2nd Internationa ICST Conference on Nano-Networks

Research Article

Thermodynamic Simulations of DNA Tile Self-Assembly

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  • @INPROCEEDINGS{10.4108/ICST.NANONET2007.2075,
        author={Kenichi Fujibayashi and Satoshi Murata},
        title={Thermodynamic Simulations of DNA Tile Self-Assembly},
        proceedings={2nd Internationa ICST Conference on Nano-Networks},
        proceedings_a={NANO-NET},
        year={2010},
        month={5},
        keywords={},
        doi={10.4108/ICST.NANONET2007.2075}
    }
    
  • Kenichi Fujibayashi
    Satoshi Murata
    Year: 2010
    Thermodynamic Simulations of DNA Tile Self-Assembly
    NANO-NET
    ICST
    DOI: 10.4108/ICST.NANONET2007.2075
Kenichi Fujibayashi1,*, Satoshi Murata1,*
  • 1: Department of Computational Intelligence and Systems Science Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
*Contact email: fuji@mrt.dis.titech.ac.jp, murata@dis.titech.ac.jp

Abstract

Self-assembling DNA complexes have been intensively studied in recent years aiming to achieve bottom-up construction of nanoscale objects. Among them, a DNA complex called DNA tile is known for its high programmability. By using a set of DNA tiles, we are able to self-assemble two-dimensional crystals with programmable patterns. This is called algorithmic self-assembly. In order to create a wide range of complex objects by this self-assembly process, we need a methodology to predict its behavior. Especially, the relationship between the error rates and growth speed is of our interest. To estimate these properties, we use thermodynamic simulations based on the Monte Carlo method. However, conventional simulation models assume some much simplified conditions, therefore cannot explain the results of crystal growth experiments. Here, we propose Realistic Tile Assembly Model (R-TAM), in which we model the detailed conditions of the experimental protocol. We will show that the simulation can explain growth process of DNA tile crystals in experiment.