Heuristic solution to a 10-city asymmetric traveling salesman problem using probabilistic DNA computing

David Spetzler, Fusheng Xiong, Wayne Frasch

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

DNA hybridization was used to make a probabilistic computation to identify the optimal path for a fully connected asymmetric 10 city traveling salesman problem. Answer set formation was achieved using a unique DNA 20mer for each edge capable of hybridizing to half of each neighboring vertex. This allowed the vertex 20mers to be linked in all possible combinations to form paths through the network. Hybridization occurred in the presence of an excess of vertex 20mers, while edge 20mers were added in limiting amounts inversely proportional to the weight of each edge, resulting in the paths with the least cumulative weight being the most abundant. Correct answers, 230bp in length, contained a single copy of each vertex and were purified by PAGE and by successive magnetic bead affinity separations with probes for each vertex. Answer detection was accomplished using LCR of probes complementary to each vertex in a manner that identified the sequential order of vertices in each path by identifying vertex pairs. Optimal answer identification was accomplished using a conventional computer by normalizing the abundance of vertex pairings, and was found to be the same as that calculated by in silico.

Original languageEnglish (US)
Title of host publicationDNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers
Pages152-160
Number of pages9
DOIs
StatePublished - Aug 27 2008
Event13th International Meeting on DNA Computing, DNA13 - Memphis, TN, United States
Duration: Jun 4 2007Jun 8 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4848 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other13th International Meeting on DNA Computing, DNA13
CountryUnited States
CityMemphis, TN
Period6/4/076/8/07

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Keywords

  • DNA computing
  • Denaturing PAGE
  • Hybridization
  • Ligation
  • Magnetic affinity
  • Traveling salesman problem

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Spetzler, D., Xiong, F., & Frasch, W. (2008). Heuristic solution to a 10-city asymmetric traveling salesman problem using probabilistic DNA computing. In DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers (pp. 152-160). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4848 LNCS). https://doi.org/10.1007/978-3-540-77962-9_16