423 citations · 1k across the 18 of their papers we have counts for
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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…
Characterizing the free-energy landscapes of DNA origamis
Chak Kui Wong, Chuyan Tang, John S. Schreck +1
We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mech…
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.
Coarse-grained modelling of the structural properties of DNA origami
Benedict E. K. Snodin, John S. Schreck, Flavio Romano +2
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. T…
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
Pedro Fonseca, Flavio Romano, John S. Schreck +3
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculat…
Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal
Aleks Reinhardt, John S. Schreck, Flavio Romano +1
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable…