Development of a bacteria computer: From in silico finite automata to in vitro and in vivo

研究成果: Conference contribution


We overview a series of our research on implementing finite automata in vitro and in vivo in the framework of DNA-based computing [1,2]. First, we employ the length-encoding technique proposed and presented in [3,4] to implement finite automata in test tube. In the length-encoding method, the states and state transition functions of a target finite automaton are effectively encoded into DNA sequences, a computation (accepting) process of finite automata is accomplished by self-assembly of encoded complementary DNA strands, and the acceptance of an input string is determined by the detection of a completely hybridized double-strand DNA. Second, we report our intensive in vitro experiments in which we have implemented and executed several finite-state automata in test tube. We have designed and developed practical laboratory protocols which combine several in vitro operations such as annealing, ligation, PCR, and streptavidin-biotin bonding to execute in vitro finite automata based on the length-encoding technique. We have carried laboratory experiments on various finite automata with 2 up to 6 states for several input strings. Third, we present a novel framework to develop a programmable and autonomous in vivo computer using Escherichia coli (E. coli), and implement in vivo finite-state automata based on the framework by employing the protein-synthesis mechanism of E. coli. We show some successful experiments to run an in vivo finite-state automaton on E. coli.

ホスト出版物のタイトルPrograms, Proofs, Processes - 6th Conference on Computability in Europe, CiE 2010, Proceedings
出版ステータスPublished - 2010 7 29
イベント6th Conference on Computability in Europe, CiE 2010 - Ponta Delgada, Azores, Portugal
継続期間: 2010 6 302010 7 4


名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
6158 LNCS


Other6th Conference on Computability in Europe, CiE 2010
CityPonta Delgada, Azores

ASJC Scopus subject areas

  • 理論的コンピュータサイエンス
  • コンピュータ サイエンス(全般)


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