Abstract
In attempting to automate the computation of n-variable 3-CNF SAT problems using DNA, two physical architectures were scrutinized, the "in-line" architecture and the "waste-well" architecture. Computer modeling of the effects of non-specific binding predicted that the in-line version would not work for problems of more than 7 variables. According to the model, the "wrong answer" DNA strands would swamp out the "correct answer" DNA strands in the final computation module. And in fact, the in-line architecture never performed a computation higher than 6 variables.
To perform a 20 variable instance of the 3-CNF SAT problem a manual version of the waste-well architecture was employed. Surprisingly though, after analysis of the modeling results, it appears that through a simple protocol change, the in-line architecture may have been able to perform higher order computations.
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Johnson, C.R. (2008). Modeling Non-specific Binding in Gel-Based DNA Computers. In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_18
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DOI: https://doi.org/10.1007/978-3-540-77962-9_18
Publisher Name: Springer, Berlin, Heidelberg
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