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Biology 103
2000 First Web Report
On Serendip

DNA COMPUTING

Nimia Barrera

DNA computing, also known as molecular computing, is a new approach to massively parallel computation based on groundbreaking work by Adleman (1). 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 (2)..

Computers today all use binary codes - 1's and 0's or on'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 (2).

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 (1).

Thus far, Adleman has only tested his DNA model with six vertices and is uncertain as to how to proceed with paths of more than six vertices. But as far as speed is concerned, DNA clearly wins. The fastest supercomputers today execute about 1,012 operations per second, while the DNA models perform 1,000 times faster than the fasters super computer (2). A clearer picture of this - and probably one that we can relate to better - is that of the typical desktop computer. Our desktops execute 106 operations per second, which is a thousand million times slower than the DNA.

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 (3). 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(3).

The research on DNA computers is ongoing still. All over the country, research teams like the one at the University of Wisconsin are concentrating their efforts in order to put this new nanotechnology to good use. And even though Adleman's DNA computer would have a hard time computing two 100-digit integers - an easy task for a supercomputer - its ability to solve complex problems is unmatched. As this new nanotechnology continues to evolve, we might yet be surprised again. The DNA based system of computing has had millions of years to evolve, while the man-made systems have only been around for a small fraction of that time (2). The future of DNA computing has yet to be decided. Anne Condon, a computer scientist on the Wisconsin team, likens compares current DNA computing to that of ENIAC computers. Built in 1946, ENIAC computers used punch cards and closets full of vacuum tubes to solve simple arithmetical problems (3).

WWW Sources

1) What is DNA Computing , on the RSA Security web site

2) http://www.englib.cornell.edu/scitech/w96/DNA.html , the server home page

3) Research article , on the University of Wisconsin web site




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