DNA COMPUTING

DNA COMPUTING

• What is a DNA computer?
With advancement in technology and research we have come to know that millions of natural supercomputers exist inside living organisms, including our body. DNA (deoxyribonucleic acid) molecules, the material our genes are made of, have the potential to perform calculations many times faster than the world's most powerful human-built computers. DNA might one day be integrated into a computer chip to create a so-called biochip that will push computers even faster. DNA molecules have already been harnessed to perform complex mathematical problems. While still in their infancy, DNA computers will be capable of storing billions of times more data than our personal computer.

A DNA computer is a molecular computer that works biochemically. It "computes" using enzymes that react with DNA strands, causing chain reactions. The chain reactions act as a kind of simultaneous computing or parallel processing, whereby many possible solutions to a given problem can be presented simultaneously with the correct solution being one of the results.


• DNA Computing Technology-

In 1994, Leonard Adleman introduced the idea of using DNA to solve complex mathematical problems. Adleman, a computer scientist at the University of Southern California, came to the conclusion that DNA had computational potential after reading the book "Molecular Biology of the Gene," written by James Watson, who co-discovered the structure of DNA in 1953. In fact, DNA is very similar to a computer hard drive in how it stores permanent information about your genes.

Adleman outlined how to use DNA to solve a well-known mathematical problem, called the directed Hamilton Path problem, also known as the "traveling salesman" problem. The goal of the problem is to find the shortest route between a number of cities, going through each city only once. As we add more cities to the problem, the problem becomes more difficult. Adleman chose to find the shortest route between seven cities.

The steps taken in the Adleman DNA computer experiment are:-
1. Strands of DNA represent the seven cities. In genes, genetic coding is represented by the letters A, T, C and G. Some sequence of these four letters represented each city and possible flight path.
2. These molecules are then mixed in a test tube, with some of these DNA strands sticking together. A chain of these strands represents a possible answer.

3. Within a few seconds, all of the possible combinations of DNA strands, which represent answers, are created in the test tube.
4. Adleman eliminates the wrong molecules through chemical reactions, which leaves behind only the flight paths that connect all seven cities.

The following algorithm solves the Hamilton Path problem, regardless of the type of computer used:
1. Generate all possible routes.
2. Select itineraries that start with the proper city and end with the final city.
3. Select itineraries with the correct number of cities.
4. Select itineraries that contain each city only once.


The success of the Adleman DNA computer proves that DNA can be used to calculate complex mathematical problems. However, this early DNA computer is far from challenging silicon-based computers in terms of speed. The Adleman DNA computer created a group of possible answers very quickly, but it took days for Adleman to narrow down the possibilities. Another drawback of his DNA computer is that it requires human assistance. The goal of the DNA computing field is to create a device that can work independent of human involvement.

Three years after Adelman’s experiment, researchers at the University of Rochester developed logic gates made of DNA. Logic gates are a vital part of how your computer carries out functions that you command it to do. These gates convert binary code moving through the computer into a series of signals that the computer uses to perform operations. Currently, logic gates interpret input signals from silicon transistors, and convert those signals into an output signal that allows the computer to perform complex functions.
The Rochester team's DNA logic gates are the first step toward creating a computer that has a structure similar to that of an electronic PC. Instead of using electrical signals to perform logical operations, these DNA logic gates rely on DNA code. They detect fragments of genetic material as input, splice together these fragments and form a single output. For instance, a genetic gate called the "And gate" links two DNA inputs by chemically binding them so they're locked in an end-to-end structure, similar to the way two Legos might be fastened by a third Lego between them. The researchers believe that these logic gates might be combined with DNA microchips to create a breakthrough in DNA computing.
DNA computer components -- logic gates and biochips -- will take years to develop into a practical, workable DNA computer. If such a computer is ever built, scientists say that it will be more compact, accurate and efficient than conventional computers

• Comparison between silicon & DNA computers-
 As long as there are cellular organisms, there will always 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's key advantage is that it will make computers smaller than any computer that has come before them, while at the same time holding more data. One pound of DNA has the capacity to store more information than all the electronic computers ever built; and the computing power of a teardrop-sized DNA computer, using the DNA logic gates, will be more powerful than the world's most powerful supercomputer. More than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter (0.06 cubic inches). With this small amount of DNA, a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations at a time. By adding more DNA, more calculations could be performed.

Unlike conventional computers, DNA computers perform calculations parallel to other calculations. Conventional computers operate linearly, taking on tasks one at a time. It is parallel computing that allows DNA to solve complex mathematical problems in hours, whereas it might take electrical computers hundreds of years to complete them.




• Olympus Develops DNA computer-

In starting of year 2002 the Olympus Optical Co. Ltd. Developed what the company claimed the commercially practical DNA computer that specializes in gene analysis. The computer was developed in conjunction with Akira Toyama, an assistant professor at Tokyo University.
Gene analysis has been usually done manually, by arranging DNA fragments and observing the chemical reactions. But that was time-consuming, said Satoshi Ikuta, a spokesman of Olympus Optical. When DNA computing is applied to gene analysis what used to take three days can now be done in six hours, he said. DNA computing also allows scientists to observe chemical reaction that occur simultaneously, lowering the research costs.
The bottleneck was that engineers were required to have expert knowledge in two specific fields, in order to develop a gene analysis DNA computer.
I. Information Processing Engineering
II. Molecular Biology
This is called genome informatics as a whole.
To achieve this, the company formed a joint venture Novous Gene Inc. Which specializes in genome informatics, in February 2001? The principles for a DNA computer that works for gene analysis were provided by Tokyo University’s Toyama.
The computer Olympus Optical has developed is divided into two sections, a molecular calculation component and an electronic calculation component. He former calculates DNA combinations of molecules, implements chemical reactions, searches and pulls out the right DNA the latter executes processing programs and analyzes these results.
The company was started gene analysis using the DNA computer on a trial basis for a year, and form this year hopes to offer the service on a commercial basis for researchers.



• Example of an application-

For example, a DNA computer as a tiny liquid computer —- DNA in solution -- that could conceivably do such things as monitor the blood in vitro. If a chemical imbalance were detected, the DNA computer might synthesize the needed replacement and release it into the blood to restore equilibrium. It might also eliminate unwanted chemicals by disassembling them at the molecular level, or monitor DNA for anomalies. This type of science is referred to as nanoscience, or nanotechnology, and the DNA computer is essentially a nanocomputer.

• Conclusion-
The DNA computer is only in its early stages of development. Though rudimentary nanocomputer perform computations, human interaction is still required to separate the correct answer out by ridding the DNA computer solution of all false answers. This is accomplished through a series of chemical steps. However, experts are encouraged by the innate abilities of a DNA computer and see a bright future.