498 citations · 3.5k across the 66 of their papers we have counts for
16 papers · 1 filter
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…
Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions
Jordan Juritz, Jenny M Poulton, Thomas E Ouldridge
The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthe…
Coarse-Grained Simulation of DNA using LAMMPS
Oliver Henrich, Yair Augusto Gutierrez-Fosado, Tine Curk +1
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, se…
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…
Modelling DNA Origami Self-Assembly at the Domain Level
Frits Dannenberg, Katherine E. Dunn, Jonathan Bath +3
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does no…
Force-induced rupture of a DNA duplex
Majid Mosayebi, Ard A. Louis, Jonathan P. K. Doye +1
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a sy…