Coarse-grained simulations of DNA overstretching
 Romano, F Chakraborty, D Doye, J Ouldridge, T Louis, A (26 Sep 2012) doi:10.48550/arxiv.1209.5892
Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
 Šulc, P Ouldridge, T Romano, F Doye, J Louis, A (18 Dec 2012) doi:10.48550/arxiv.1212.4536
Coarse-graining DNA for simulations of DNA nanotechnology
 Doye, J Ouldridge, T Louis, A Romano, F Sulc, P Matek, C Snodin, B Rovigatti, L Schreck, J Harrison, R Smith, W (18 Aug 2013) doi:10.48550/arxiv.1308.3843
DNA hybridization kinetics: zippering, internal displacement and sequence dependence
 Ouldridge, T Šulc, P Romano, F Doye, J Louis, A (14 Mar 2013) doi:10.48550/arxiv.1303.3370
The role of loop stacking in the dynamics of DNA hairpin formation
 Mosayebi, M Romano, F Ouldridge, T Louis, A Doye, J (05 Oct 2014) doi:10.48550/arxiv.1410.1218
Modelling toehold-mediated RNA strand displacement
 Šulc, P Ouldridge, T Romano, F Doye, J Louis, A (12 Nov 2014) doi:10.48550/arxiv.1411.3239
A nucleotide-level coarse-grained model of RNA
 Šulc, P Romano, F Ouldridge, T Doye, J Louis, A (17 Mar 2014) doi:10.48550/arxiv.1403.4180
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
 Matek, C Ouldridge, T Doye, J Louis, A (10 Apr 2014) doi:10.48550/arxiv.1404.2869
DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
 Schreck, J Ouldridge, T Romano, F Sulc, P Shaw, L Louis, A Doye, J (19 Aug 2014) doi:10.48550/arxiv.1408.4401
Characterizing the bending and flexibility induced by bulges in DNA duplexes
 Schreck, J Ouldridge, T Romano, F Louis, A Doye, J (19 Dec 2014) doi:10.48550/arxiv.1412.6309
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