing speed compared to electronic computers for certain tasks and the complexity in programming and interpreting biological systems. Other concerns involve the scalability of DNA manipulation and ethical considerations surrounding genetic materials .

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