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

Masahiro Takinoue, Daisuke Kiga, Koh Ichiroh Shohda, Akira Suyama

Research output: Contribution to journalArticle

35 Citations (Scopus)

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 languageEnglish
Article number041921
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume78
Issue number4
DOIs
Publication statusPublished - 2008 Oct 29
Externally publishedYes

Fingerprint

Molecular Computing
Transcription
Simulation Model
Experiment
Reverse
simulation
Computing
deoxyribonucleic acid
Molecules
Modeling Method
Mathematical Modeling
molecules

ASJC Scopus subject areas

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

Cite this

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

In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, Vol. 78, No. 4, 041921, 29.10.2008.

Research output: Contribution to journalArticle

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