9 massive parallelism nevertheless adlemans algorithm

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Unformatted text preview: ill defeated by exponential explosion. ¶8. Lipton (1995) estimates that it is feasible for n 70, but this is also within the range of conventional computer. ¶9. Massive parallelism: Nevertheless, Adleman’s algorithm illustrates the massive parallelism of molecular computation. Step 1 (generation of all possible paths) took about an hour for n = 7. Adleman estimates that about 1014 ligation operations were performed, and that it could be scaled up to 1020 operations. Therefore, speeds of about 1015 to 1016 ops/sec (1–10 peta-operations/s) should be achievable. That is, digital supercomputer range. 236 CHAPTER IV. MOLECULAR COMPUTATION ¶10. Energy: Adlemen estimates that 2 ⇥ 1019 ligation operations were performed per joule of energy. Contemporary supercomputer perform only 109 operations per joule, so MC is 1010 more energy e cient. ¶11. It is near the thermodynamic limit of 34 ⇥ 1019 operations per joule. Recall (Ch. II, Sec. B.1) kT ln 2 ⇡ 3 ⇥ 10 9 pJ = 3 ⇥ 10 21 J, so there can be about 3.3 ⇥ 1020 bit changes/J. ¶12. Space: One bit of information occupies about 1 cubic nm. Contemporary disks store a bit in about 1010 cubic nm. That is, a 1010 improvement in density. ¶13. Inherent error: A more pervasive problem is the inherent error in the filtering processes (due to incorrect hybridization). Some strands we don’t want, get through; and some that we do want, don’t. With many filtering stages the errors accumulate to the extent that the algorithms fail. ¶14. There are some approaches to error-resistant DNA computing....
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