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cond-mat.softApr 10, 2020
31
citations (OpenAlex)
authors
  • Jonathan P. K. Doye
  • Hannah Fowler
  • Domen Prešern
  • Joakim Bohlin
  • Lorenzo Rovigatti
  • Flavio Romano
  • Petr Šulc
  • Chak Kui Wong
  • Ard A. Louis
  • John S. Schreck
  • Megan C. Engel
  • Michael Matthies
  • Erik Benson
  • Erik Poppleton
  • Benedict E. K. Snodin
institutions
  • Arizona State University
  • Harvard University
  • NSF National Center for Atmospheric Research
  • NSF NCAR Computational & Information Systems Laboratory
  • Sapienza University of Rome
  • University of Oxford
arXiv abstractPDF
paper

The oxDNA coarse-grained model as a tool to simulate DNA origami

arXiv:2004.05052 · doi:10.1007/978-1-0716-3028-0_6

Abstract

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

arXiv comment17 pages, 5 figures

References in corpus (10)

  • Canonical sampling through velocity-rescaling
  • Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
  • Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
  • Sequence-dependent thermodynamics of a coarse-grained DNA model
  • A nucleotide-level coarse-grained model of RNA
  • Molecular engineering of chiral colloidal liquid crystals using DNA origami
  • Coarse-grained modelling of the structural properties of DNA origami
  • Coarse-Grained Simulation of DNA using LAMMPS
  • Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis
  • Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
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