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The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

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DNA and RNA Origami

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2639))

Abstract

This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.

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Acknowledgments

We are grateful for support from the EPSRC Centre for Doctoral training, Theory and Modelling in Chemical Sciences, under grant EP/L015722/1.

Author information

Authors and Affiliations

  1. Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK

    Jonathan P. K. Doye, Hannah Fowler, Domen Prešern & Chak Kui Wong

  2. Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK

    Joakim Bohlin & Erik Benson

  3. Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy

    Lorenzo Rovigatti & Flavio Romano

  4. School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA

    Petr Šulc, Michael Matthies & Erik Poppleton

  5. Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford, UK

    Ard A. Louis

  6. School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA

    Megan C. Engel

  7. Department of Philosophy, Future of Humanity Institute, University of Oxford, Oxford, UK

    Benedict E. K. Snodin

  8. Computational and Information Systems Laboratory, National Center for Atmospheric Research (NCAR), Boulder, USA

    John S. Schreck

Authors
  1. Jonathan P. K. Doye
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  2. Hannah Fowler
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  3. Domen Prešern
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  4. Joakim Bohlin
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  5. Lorenzo Rovigatti
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  6. Flavio Romano
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  7. Petr Šulc
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  8. Chak Kui Wong
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  9. Ard A. Louis
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  10. John S. Schreck
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  11. Megan C. Engel
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  12. Michael Matthies
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  13. Erik Benson
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  14. Erik Poppleton
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  15. Benedict E. K. Snodin
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Corresponding author

Correspondence to Jonathan P. K. Doye .

Editor information

Editors and Affiliations

  1. Aarhus university, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus, Denmark

    Julián Valero

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Doye, J.P.K. et al. (2023). The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami. In: Valero, J. (eds) DNA and RNA Origami. Methods in Molecular Biology, vol 2639. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3028-0_6

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  • DOI: https://doi.org/10.1007/978-1-0716-3028-0_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3027-3

  • Online ISBN: 978-1-0716-3028-0

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