Automatic design of DNA logic gates based on kinetic simulation

Ibuki Kawamata, Fumiaki Tanaka, Masami Hagiya

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

7 Citations (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.

Original languageEnglish
Title of host publicationDNA Computing and Molecular Programming - 15th International Conference, DNA 15, Revised Selected Papers
Number of pages9
Publication statusPublished - 2009
Event15th International Conference on DNA Computing and Molecular Programming, DNA 15 - Fayetteville, AR, United States
Duration: 2009 Jun 82009 Jun 11

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5877 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference15th International Conference on DNA Computing and Molecular Programming, DNA 15
Country/TerritoryUnited States
CityFayetteville, AR


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