Recent Developments

Bigger is Better
The largest problem yet solved by a DNA computer was a 20-variable 3-SAT problem run by Adleman and others in 2002. Using a similar encoding scheme to the one Lipton proposed in his 1995 article on solving SAT, the team of researchers performed an exhaustive search of over 1 million possibilities; a dataset eleven times bigger than the one used in the Knights Problem (2^9 vs 2^20). To narrow down the massive data set, the researchers built a "computer" consisting of an electrophoresis box containg a "hot" and a "cold" chamber. The current dataset is contained in the hot chamber while the "clause" (describing one truth statement) is in the cold chamber. Theoretically, during electrophoresis, the strands that satisfy the clause in the cold chamber will migrate across and be "captured" in a special layer of gel. These strands then become the "dataset" for the next clause and the next clause is then "executed." Doing this for all twenty clause should result in the results that satisfy the entire statement. It did, as the researchers were left the with the unique result to the 20 clause problem.

Other avenues in modern day research involve finding more efficient ways of performing the “test tube” chemical operations used by Adleman and others to extract the correct solution strand. A group of researchers at the University of Wisconsin are working on the design for a “high density, chemically complex surfaces that can replace the test tube/magnetic bead methodology and simplify the task of performing the thousands of successive separations by hybridization that will be required in any DNA computing scheme.”

The first "real" DNA computer?
Last year (2002), a group of Japanese researchers at Olympus Optical Co. announced that they had created the “world's first DNA computer for gene analysis.” Built on the work done by University of Tokyo Professor, Akira Suyama, Olympus claims to have built the first fully automated DNA computer boasting huge computational capacity, low energy consumption, and massively parallel processing capabilities. An important feature of the system is the electric computer, which handles the lengthy process and complicated process of creating the complete set of answers and then using DNA manipulation to remove incorrect answers. The computer also increases accuracy as it cuts out human error. Olympus also introduced many important technological advances. Most notably, artifical DNA that behaves in the same way as real DNA, but hybridzes without interfering with eachother (in other words. virtually no mutations and no error). The other notable technology is a technology called Magtration(R), which facilitates precise seperation of specific DNA strands using magnetic microparticles. The creator says the computer can be used to solve many different types of problems (unlike previous experiments which were designed to solve a single instance of a problem) by simply changing the “source program” of the electronic computer that controls sample handling and processing. Although experts are cautious of calling this machine a real computer, it's a huge step in DNA computing. Not only is it the first practical application of DNA computing in the commercial sphere, it leads the way in what some consider the future of the field, namely integrating DNA's massive parallelism with "traditional" digital computers to solve certain large/hard problems that are very difficult (or impossible) to solve using digital computers alone.

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