Automatic design of DNA logic gates based on kinetic simulation

Ibuki Kawamata, Fumiaki Tanaka, Masami Hagiya

研究成果: Conference contribution

7 被引用数 (Scopus)


Recently, DNA logic gates and DNA machines have been developed using only a simple complementary base pairing of DNA, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. The purpose of this research is to develop a method for automatically searching and designing DNA logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted DNA molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. The effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.

ホスト出版物のタイトルDNA Computing and Molecular Programming - 15th International Conference, DNA 15, Revised Selected Papers
出版ステータスPublished - 2009 12 11
イベント15th International Conference on DNA Computing and Molecular Programming, DNA 15 - Fayetteville, AR, United States
継続期間: 2009 6 82009 6 11


名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
5877 LNCS


Conference15th International Conference on DNA Computing and Molecular Programming, DNA 15
CountryUnited States
CityFayetteville, AR

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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