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Maze Exploration with Molecular-Scale Walkers

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Theory and Practice of Natural Computing (TPNC 2012)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7505))

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Abstract

Molecular spiders are nanoscale walkers made with catalytic DNA legs attached to a rigid body. They move in a matrix of DNA substrates, cleaving them and leaving behind product DNA strands. Unlike a self-avoiding walker, a spider is able to revisit the products. However, the legs cleave and detach from substrates more slowly than they detach from products. This difference in residence time and the presence of multiple legs make a spider move differently from an ordinary random walker. The number of legs, and their lengths, can be varied, and this defines the spider’s local gait, which affects its behavior in global tasks. In this work we define an abstract model of molecular spiders, and within it we study the efficiency of maze exploration as a function of the spider structure. For a fixed geometry, there is an optimal setting of chemical kinetics parameters that minimizes the mean time to traverse a maze.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of New Mexico, USA

    Darko Stefanovic

  2. Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA

    Darko Stefanovic

Authors
  1. Darko Stefanovic
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Editor information

Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Universitat Rovira i Virgili, Avinguda Catalunya, 35, 43002, Tarragona, Spain

    Adrian-Horia Dediu  & Carlos Martín-Vide  & 

  2. Fakultät für Informatik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany

    Bianca Truthe

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Stefanovic, D. (2012). Maze Exploration with Molecular-Scale Walkers. In: Dediu, AH., Martín-Vide, C., Truthe, B. (eds) Theory and Practice of Natural Computing. TPNC 2012. Lecture Notes in Computer Science, vol 7505. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33860-1_18

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  • DOI: https://doi.org/10.1007/978-3-642-33860-1_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33859-5

  • Online ISBN: 978-3-642-33860-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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