Coarse-Grained Modelling of DNA and DNA Self-Assembly

  • Thomas E. Ouldridge

Part of the Springer Theses book series (Springer Theses)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Thomas E. Ouldridge
    Pages 1-20
  3. Thomas E. Ouldridge
    Pages 21-37
  4. Thomas E. Ouldridge
    Pages 39-49
  5. Thomas E. Ouldridge
    Pages 51-58
  6. Thomas E. Ouldridge
    Pages 59-69
  7. Thomas E. Ouldridge
    Pages 71-92
  8. Thomas E. Ouldridge
    Pages 93-100
  9. Thomas E. Ouldridge
    Pages 101-117
  10. Thomas E. Ouldridge
    Pages 119-122
  11. Back Matter
    Pages 123-176

About this book


This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker — the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.


Biological Motors Coarse Grained Molecular Simulation DNA Nanotechnology DNA Tweezers DNA Walker Molecular Self-Assembly Monte Carlo Algorithms

Authors and affiliations

  • Thomas E. Ouldridge
    • 1
  1. 1.University of OxfordOxfordUnited Kingdom

Bibliographic information

  • DOI
  • Copyright Information Springer-Verlag Berlin Heidelberg 2012
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Physics and Astronomy
  • Print ISBN 978-3-642-30516-0
  • Online ISBN 978-3-642-30517-7
  • Series Print ISSN 2190-5053
  • Series Online ISSN 2190-5061
  • Buy this book on publisher's site
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