Note : (Cover Page)

Technical Seminar Report On

DNA COMPUTING
Submitted in partial fulfillment of the Requirements for the award of the degree of

Bachelor of Technology In Computer Science & Engineering

By

N.Manasa Reddy 08M51A0564

T h e P a th o f S u c c e ss

Department of Computer Science & Engineering

RRS COLLEGE OF ENGINEERING & TECHNOLOGY
(Affiliated to Jawaharlal Nehru Technological University, Hyderabad) Muthangi (V), Patancheru (Mdl), Medak (Dist) -502300.

Technical Seminar Report ON

DNA COMPUTING
Submitted in partial fulfillment of the Requirements for the award of the degree of

Bachelor of Technology In Computer Science & Engineering

By

N.Manasa Reddy
08M51A0564
Under The Guidance of Mr. B.Ravi Prasad Assistant professor

T h e P a th o f S u cc e s s

Department of Computer Science & Engineering

RRS COLLEGE OF ENGINEERING & TECHNOLOGY
(Affiliated to Jawaharlal Nehru Technological University, Hyderabad)

Muthangi (V), Patancheru (Mdl), Medak (Dist) -502300.

Department of Computer Science & Engineering

RRS COLLEGE OF ENGINEERING & TECHNOLOGY
(Affiliated to Jawaharlal Nehru Technological University, Hyderabad) Muthangi (Vill), Patancheru (Mdl), Medak (Dist) -502300.
T h e P a th o f S u c c e ss

CERTIFICATE
This is to certify that the technical seminar entitled DNA COMPUTING has been presented by N.Manasa Reddy(08M51A0564) in partial fulfillment of the requirements for the award of degree of Bachelor of Technology in Computer Science and Engineering from Jawaharlal Nehru Technological University, Hyderabad.

GUIDE

HEAD OF THE DEPARTMENT

Mr.B.Ravi Prasa
Assistant Professor

Prof. K.Nagi Reddy

ABSTRACT
Silicon microprocessors have been the heart of computing world for more than forty years. Computer chip manufacturers are furiously racing to make the next microprocessor that will topple speed records and in the process are cramming more and more electronic devices onto the microprocessor. Sooner or later the physical speed and miniaturization limits of silicon microprocessors are bound to hit a wall. Chipmakers need a new material to produce faster computing speed with fewer complexities. You wont believe where scientists have found this new material. DNA, the material our genes are made of, is being used to build the next generation of microprocessors. Scientists are using this genetic material to create nano-computers that might take the place of silicon computers in the next decade. A nascent technology that uses DNA molecules to build computers that are faster than the worlds most powerful human-built computers is called DNA computing. Molecular biologists are beginning to unravel the information processing tools such as enzymes, copying tools, proofreading mechanisms and so on, that evolution has spent millions of years refining. Now we are taking those tools in large numbers molecules and using them as biological computer processors. DNA computing has a great deal of advantage over conventional silicon-based computing. DNA computers can store billions of times more data than your personal computer. DNA computers have the ability to work in a massively parallel fashion, performing many calculations simultaneously. DNA molecules that provide the input can also provide all the necessary operational energy. DNA computing has made a remarkable progress in almost every field. It has found application in fields like biomedical, pharmaceutical, information security, cracking secret codes, etc. Scientists and researchers believe that in the foreseeable future DNA computing could scale up to great heights!

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CONTENTS
Certificate Abstract 1. Introduction 2. Literature survey 3. Title Description 4. Conclusion Bibliography i ii 1 2 3 11

INTRODUCTION
DNA computing, also known as molecular computing, is a new approach to massively parallel computation based on groundbreaking work by Adleman. In November of 1994, Dr. Leonard Adleman wrote the first paper on DNA computing. In this paper, he found a way to solve the "Hamiltonian path problem," which involves finding all the possible paths between a certain number of vertices. It is also known as the "traveling salesman problem." This name comes from viewing each vertex as a city, with the problem to find all possible routes for a salesman passing through each of these cities. Computers today all use binary codes - 1's and 0's or one's and off's. These codes are the basis for all possible calculations a computer is able to perform. Because the DNA molecule is also a code, Adleman saw the possibility of employing DNA as a molecular computer. However, rather than relying in the position of electronic switches in a microchip, Adleman relied on the much faster reactions of DNA nucleotides binding with their complements, a brute force method that would indeed work. A DNA computer is a collection of DNA strands that have been specially selected to aid in the search of solutions for some problems. DNA computing results in parallelism, which means that when enough DNA information is given, huge problems can be solved by invoking a parallel search. In DNA Computing, the input data is encoded as DNA sequences which are transformed by means of a series of biochemical operations (taking place in a test tube) into a certain form that represents the output of the computation. DNA Computing is interesting for the following reasons:

The (DNA) computer uses unusually small processing elements.

The computer knows things that are not even programmed.

LITERATURE SURVEY
The aim of this report is to make a review on DNA computing: molecular biology is used to suggest a new way of solving a NP-complete problem. The idea (due to Leonard Adleman in [Adl94]) is to use strands of DNA to encode the (instance of the) problem, and to manipulate them using techniques commonly available in any molecular biology laboratory, in order to simulate operations that select the solution of the problem, if it exists. After Adleman''s paper (appeared on "Science" in November 1994), many authors have been interested in DNA computing. We will try to give a description of the discussions and the results which appeared in literature. Currently, at the University of Wisconsin, a research team is looking into DNA computing. The university team created a crude molecular computer "chip" made of a small glass plate covered with a thin layer of gold. Strands of DNA were coded to represent solutions to a computational problem with 16 possible answers. Then, enzymes were applied to the gold slide to strip out all the DNA with the incorrect answers and, and thus, solving the calculation. "It opens up the possibility of ultrahigh-capacity storage and massively parallel searches," explains Robert Corn, a professor of chemistry and a member of the research team. A DNA computer the size of a penny, for example, could hold up to 10 terabytes of data, far exceeding the capacity of any computer storage medium available today.

TITLE DESCRIPTION
Adlemans Experiment:
The field of DNA computing is generally considered to have begun with Leonard Adleman's 1994 experiment involving the Hamiltonian Path (HP) problem. Simply stated, the HP problem is to determine whether or not a graph, with fixed starting and ending vertices, has some sequence of steps by which every vertex in the graph is visited exactly once. Formally, an instance of HP takes the form (V, E, s, d), where V and E are the sets of vertices and edges that define the graph's topology and s and d are the start and destination vertices. Adleman found a DNA algorithm by which one could determine, in linear time, whether or not such an instance belonged to HP (membership meaning that there is some path satisfying the criteria above). The choice of this problem is rather important in light of the fact that HP is known to be NP-complete, which is to say that any problem whose solution can be verified in polynomial time may be reduced to HP by some polynomial time algorithm. This is a truly remarkable result, as it shows that all problems in NP can be solved, by reduction, in polynomial time (due mostly to the reduction) by a DNA-based computer.

Adleman's algorithm:
1. Generate random paths through the graph 2. Remove those paths that begin with vertices other than s and those that end with vertices other than d. 3. Remove those paths that visit a number of vertices unequal to the size of the set V. 4. Remove those paths that visit some vertex more than once. (Note: this is the step that makes the overall algorithm execute in linear time. This step is a 3

loop, executed once for each vertex, whose body goes about removing paths that contain that vertex more than once.) 5. If there are any paths left, answer "yes," otherwise "no."

Is there any Hamiltonian path from Darwin to Alice Spring?

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.

1.Encode each city with complementary base - vertex molecules Sydney - TTAAGG Perth - AAAGGG Melbourne - GATACT Brisbane - CGGTGC Alice Spring CGTCCA Darwin - CCGATG 2. Encode all possible paths using the complementary base edge molecules Sydney Melbourne AGGGAT Melbourne Sydney ACTTTA Melbourne Perth ACTGGG etc 3. Marge vertex molecules and edge molecules. All complementary base will adhere to each other to form a long chains of DNA molecules

Long chains of DNA molecules (All possible paths exist in the graph)

The solution is a double helix molecule

OPERATIONS ON DNA
1. Merge - This is the simple operation of combining the contents of two test tubes in a third tube. 2. Anneal - This is the process by which complementary strands of DNA are paired to form the famous double-helix structure of Watson and Crick. Annealing is achieved by cooling a DNA solution, which encourages pairing. Adleman uses this in step 1 to generate all legal paths through the graph. 3. Melt - Melting is the inverse operation of annealing. By heating the contents of a tube, double-stranded DNA sequences are denatured, or separated into its two single-stranded parts. 4. Separation by length - The contents of a test tube can be separated by increasing length. This is achieved by gel electrophoresis, whereby longer strands travel more slowly through the gel. This operation was used by Adleman in step 3 of his solution to HP. 5. Separation by sequence - This operation allows one to remove from solution all DNA strands that contain a desired sequence. This is performed by generating the strand whose complement is the desired sequence. This newly generated strand is attached to a magnetic substance which is used to extract the sequences after annealing. This operation is the crux of Adleman's step 4. 6. Copying/Amplification - Copies are made of DNA strands in a test tube. The strands to be copied must have known sequences at both the beginning and end in order for this operation to be performed.

7. Append - This process makes a DNA strand longer by adding a character or strand to the end of each sequence. 8. Detect - It is also possible to analyze a test tube in order to determine whether or not it contains at least one strand of DNA. This operation, for example, is the last in Adleman's algorithm where we attempt to find a DNA sequence that has survived the previous steps.

Analysis
In analyzing these operations, it becomes obvious that the power of DNA computing comes from its ability to perform the same operation simultaneously on the contents of a test tube. Since the duration of the operation does not depend on the size of the test tube, operations can be performed in parallel with no added cost. While it may seem that this parallelism is potentially unbounded, it should be noted that the restricting concern is that the volume of the test tubes must increase in order to accommodate more simultaneous computations. It almost seems, then, that the time complexity of NP problems solved by Turing machines is being traded for a type of volume complexity in DNA computing. Noticing that DNA computing allows massive parallelism in constant time leads one to a comparison with quantum computing. Quantum computing, a topic of much recent research, performs parallel operations by means of a quantum register. Such registers, in a certain configuration, are thought to be in all possible states simultaneously. As a consequence of this, operations on this register can be thought of as being performed in parallel on all possible states of the register. The mechanisms of such registers, though beyond the scope of this report, allow one to extract the result corresponding to certain states in an attempt to find the answer to a specific computation. The primary difference between DNA and Quantum computing, we see, is that DNA increases parallelism at the expense of additional volume (the contents of a test tube) while the quantum register allows these parallel computations to be performed in a fixed physical area. One other important distinction between the two is that they afford different levels of assurance. DNA computing generates solutions in a 7

probabilistic manner, where any particular solution is generated with some probability based on the complex dynamics of the bonding process. Despite these differences, the similarities between these two methods are important to note. Most importantly, neither of these computing paradigms has been successfully implemented fully in an operational computer for public use. Secondly, the structure of algorithms for these two types of computer is fairly similar. The first phase typically involves the generation of all possible solutions to a problem and the second involves some method to extract the desired answer from all possibilities. This has been formalized by Claude and Paun in the notion of solutions by carving.

Advantages
The advantage of DNA approach is that it works in parallel, processing DNA computing is an example of computing at a molecular level,

all possible answers simultaneously. potential a size limit that may never be reached by the semiconductor industry. It can be used to solve a class of problems that are difficult or impossible to solve using traditional computing methods. There is no power required for DNA computing while the computation is taking place. The chemical bonds that are the building blocks of DNA happen without any outside power source. Its energy-efficiency is more than a million times that of a PC. DNA computing is a cost-effective method for solving complex computational problems.

Disadvantages
DNA computers require human assistance. Technological challenges remain before DNA computing. Researchers need to develop techniques to reduce number of computational errors 8

produced by unwanted chemical reactions with the DNA strands. They need to eliminate, combine, or accelerate the steps in processing the DNA. The extrapolation and practical computational environment required are daunting. The test tube environment used for DNA computing is far from practical for everyday use. To the naked eye, DNA computer looks like clear water solution in a test tube. There is no mechanical device. Hence to make the output visible, human manipulation is needed.

The Future of DNA Computing

Since the boom in DNA computing research in the mid-1990's there has been a significant decrease in the number of technical papers and conferences related to the topic. An Internet search for DNA computing will direct the user to a number of sites, many of which haven't been updated in several years. What are some of the reasons for this precipitous fall from grace? It turns out that, while DNA computing provides a good theoretical framework within which to design algorithms, the ability to construct a DNA-based computer is limited by a number of implementation level problems. The first problem, which has already been alluded to, has to do with the volume complexity that goes along with DNA computing. In his initial paper, Adleman speculated that more useful instances of the Hamiltonian path could be solved in linear time with a manageable volume of solution. Later analysis (Calude, 41) concluded that, due to the exponential growth of the number of paths with an increase in the number of vertices, the required mass of the solution for a graph with 200 vertices would exceed 3*1025 kg! This is due, in part, to the fact that pairing of DNA strands in a test tube happens in a probabilistic manner, which requires that excess quantities be used in order to provide reasonable assurance that errors will be minimized .In general, when for example the number of vertices grows into the hundreds, selecting a large number of DNA strands that are sufficiently different from one another becomes a difficult problem.

One of the related problems with DNA computing is that there is no universal method of data representation. In todays computer systems, for example, the binary representation is universally agreed upon. DNA computing, however, has no such standard. This is primarily due to the fact that there is no DNA-based operation to extract a strand if it has a particular value at a particular position. Extraction in DNA computing is performed solely be value and without respect to the values position within the strand, meaning that position information must be built into the sequence itself. Whats worse is that DNA-based representations of binary numbers are not extensible. Given a coding standard for an n bit binary sequence, extension to greater lengths generally requires that all of the DNA representations be regenerated in the form of longer strands to accommodate the additional information. This is a particularly annoying inconvenience, since it means that algorithm designers must explicitly design representation schemes for any problem before actually going about finding a solution. Finally, one of the biggest problems facing the field of DNA computing is that no efficient implementation has been produced for testing, verification, and general experimentation. While Adlemans initial experiment was performed in a lab, many of the subsequent algorithms in DNA computing have never been implemented or tested. The reason for this is that the resources required to execute these algorithms are both expensive and hard to find. Unlike common desktop computers, computing with a DNA-based solution has a high incremental cost both in the time of the operators and the raw materials that it uses. Were these facilities more available and affordable, real progress might be made in solving an interesting (large) instance of a problem using these new methods. Despite all of the difficulties outlined above, there are still a number of researchers working on topics related to DNA computing.. Some more recent work has attempted to address the issues of data representation and others with the ability to emulate todays circuit-based computing in a DNA-based system.

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CONCLUSION
Despite its auspicious debut in 1994, it seems that DNA computing is destined to be remembered as a novel idea that was too difficult to implement practically. Much of the original hope surrounding the field had to do with the incredible data density that one could achieve with DNA, owing to the microscopic size of the sequences involved. That hope has since been limited by the reality that solutions to real life problems require, due in part to the probabilistic nature of the annealing process, many copies of each of the reactants. Overall it has been shown that the increases in the number of copies needed of each strand far outweighs the gains that one achieves by using DNA-based representations of data . Despite the identified inefficiencies, it is certainly possible that in some instances a DNA-based computing system may prove to be the best solution. One could certainly imagine that the encryption-breaking method introduced above might become a viable solution for a highly motivated institution such as the military in a time of war. Any institution, for that matter, with sufficient motivation and access to the equipment and resources to undertake such a task might be well rewarded. What is 11

less likely, however, is that DNA computing will become a replacement for electronic computing in the near future. Given the high cost and required space, it is hard to imagine the use of a DNA-based computer in many of the places where computers exist today; certainly the notion of including a DNA computer as part of a cars control system is rather laughable.

REFERENCES

(1)-http://serendip.brynmawr.edu/biology/b103/f00/web1/barrera.html (2)http://citeseerx.ist.psu.edu/viewdoc/download? doi=10.1.1.115.1357&rep=rep1&type=pdf (3)-http://www.cim.mcgill.ca/~scott/RIT/dna_computing.html (4) www.downloadppts.com (5) Molecular computation of solutions to combinatorial problems- Leonard .M. Adleman. (6)Introduction to computational molecular biology by joao setubal and joao meidans -Sections 9.1 and 9.3

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(7)DNA computing, new computing paradigms by G.Paun, G.Rozenberg, A.Salomaa-chapter 2 (8) Computing With Cells and Atom- C.S. Calude and G. Paun, Taylor & Francis, 2001

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