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cond-mat.soft2021★ 3 cited
Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling
Jonathan P. K. Doye, Ard A. Louis, John S. Schreck +5
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the…
cond-mat.soft2020
Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
Megan C. Engel, Flavio Romano, Ard A. Louis +1
We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on…
cond-mat.soft2020
The oxDNA coarse-grained model as a tool to simulate DNA origami
Jonathan P. K. Doye, Hannah Fowler, Domen Prešern +12
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.