10th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)

Research Article

Simulating Self-replicating Patterns of DNA Tiles

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  • @INPROCEEDINGS{10.4108/eai.22-3-2017.152414,
        author={Vinay K. Gautam and Rajendra Prasath},
        title={Simulating Self-replicating Patterns of DNA Tiles},
        proceedings={10th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)},
        publisher={EAI},
        proceedings_a={BICT},
        year={2017},
        month={3},
        keywords={algorithmically programmable pattern self-replication simulation of self-replication dna self-assembly dna tile},
        doi={10.4108/eai.22-3-2017.152414}
    }
    
  • Vinay K. Gautam
    Rajendra Prasath
    Year: 2017
    Simulating Self-replicating Patterns of DNA Tiles
    BICT
    EAI
    DOI: 10.4108/eai.22-3-2017.152414
Vinay K. Gautam1,*, Rajendra Prasath1
  • 1: Department of Computer and Information Science, NTNU
*Contact email: vkgautam@idi.ntnu.no

Abstract

This paper presents a simulation framework in which a pre-assembled rectangular pattern of DNA tiles can be put together with sets of other DNA tiles to autonomously assemble replicas of itself in a discrete two-dimensional grid. The simulator implements both abstract and chemical kinetics based modelling to simulate the tile pattern self-replication. While the abstract model uses only logical matching between the edges of tiles to guide the assembly process, the chemical kinetics model calculates stochastic preference for attachment and/or detachment of each tile during the self-replication. A comparison is made between pattern self-replication timing in the abstract model and cellular automata based models. Simulation of chemical kinetics behaviour shows that the physico-chemical parameters of tile self-assembly govern the tractability of self-replication process and reliability of replicating patterns. Observations are made about the limitations of the simulator, and a few suggestions for improvement and further studies are discussed.