13-06-2012, 12:33 PM
DNA COMPUTING
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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 is bound to hit a wall. Chipmakers need a new material to produce faster computing speed with fewer complexities. You won’t 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 nanocomputers 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 world’s 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 PDF created with pdfFactory pro trial version
DNA computing could scale up to great heights!
Introduction:
Man’s thirst for knowledge has driven the information revolution.
Human brain, a master processor,
Processes the information about the internal and external environment and sends signals to take appropriate actions. In nature, such controls exist at every level. Even the smallest of the cells has a
Nucleus, which controls the cell. Where does this power actually come from? It lies in the DNA. The ability to harness this computational power shall determine the fate of next generation of computing. DNA computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA, biological molecules that can store huge amounts of information and are able to perform operations similar to that of a computer, through the deployment of enzymes, biological
catalysts that act like software to execute desired operations. The appeal of DNA computing lies in the fact that DNA molecules can store far more information than any existing conventional computer chip. Also, utilizing DNA for complex computation can be much faster than utilizing a
Conventional computer, for which
Massive parallelism would require large amounts of hardware, not simply more DNA.
Structure of DNA:
All organisms on this planet
are made of the same type of genetic blueprint, which bind us together. Within the cells of any organism is a substance called Deoxyribonucleic Acid (DNA), which is a double-stranded helix
of nucleotides, which carries the genetic information of a cell. The data density of DNA is impressive. Just like a string of binary data is encoded with ones and zeros, a strand of DNA is encoded with four bases, represented by letters A
(Adenine), T (Thymine), C (Cytosine) and G (Guanine). PDF created with pdfFactory pro trial version Graphical representation of inherent bonding properties of DNA Illustration of double helix shape of DNA. The bases (nucleotides) are spaced every 0.35 nanometers along the DNA molecule, giving it a remarkable data density of nearly 18Mbits per inch. These nucleotides will only combine in such a way that C always pairs with G and T always pairs with A. This complementarity makes DNA a unique data structure for computation and can be exploited in many ways.
Computer in a test tube:
The idea of using DNA to
Store and process information took off in the year 1994 when Leonard Adleman, a computer scientist at the University of Southern California, came to the conclusion that DNA had computational potential. Adleman caused an avalanche in the fields of biology; mathematics and computers by solving a problem called the Directed Hamiltonian Path problem or sometimes referred to as the Traveling Salesman Problem. The ‘salesman’ in this problem has a map of several cities
That he must visit to sell his wares where these cities have only one-way streets between some but not all of them. The crux of the problem is that the salesman must find a route to travel that passes through each city (A through G) exactly once, with a designated beginning and end. The salesman does not want to backtrack or go more than once through any of the paths. This is a non deterministic polynomial time problem. Basic outline of Traveling Salesman Problem. Adleman used a basic seven city, thirteen street model for Traveling Salesman Problem and created randomly sequenced DNA strands 20 bases long to chemically represent each city and a complementary 20 base strand that overlaps each city’s strand half way to represent each street. This representation allowed each multi-city tour to become a piece of double stranded DNA with the cities linked in some order by the streets. PDF created with pdfFactory pro trial version Representation of 20 bases DNA
strand representing a city showing the bonding tendencies of nucleotides to DNA strands representing pathways between the cities. By placing a few grams of every DNA city and street in a test
tube and allowing the natural bonding tendencies of the DNA building blocks to occur, the DNA bonding created over 10^9 answers in less than one second. Out of the answers that came about the correct answers were determined considering that the correct path must start at A and end at G, it must pass through all cities at least once and must contain each city in turn. The correct answer was determined by filtering the strands of DNA according to their end-bases to determine which strands began from A and end in city G. The remaining strands were then measured through electrophoreic techniques to determine if the path they represent has passed through all seven cities. Finally the resulting sets of DNA were examined individually to determine if they contain each city in turn. That strand(s) that remained was then determined to be the answer(s). This process took Adleman about a week. A conventional computer is better suited for deterministic computation permitting at most one next move at any step in computation. The inherent parallel computing ability of DNA, however, is perfectly suited for solving such non-deterministic type of problems.
A Successor to Silicon:
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. Many have predicted that Moore’s law (which
states that the microprocessors would double in complexity every two years) will soon reach its end, because of the physical speed and miniaturization limits of silicon microprocessors. DNA computers have the potential to take computing to new levels, picking up where Moore’s law leave off. DNA computers could surpass PDF created with pdfFactory pro trial version their silicon-based predecessors. The several advantages of DNA over silicon are: As long as there are cellular organisms, there will be a supply of DNA. The large supply of DNA makes it a cheap resource. Unlike the toxic materials used to make traditional microprocessors, DNA biochips can be made cleanly. DNA computers are many times smaller than today’s computers. DNA molecules have a potential to store extensively large amount of information. It has been estimated that a gram of dried DNA can hold as much information as a trillion CD’s. More than 10 trillion DNA molecules can fit into an area of 1 cubic centimeter. With this small amount if DNA a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations at a time. In a biochemical reaction-taking place in a tiny surface area, a very large
number of DNA molecules can operate in concert, creating a parallel processing system that mimics the ability of the most powerful supercomputer. DNA computers have the ability to perform many calculations simultaneously; specifically, on the order of 10^9 calculations per ml of DNA per second! A calculation that would take 10^22
modern computers working in parallel to complete in the span of one human’s life would take one DNA computer only 1 year to polish off!
Scope and recent updates:
Scientists have taken DNA from the free-floating world of the test tube and anchored it securely to a surface of glass and gold. University of Wiscosnin- Madison researchers have developed a thin, gold-coated plate of glass about an
Inch square. They believe it is the optimum working surface on which they can attach trillions of strands of DNA. Putting DNA computing on a solid surface greatly simplifies the complex and repetitive steps previously used in rudimentary DNA computers. Importantly it takes DNA out of the test tube and puts it on a solid surface, making the technology simpler, more accessible and more amenable to the development of large DNA computers capable of tackling the kind of complex problems that conventional computers now handle routinely. Researchers believe that by the year 2010 the first PDF created with pdf Factory Pro trial version DNA chip will be commercially available.