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Multiple Molecular Spiders with a Single Localized Source—The One-Dimensional Case

(Extended Abstract)
  • Oleg Semenov
  • Mark J. Olah
  • Darko Stefanovic
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6937)

Abstract

Molecular spiders are nanoscale walkers made with DNA enzyme legs attached to a common body. They move over a surface of DNA substrates, cleaving them and leaving behind product DNA strands, which they are able to revisit. Simple one-dimensional models of spider motion show significant superdiffusive motion when the leg-substrate bindings are longer-lived than the leg-product bindings. This gives the spiders potential as a faster-than-diffusion transport mechanism. However, analysis shows that single-spider motion eventually decays into an ordinary diffusive motion, owing to the ever increasing size of the region of cleaved products. Inspired by cooperative behavior of natural molecular walkers, we propose a model for multiple walkers moving collectively over a one-dimensional lattice. We show that when walkers are sequentially released from the origin, the collective effect is to prevent the leading walkers from moving too far backwards. Hence there is an effective outward pressure on the leading walkers that keeps them moving superdiffusively for longer times, despite the growth of the product region.

Keywords

Molecular Motor Common Body Mean Square Displace Feasible Transition Kinetic Monte Carlo Method 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Oleg Semenov
    • 1
  • Mark J. Olah
    • 1
  • Darko Stefanovic
    • 1
  1. 1.Department of Computer ScienceUniversity of New MexicoMexico

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