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

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

Abstract

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.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages362-371
Number of pages10
Volume6158 LNCS
DOIs
Publication statusPublished - 2010
Event6th Conference on Computability in Europe, CiE 2010 - Ponta Delgada, Azores, Portugal
Duration: 2010 Jun 302010 Jul 4

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6158 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other6th Conference on Computability in Europe, CiE 2010
CountryPortugal
CityPonta Delgada, Azores
Period10/6/3010/7/4

Fingerprint

Finite Automata
Finite automata
Bacteria
Finite State Automata
Escherichia Coli
Encoding
Escherichia coli
Tube
DNA
Strings
Experiment
Protein Synthesis
Self-assembly
State Transition
Annealing
DNA Sequence
Experiments
DNA sequences
Self assembly
Target

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Sakakibara, Y. (2010). Development of a bacteria computer: From in silico finite automata to in vitro and in vivo. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6158 LNCS, pp. 362-371). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6158 LNCS). https://doi.org/10.1007/978-3-642-13962-8_40

Development of a bacteria computer : From in silico finite automata to in vitro and in vivo. / Sakakibara, Yasubumi.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6158 LNCS 2010. p. 362-371 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6158 LNCS).

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

Sakakibara, Y 2010, Development of a bacteria computer: From in silico finite automata to in vitro and in vivo. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 6158 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6158 LNCS, pp. 362-371, 6th Conference on Computability in Europe, CiE 2010, Ponta Delgada, Azores, Portugal, 10/6/30. https://doi.org/10.1007/978-3-642-13962-8_40
Sakakibara Y. Development of a bacteria computer: From in silico finite automata to in vitro and in vivo. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6158 LNCS. 2010. p. 362-371. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-13962-8_40
Sakakibara, Yasubumi. / Development of a bacteria computer : From in silico finite automata to in vitro and in vivo. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6158 LNCS 2010. pp. 362-371 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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