### Abstract

Autonomous DNA computers have been attracting much attention because of their ability to integrate into living cells. Autonomous DNA computers can process information through DNA molecules and their molecular reactions. We have already proposed an idea of an autonomous molecular computer with high computational ability, which is now named Reverse-transcription-and- TRanscription-based Autonomous Computing System (RTRACS). In this study, we first report an experimental demonstration of a basic computation element of RTRACS and a mathematical modeling method for RTRACS. We focus on an AND gate, which produces an output RNA molecule only when two input RNA molecules exist, because it is one of the most basic computation elements in RTRACS. Experimental results demonstrated that the basic computation element worked as designed. In addition, its behaviors were analyzed using a mathematical model describing the molecular reactions of the RTRACS computation elements. A comparison between experiments and simulations confirmed the validity of the mathematical modeling method. This study will accelerate construction of various kinds of computation elements and computational circuits of RTRACS, and thus advance the research on autonomous DNA computers.

Original language | English |
---|---|

Article number | 041921 |

Journal | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics |

Volume | 78 |

Issue number | 4 |

DOIs | |

Publication status | Published - 2008 Oct 29 |

Externally published | Yes |

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### ASJC Scopus subject areas

- Condensed Matter Physics
- Statistical and Nonlinear Physics
- Statistics and Probability

### Cite this

*Physical Review E - Statistical, Nonlinear, and Soft Matter Physics*,

*78*(4), [041921]. https://doi.org/10.1103/PhysRevE.78.041921

**Experiments and simulation models of a basic computation element of an autonomous molecular computing system.** / Takinoue, Masahiro; Kiga, Daisuke; Shohda, Koh Ichiroh; Suyama, Akira.

Research output: Contribution to journal › Article

*Physical Review E - Statistical, Nonlinear, and Soft Matter Physics*, vol. 78, no. 4, 041921. https://doi.org/10.1103/PhysRevE.78.041921

}

TY - JOUR

T1 - Experiments and simulation models of a basic computation element of an autonomous molecular computing system

AU - Takinoue, Masahiro

AU - Kiga, Daisuke

AU - Shohda, Koh Ichiroh

AU - Suyama, Akira

PY - 2008/10/29

Y1 - 2008/10/29

N2 - Autonomous DNA computers have been attracting much attention because of their ability to integrate into living cells. Autonomous DNA computers can process information through DNA molecules and their molecular reactions. We have already proposed an idea of an autonomous molecular computer with high computational ability, which is now named Reverse-transcription-and- TRanscription-based Autonomous Computing System (RTRACS). In this study, we first report an experimental demonstration of a basic computation element of RTRACS and a mathematical modeling method for RTRACS. We focus on an AND gate, which produces an output RNA molecule only when two input RNA molecules exist, because it is one of the most basic computation elements in RTRACS. Experimental results demonstrated that the basic computation element worked as designed. In addition, its behaviors were analyzed using a mathematical model describing the molecular reactions of the RTRACS computation elements. A comparison between experiments and simulations confirmed the validity of the mathematical modeling method. This study will accelerate construction of various kinds of computation elements and computational circuits of RTRACS, and thus advance the research on autonomous DNA computers.

AB - Autonomous DNA computers have been attracting much attention because of their ability to integrate into living cells. Autonomous DNA computers can process information through DNA molecules and their molecular reactions. We have already proposed an idea of an autonomous molecular computer with high computational ability, which is now named Reverse-transcription-and- TRanscription-based Autonomous Computing System (RTRACS). In this study, we first report an experimental demonstration of a basic computation element of RTRACS and a mathematical modeling method for RTRACS. We focus on an AND gate, which produces an output RNA molecule only when two input RNA molecules exist, because it is one of the most basic computation elements in RTRACS. Experimental results demonstrated that the basic computation element worked as designed. In addition, its behaviors were analyzed using a mathematical model describing the molecular reactions of the RTRACS computation elements. A comparison between experiments and simulations confirmed the validity of the mathematical modeling method. This study will accelerate construction of various kinds of computation elements and computational circuits of RTRACS, and thus advance the research on autonomous DNA computers.

UR - http://www.scopus.com/inward/record.url?scp=56149111222&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=56149111222&partnerID=8YFLogxK

U2 - 10.1103/PhysRevE.78.041921

DO - 10.1103/PhysRevE.78.041921

M3 - Article

VL - 78

JO - Physical review. E

JF - Physical review. E

SN - 1539-3755

IS - 4

M1 - 041921

ER -