Darpa Progress Report  April 25, 1999

  1. We have developed an approach to DNA computation in which we 'write' on circular double stranded DNA molecules (plasmids) using biochemical processes. We have now confirmed in the laboratory that we can carry out three of our 'write' operations in sequence - and then 'read' the result. This preliminary laboratory work is reported in paper #2 below, where it is also explained how we plan to solve several hard algorithmic problems by these means. New theoretical results concerning the splicing operations used in our laboratory work have been obtained.
  2. Papers written since Aug.1998 (three others have appeared in print since Aug.1998):
    1. T.Head, Circular suggestions for DNA computing, in: Eds. M.Gromov & A.Carbone, Pattern Formation, World Scientific (invited paper - to appear) (abstract, dvi or postscript).
      T.Head, M.Yamamura & S.Gal, Aqueous computing: writing on molecules, Proceedings of the Congress on Evolutionary Computing (CEC'99), July 6-9, 1999 (invited paper - to appear)  (abstract, dvi or postscript).
  3. Using our tested method of 'writing' (cut & paste) we expect to solve small instances of hard algorithmic problems. Our next step will be to develop a method of 'writing' on our plasmids that will allow the solution of large scale instances of similar problems. We plan to 'write' by attaching short single stranded PNA molecules (P: protein backbone) to the plasmids and to 'read' by separation based on mass of the resulting complexes. New theoretical results on splicing and test tube computing will be written by two Ph.D. candidates working with us.
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