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The thesis I have chosen to do is DNA computing and its applications which would change the way we perceive technology.DNA is also called as the molecule of life. It carries information from generations together. DNA has self replicating properties, that is, it can create multiple copies of itself. The reason behind this to happen is because cells replicate and each cell would need a copy of the DNA so that it can propagate the information of life.
DNA as its basic building blocks have four different bases.They are Adenine ,Cytosine ,Guanine and Thymine.Adnine is represented by A,Cytosine is represented by C,Guanine is represented by G and Thymine is represented by T. Each one of these bases are also associated with sugar and phosphate molecule. Together they form what is known as nucleotides. These nucleotides arrange themselves in a double helix kind of structure or twisted staircases as is shown in the diagram above. These bases have the same chemical constituent in each and every living person .But the part where it differs is the way the bases are arranged in different sequences. That is what sets each and every individual apart.
These bases in them carry a lot of valuable information that determines how an organism is formed. This information is represented by millions of such chemical bases intertwined into a specialized structure. It is this fundamental nature of the DNA to carry millions of data that has inspired scientist Dr Leonard Adleman to use them in solving certain computing problems. The 4 different bases have resulted in a new kind of number system which would involve information being represented by 4 numbers corresponding to the 4 bases of the DNA ââ‚¬" A,C,T,H.
DNA was used as a tool to solve an instance of a computing problem by Dr Leonard Adleman .He used DNA molecule to solve the Hamiltonian path problem, which happens to be finding the shortest path through the cities in a graph theory kind of puzzle.. This experiment proved to be a cornerstone in proving that the molecule of life could be used to a lot more applications other than carrying the information of life.
Statement of the need :
As the need for better computing methods have grown over a period of time, there have been a lot of attempts made to find ways and means to make the logic circuits smaller and faster and reduce the processing time by an appreciable amount.DNA molecule has evolved as a strong candidate by virtue of its capacity to carry huge treasure trove of information and its magical self replicating capacity. At the moment DNA has to go hand in hand with silica,viz carbon nanotubes, but there would come a day when DNA would be able to take over completely from silica and thereby give technology a true eco friendly brand value.
Goals of Thesis:
The goal of this thesis is to enumerate the benefits of DNA computing in solving engineering problems. The thesis sheds some light as to how DNA computing technology can be used to provide for better improved encryption standards. It also provides useful insights about the work done by some multinationals on formulating and fabrication a chip with DNA as the substrate material.
Description of the Thesis:
DNA molecules have the potential to solve complicated mathematical problems faster and better than any silicon transistors of highest quality and repute.It has the potential to radically change computing as we perceive it. It all began when Dr Adleman solved the NP problem with the wet DNA experiment. NP problems have been the toughest problems to solve for ages in the field of computer science. One of the NP problems that happens to be solved or complete is the travelling salesman problem. Dr Adlemann used wet DNA experiment to solve the travelling salesman problem thus proving that DNA molecules could be used to solve complex computing problems.
Dr Adleman developed a technique for solving combinatorial problems. He made use of hybridization, ligation and amplification. Hybridization is the process of combining two DNA strands which are complementary .Ligation is where two DNA strands are combined together to make up a single strand. This involves the use of molecules like enzymes. Amplification involves a method called PCR(Polymerase chain reaction).In the PCR technique, the DNA strands are amplified by enzymes called polymerase which after a series of lab experiments provide the desired result of DNA amplification.
DNA has four different molecules that make up its basic constitution. They are the Adenine, Guanine, Cytosine and Thymine. By virtue of its inherent nature Adenine can only link up to Thymine and Guanine to Cytosine. The various combinations of these molecules make up the sequence of life.
The very first problem that Dr Adlemann solved was the Hamiltonian problem. Hamiltonian path problem is a type of graph problem. It could be both directed or undirected. Given a set of vertices and edges, this problem involves finding ways and means to traverse all the vertices exactly once through the edges.
By using DNA molecules it can be solved in the following sequence. To begin with vertices and edges are represented by the DNA polymers. The technique of ligation helps create those DNA strands. They would denote the pathways in the graph. Next DNA strands are isolated using enzymatic reactions.The last step involves checking for all the vertices which would form a Hamiltonian path.Then by chemical reactions, checks are made to see if any DNA strands are left on those vertices.In every step of the way PCR (polymerase chain reaction) is used to enlarge or amplify results for processing.
Advantages of DNA computer :
The technology for DNA computer is under development. However, it is clear that molecular computers have many attractive properties. While modern supercomputers perform 1012 operations persecond, Adleman estimates 1020 operations per second to be realistic for molecular manipulations. Similar impressive views concern the consumption of energy and the capacity of memory; A supercomputer needs one joule for 109 operations, whereas the same energy is sufficient to perform 2*10^19 ligation operations. On a videotape, every bit needs 1012 cubic nanometers storage; DNA stores information with a density of one bit per cubic nanometer . Although the execution time for DNA molecular reactions are relatively slower than conventional computers, the total performance of DNA computers can outshine the
conventional electronic computers. (Watada & Bakar, 2008)( CITATION needed)
FIRST REAL BREAKTHROUGH:
It all began when Dr Adleman proved the WET DNA experiment .This experiment made people sit up and take notice of the fact that DNA and molecular engineering could play a significant role in the realm of computing. Dr Adleman was able to solve the Hamiltonian problem which involved choosing the shortest paths between seven cities. Hamiltonian problem of paths is a kind of travelling salesman puzzle. It is achieved by fixing the distance between two cities to constants that are finite in value ,provided the cities are adjacent. Else they are set to infinity.This problem involves a graph with a set of vertices and a starting point and a end point.The algorithm that was employed by Dr Adlemann to solve this problem was as follows.
A. Paths were made throughout the whole graph.
B. Paths with a starting and stopping point were considered.
C. Among the vertices of number S, only those paths which were going through S number of vertices were selected. And those that made the cut were the ones that traversed through all of those vertices only once.
The same was carried out with the DNA in the laboratory. The cities were represented by DNA of length and size 25 mer. The vertex was represented by DNA strands that would encapsulate two adjacent cities.In the beginning DNA strands were fabricated by the appropriate chemical reaction.A certain equal quantity of both DNA strands,one representing a city A and and another representing an adjacent city B were taken.They were mixed in a test tube.This was done using the Ligation process.The end result was that there were different permutations and combinations of the solution to the Hamiltonian puzzle.
An appropriate solution was vertex that passed through each and every city.PCR method was used to check if the strands made it through every city in the reckoning. By another chemical reaction, strands that made it through every city were separated from the ones that didnââ‚¬â„¢t. Finally the result had strands that passed through every city.
In the next stage of the experiment was called electrophoresis. This process would separate DNA strands according to their sizes. Only strands of specific size were isolated and immersed in a specialized H2O solution. Strands that have made it through all the seven cities would be recovered with this procedure.This would then be fodder for the next stage of the experiment.
The last step of the process involves a tedious method called magnetic beads separation.(CITATION MAY BE NEEDED).It involved an exhaustive process. It was to check if any of the cities were left behind on the strands. The step was repeated until the output was attained. The whole procedure took a lot of time but the end answers justified the means.
Progress made in the field so far:
After the advent of DNA computing scores of new findings have been made in the same technology. Rapid strides have been made in terms of both the conceptual and the implementation aspects of the technology. There are various sections of the academia and research world that are bifurcated into ones that are looking into the laboratory experiments and a another sect of denizens who are exploring unchartered territories hitherto unknown in the fabrication of a DNA computer. The latter half of the Samaritans have been focusing their time and energy so far in developing algorithms for this unique type of computer. The reason for them to do so is when this wonder machine is ready for inception into the realm of practical application, it would have algorithms to be tested with. Also the specialized form of computer would have a head start in terms of solving various computing issues head long without any more gestation period.
Over a period of time researchers have faced certain restrictions and roadblocks in the certain algorithms and methods used in DNA computing. But there have also been lot of vital breakthroughs. There have been those that have happened at the molecular level and those that have happened at the engineering domain.
Most of the research work on computation revolves around variables. These variables provide a part and parcel of the solution for many engineering problems. They are variables that represent some numbered representations. The progress this specialized form of computing has been able to do is highlighted next.
DNA computing involves four different methods to represent numerical values
in DNA computing.The value of the numeral must be represented as accurately as
possible. This is critical to getting good solutions for graph theory puzzles. If there were
to be mistakes in representing the numerals it could throw the graph theory calculations
out of order. The four ways of presenting numerical value in DNA computing are widely
employed as (i) constant length based (ii) direct proportional length based (iii)
concentration control and iv) gradient temperature method  (CITATION NEEDED)
Dr Adlemann made use of constant based length method to provide distances between two cities. However no markings were used to represent arcs between cities.The work done by Dr Lipton did not include any such work on arc labeling.The first prominent work on arc labeling was done by Narayanan and Zorbalas in 1998.
They proposed constant based length method to show the arcs ,that is the length between cities. They used DNA of length 3 mer to provide for the shorter distance and the length of 6mer to provide for the longer distance. Therefore the longer distance are provided for by the larger strands and shorter ones by smaller strands. The smaller strand would be the expected output.(CITATION NEEDED)
The distances here are limited and are not too long. The reason is because too much of distances would result in longer sizes of DNA strands. This would result in erroneous results creeping into the final scheme of things.
There were other techniques proposed by a few other scientists to solve weighted graph problem. Dr Yamamoto proposed method of concentration of chemicals. The DNA chemical mix was used as the input and the output. This was basically going to make it easy on the expenses of the set up as it would result in only a few wavelengths being put through severe introspection.(citation)
About 6 years back,a new method was proposed by scientist named Dr Lee to find a solution for the weighted graph problem.The varying levels of temperature was used a tool to overcome the drawbacks of the previous few methods. Melting temperatures decide the shape and the cost of these arcs. Economy is attained by DNA arcs that fall in the lower melting range and thereby provide the effective solution we are looking for.
The temperature stability for each city and its paths are kept in equilibrium. This is because temperature consistency provides a proper balance to the set up. The roads directions or pathways are prepared based on certain criteria like arrival, departures and the logistics ,costs that comes along with it.
But lot of work still remains a finding a fool proof solution for finding the numerical consistency. Any kind of breakthrough would really help in opening new vistas in the real world implementation.
Developments in the Engineering Sector:
Most of the work involving DNA computing has been done in providing a solution for the Hamiltonian problem. But inroads are being made in the field of cryptography ,encryption and many more .Some of the computing problems have been solved using DNA computing. We are going to throw some light on a few of them.
The very first work that was done was to solve the issue of scheduling. The solution involved taking up 6 different errands and trying to find a proper scheduling method for them. Hamiltonian path problem was used as a reference. The name of the scientist who proposed this solution was Dr Zhixing (CITATION NEEDED).But owing to limitations of the size of the numerical values that could be supported by this form of computing only scheduling algorithms of limited scope could be solved by this method.
Another field which has grown in prominence of late is the field of information security. With lot of data and information that flows through the internet cloud, providing good encryption has become a keystone project for all banks concerned. It has been proposed by Dr Boneh and Dr Adleman that the best way to go about developing a sound encryption algorithm is to break one. They had come up with a design plan to break the DES(Data Encryption Standard ) algorithm. (CITATION NEEDED).
DNA cryptography has been proposed by Gehani et al, Kartalopoulos and Tanaka et al as a new born cryptography field (CITATION NEEDED).There have been rapid strides made of late with DNA computing in the field of steganography and certification. DNA has also been employed in the field of telecommunication and computer systems.DNA computing methods have also helped in solving complex problems which require huge number crunching and processing capabilities to solve. On the other hands, Jeng et al. have introduced a merging technique between DNA computing and fuzzy set to forecast a money exchange rate . (CITATION NEEDED).
It has been found that DNA computing is capable of providing massive parallel computing and can store huge amount of data.It has the capability to take solving problems to a new level as it can perform parallel computation with elan and therefore can pose a serious challenge to all conventional encryption technologies.A testament of this processing superiority is the cracking of DES encryption algorithm by this technology.DNA is extremely supreme in terms of volume of information that it can store and propogate.
Cryptography using DNA computing is now in its infancy .It is still limited to the laboratory and is finding its feet. It has been observed that a message encrypted using DNA components is very hard to decipher unless or until the key is not present. It is the presence of DNA primers that play a significant role in the decryption.DNA primers are like the raw materials for procreation. It is from them that other DNA strands spawn in numbers. It is these primers that is the key and needs to be used for the purpose of encrypting. Also there have been well established conventional encryption algorithms that can still be used to perfection while dealing with data security. Therefore DNA computing and conventional encryption technology could go hand in hand and form a significant union for data protection.
DNA computing involves playing around with 4 basic numbers unlike binary number system which involves 2.The basic components of DNA are the 4 molecules. They are Adenosine, Cytosine, Thyamine and Guanine.DNA computing is all about the permutation and combination of these 4 molecules. In the binary notation the complements are in such a way that complement of zero is one and that of one is zero. But as per the DNA physiology the molecule of ADENOSINE can only be linked with THYMINE and CYTOSINE WITH GUANINE. Therefore it has been planned that the complement of ADENOSINE would be THYMINE and that of CYTOSINE would be GUANINE. So which every arbitrary number they would be represented with, say if the number representing Adenosine is complemented then that would be equal to the number representing Thymine. Similarly the number representing Cytosine is complemented , we would get the number which would represent guanine. That is because they are interlinked by nature.
DNA ENCRYPTION DESIGN : ( CITATION NEEDED)
Senderââ‚¬â„¢s End :
The following system has been proposed by an author for a encryption system design. For the process of encryption, at the senders end the message is first converted to hex representation internally .The hexadecimal value is then converted to binary number format. This binary format is converted to cipher representation. This is done by virtue of a key. As and when this is done the whole message is changed to look radically different , almost unrecognizable. It almost looks like gibberish. Next by means of DNA coding principles, the data is converted to another form of representation. This new information generated would be tagged with DNA primers.
The receiver receives the DNA technology coded message. The DNA primers that accompany the encrypted message helps in DNA encoded information to be read. This message is then converted to binary numbers by means of DNA coding. The binary cipher is then converted to binary text data. This is achieved by using secret key which is at the receivers end. The final step is of course to convert binary data to original message.
Formulating the Key:
The most important fundamental part in an encryption design architecture is the key formulation. The key decides how robust and safe the delivery of the message from the sender to the receiver is going to be. At first the sender generates a sequence of DNA information which is transmitted over a secure channel to the receiver. The receiver then does the same from his end. Once both of them finish sending this data to each other the key is calculated by a combination of the public key at the senders end, private key at the receivers end and the exchanged DNA sequence information present at both the ends.
DNA chip fabrication : CITATION NEEDS TO BE EXPLORED
According to PC world website, engineers at IBM have already started to work on the chip that is being manufactured with DNA materials interspersed with carbon nanotubes. The DNA would form the substrate and the carbon nanotubes would be the bridges or information carriers in the circuit. The chips have been reducing in size substantially over the years and as it gets miniaturized to such levels that the etching process is less than 22nm.This would in turn result in complications growing manifold .
Based on the technique suggested by a scientist named Paul Rothmund at California Institute of Technology,who found that DNA could assemble by themselves into different shapes. These shapes could be of any geometry like a Triangle or circle. The first stage is the lithography which involves shaping up the circuits. On top of these lithographic circuits are poured the DNA solution which by its virtue of self assembling mechanism would carve into shapes pronounced by the lithographic module. The DNA with carbon nanotubes were assembled to emulate logic circuits.
If this technology could find a breakthrough it would change the way we (Placeholder1) (SHAH, 2009)intervention for companies looking to cut costs and improve quality at the same time.
DNA computing is revolutionary in the way in which it is conceptualized. But there are other innovative ideas brimming to the surface as well. One of them is called quantum computing. Quantum computing is envisioned as a technology that would make use of atoms and molecules to do its processing and computation. This would result in speeds of operation hitherto unknown to mankind. But a quantum computer still exists in theory and is far from being put into practice.
Advantages of DNA computing :
DNA computing is believed by many to be the harbinger of clean processing technology. The self replicating nature of the DNA molecule provides us with a powerful tool to be used in information theory. The bases of DNA molecule carry information that has been passed from millions of generation together. There are about a million bases arranged in different sequences in just one strand of the DNA.A single strand of DNA is as puny as 10 Angstorm . Angstorm is ten to the power of minus ten. Thereby by virtue of their small sizes and capacity to carry information in gigantic amount , they would help in miniaturizing circuits to whole new dimensions.
The Cons far outweighs the pros. The few drawbacks it could have would be laboratory costs associated with the technology. Also DNA used for the technology must be taken through several stages of processing before it can be used for the final scheme of things.