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#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Phys. Condens. Matter''. '''22''', 104102 (2010)
#:[http://dx.doi.org/10.1088/0953-8984/22/10/104102 Extracting bulk properties of self-assembling systems from small simulations] ([https://arxiv.org/abs/0910.1201 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#:[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
#:[http://aip.scitation.org/doi/abs/10.1063/1.3552946?journalCode=jcp Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
#T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
#T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
#:[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 Coarse-grained modelling of DNA and DNA self-assembly]
#:[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 Coarse-grained modelling of DNA and DNA self-assembly]
#F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''136''', 215102 (2012)
#F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''136''', 215102 (2012)
#:[http://jcp.aip.org/resource/1/jcpsa6/v136/i21/p215102_s1 The effect of topology on the structure and free energy landscape of DNA kissing complexes] ([http://arxiv.org/abs/1203.3577 arXiv])
#:[http://dx.doi.org/10.1063/1.4722203 The effect of topology on the structure and free energy landscape of DNA kissing complexes] ([http://arxiv.org/abs/1203.3577 arXiv])
#C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, ''Soft Matter'' '''8''', 8388 (2012)
#C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, ''Soft Matter'' '''8''', 8388 (2012)
#:[http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25845e Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link] ([http://arxiv.org/abs/1204.0985 arXiv])
#:[http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25845e Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link] ([http://arxiv.org/abs/1204.0985 arXiv])
#C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, ''J. Phys. Chem. B'' (2012)
#C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, ''J. Phys. Chem. B'' '''116''', 1161-11625 (2012)
#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#:[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])  
#:[http://dx.doi.org/10.1063/1.4754132 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])
#T.E. Ouldridge, ''J. Chem. Phys.'' '''137''', 144105 (2012)
#:[https://doi.org/10.1063/1.4757267 Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble] ([https://arxiv.org/abs/1204.5716 arXiv])
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#:[http://jcp.aip.org/resource/1/jcpsa6/v138/i8/p085101_s1 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
#:[http://dx.doi.org/10.1063/1.4792252 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
#P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, ''Natural Computing'' (2013)
#T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ''ACS Nano'' '''7''', 2479-2490  (2013)  
#:[http://link.springer.com/article/10.1007%2Fs11047-013-9391-8 Simulating a burnt-bridges DNA motor with a coarse-grained DNA model] ([http://arxiv.org/abs/1212.4536 arXiv])
#T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ''ACS Nano'' (2013)  
#:[http://pubs.acs.org/doi/abs/10.1021/nn3058483 Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker]
#:[http://pubs.acs.org/doi/abs/10.1021/nn3058483 Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker]
#T. E. Ouldridge, P. Šulc,  F. Romano, J. P. K. Doye, A. A. Louis, ''Nucleic Acids Res.'', (2013)  
#T. E. Ouldridge, P. Šulc,  F. Romano, J. P. K. Doye, A. A. Louis, ''Nucleic Acids Res.'' '''41''', 8886-8895 (2013)  
#:[http://nar.oxfordjournals.org/content/early/2013/08/08/nar.gkt687 DNA hybridization kinetics: zippering, internal displacement and sequence dependence] ([http://arxiv.org/abs/1303.3370 arXiv])
#:[https://dx.doi.org/10.1093%2Fnar%2Fgkt687 DNA hybridization kinetics: zippering, internal displacement and sequence dependence] ([http://arxiv.org/abs/1303.3370 arXiv])
#J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, ''Phys. Chem. Chem. Phys'' (2013)
#J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, ''Phys. Chem. Chem. Phys'' '''15''', 20395-20414 (2013)
#:[http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp53545b#!divAbstract Coarse-graining DNA for simulations of DNA nanotechnology] ([http://arxiv.org/abs/1308.3843 arXiv])
#:[http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp53545b#!divAbstract Coarse-graining DNA for simulations of DNA nanotechnology] ([http://arxiv.org/abs/1308.3843 arXiv])
# N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, ''Nucleic Acids Res.'', (2013)
# N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, ''Nucleic Acids Res.'' '''41''', 10641-10658 (2013)
#:[http://nar.oxfordjournals.org/content/early/2013/09/07/nar.gkt801.full?sid=762d341b-b72f-4a09-9235-20ad3ef8aeed  On the biophysics and kinetics of toehold-mediated DNA strand displacement]
#:[http://dx.doi.org/10.1093/nar/gkt801 On the biophysics and kinetics of toehold-mediated DNA strand displacement]
#P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, ''Natural Computing'' '''13''', 535  (2014)
#:[http://link.springer.com/article/10.1007%2Fs11047-013-9391-8 Simulating a burnt-bridges DNA motor with a coarse-grained DNA model] ([http://arxiv.org/abs/1212.4536 arXiv])
#L. Rovigatti, F. Bomboi, F. Sciortino, ''J. Chem. Phys.'' '''140''', 154903 (2014)
#L. Rovigatti, F. Bomboi, F. Sciortino, ''J. Chem. Phys.'' '''140''', 154903 (2014)
#:[http://dx.doi.org/10.1063/1.4870467 Accurate phase diagram of tetravalent DNA nanostars] ([http://arxiv.org/abs/1401.2837 arXiv])
#:[http://dx.doi.org/10.1063/1.4870467 Accurate phase diagram of tetravalent DNA nanostars] ([http://arxiv.org/abs/1401.2837 arXiv])
# L. Rovigatti, P. Šulc, I. Reguly, F. Romano, ''arXiv'', (2014)
#P. Šulc, F. Romano, T. E. Ouldridge,  J. P. K. Doye, A. A. Louis,  ''J. Chem. Phys.'' '''140''', 235102 (2014)
#:[http://arxiv.org/abs/1401.4350 A comparison between parallelization approaches in molecular dynamics simulations on GPUs]
#P. Šulc, F. Romano, T. E. Ouldridge,  J. P. K. Doye, A. A. Louis,  ''J. Chem. Phys.'' 140, 235102 (2014)
#:[http://scitation.aip.org/content/aip/journal/jcp/140/23/10.1063/1.4881424 A nucleotide-level coarse-grained model of RNA] ([http://arxiv.org/abs/1403.4180 arXiv])
#:[http://scitation.aip.org/content/aip/journal/jcp/140/23/10.1063/1.4881424 A nucleotide-level coarse-grained model of RNA] ([http://arxiv.org/abs/1403.4180 arXiv])
#L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ''ACS Nano'', (2014)
#L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ''ACS Nano'' '''8''', 3567-3574 (2014)
#:[http://pubs.acs.org/doi/abs/10.1021/nn501138w Gels of DNA Nanostars Never Crystallise]
#:[http://pubs.acs.org/doi/abs/10.1021/nn501138w Gels of DNA Nanostars Never Crystallise]
#C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis,''arXiv'', (2014)
#:[http://arxiv.org/abs/1404.2869 Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA]
#Q. Wang, B. M. Pettitt, ''Biophys. J.'' '''106''', 1182–1193 (2014)
#Q. Wang, B. M. Pettitt, ''Biophys. J.'' '''106''', 1182–1193 (2014)
#:[http://www.sciencedirect.com/science/article/pii/S0006349514000927 Modeling DNA Thermodynamics under Torsional Stress]
#:[http://www.sciencedirect.com/science/article/pii/S0006349514000927 Modeling DNA Thermodynamics under Torsional Stress]
#  J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, ''Nucleic Acids Res.'' '''43''', 6181-6190 (2014)
#:[http://nar.oxfordjournals.org/content/43/13/6181 DNA hairpins primarily promote duplex melting rather than inhibiting hybridization] ([http://arxiv.org/abs/1408.4401 arXiv])
# R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, ''Nature Comm.'' '''5''', 5324 (2014)
#:[http://www.nature.com/ncomms/2014/141110/ncomms6324/full/ncomms6324.html Programmable energy landscapes for kinetic control of DNA strand displacement]
# M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ''J. Phys. Chem. B'' '''118''', 14326-14335 (2014)
#:[http://arxiv.org/ct?url=http%3A%2F%2Fdx.doi.org%2F10%252E1021%2Fjp510061f&v=13bb91c1 The role of loop stacking in the dynamics of DNA hairpin formation] ([http://arxiv.org/abs/1410.1218 arXiv])
# I. Y. Loh, J.Cheng, S. R. Tee, A. Efremov, and Z. Wang, ''ACS Nano'' '''8''', 10293–10304 (2014)
#:[http://pubs.acs.org/doi/abs/10.1021/nn5034983 From bistate molecular switches to self-directed track-walking nanomotors]
# C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, ''Sci. Rep.'', '''5''', 7655 (2015)
#:[http://dx.doi.org/10.1038/srep07655 Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA] ([http://arxiv.org/abs/1404.2869 arXiv])
# L. Rovigatti, P. Šulc, I. Reguly, F. Romano, ''J. Comput. Chem.'', '''36''', 1-8 (2015)
#:[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23763/abstract A comparison between parallelization approaches in molecular dynamics simulations on GPUs] ([http://arxiv.org/abs/1401.4350 arXiv])
# P. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', '''26''', 084001 (2015)
#:[http://dx.doi.org/10.1088/0957-4484/26/8/084001 Physical model for recognition tunneling]
# F. Romano and F. Sciortino, ''Phys. Rev. Lett.'' '''114''', 078104 (2015)
#:[http://dx.doi.org/10.1103/PhysRevLett.114.078104 Switching Bonds in a DNA Gel: An All-DNA Vitrimer]
#  J. S. Schreck, T. E. Ouldridge, F. Romano, A. A. Louis, J.P.K. Doye, ''J. Chem. Phys.'' '''142''', 165101 (2015)
#:[http://scitation.aip.org/content/aip/journal/jcp/142/16/10.1063/1.4917199 Characterizing the bending and flexibility induced by bulges in DNA duplexes] ([http://arxiv.org/abs/1412.6309 arXiv])
#  M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ''ACS Nano'' '''9''', 11993 (2015)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.5b04726 Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors] ([http://arxiv.org/abs/1502.03623 arXiv])
# T. E. Ouldridge, ''Mol. Phys.'' '''113''', 1-15 (2015)
#:[http://www.tandfonline.com/doi/abs/10.1080/00268976.2014.975293 DNA nanotechnology: understanding and optimisation through simulation] ([http://arxiv.org/abs/1411.1927 arXiv])
# P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis,  ''Biophys. J.'' '''108''', 1238-1247 (2015)
#:[http://dx.doi.org/10.1016/j.bpj.2015.01.023 Modelling toehold-mediated RNA strand displacement] ([http://arxiv.org/abs/1411.3239 arXiv])
# B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, ''J. Chem. Phys.'' '''142''', 234901 (2015)
#:[http://scitation.aip.org/content/aip/journal/jcp/142/23/10.1063/1.4921957 Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/1504.00821 arXiv])
# C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis,  ''J. Chem. Phys.''  '''143''', 243122 (2015)
#:[http://dx.doi.org/10.1063/1.4933066 Coarse-grained modelling of supercoiled RNA] ([http://arxiv.org/abs/1506.02539 arXiv])
# Q. Wang, C.G. Myers, and B.M. Pettitt, ''J. Phys. Chem. B'' '''119''', 4937–4943 (2015)
#:[http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b00865 Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density]
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''J. Chem. Theor. Comput.'' '''15''' 4660-4672 (2019)
#: [https://doi.org/10.1021/acs.jctc.9b00112 Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model] ([http://arxiv.org/abs/1506.09008 arXiv]) ([http://dx.doi.org/10.5281/zenodo.1753767 data])
# J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, ''Science'' '''349''', 977-981 (2015)
#:[http://dx.doi.org/10.1126/science.aab2666  Base triplet stepping by the Rad51/RecA family of recombinases]
# B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ''ACS Nano'' '''10''', 1724-1737 (2016)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.5b05865 Direct Simulation of the Self-Assembly of a Small DNA Origami] ([https://ora.ox.ac.uk/objects/uuid:e71db18a-71f2-4806-9200-dc4cdc283ec8 data])
# V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, ''Nat. Commun.'' '''7''', 10803 (2016)
#:[http://dx.doi.org/10.1038/ncomms10803 Design principles for rapid folding of knotted DNA nanostructures]
#  J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ''ACS Nano'', '''10''', 4236-4247 (2016)
#:[http://dx.doi.org/10.1021/acsnano.5b07664 Characterizing DNA star-tile-based nanostructures using a coarse-grained model]
# M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ''ACS Nano'', '''10''', 5882–5890 (2016)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b01035 Biomimetic autonomous enzymatic nanowalker of high fuel efficiency]
# J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, ''J. Chem. Phys.'' '''145''', 084910 (2016)
#:[http://dx.doi.org/10.1063/1.4961398 Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars]
# T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, ''Nucleic Acids Res.'' '''44''', 9121-9130 (2016)
#:[http://dx.doi.org/10.1093/nar/gkw815 Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation]
# Q. Wang and B.M. Pettitt, ''J. Phys. Chem. Lett'' '''7''', 1042–1046 (2016)
#:[http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b00246 Sequence affects the cyclization of DNA minicircles]
# A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, ''J. Phys: Condens. Matter'' '''29''', 014006 (2017).
#:[http://iopscience.iop.org/article/10.1088/0953-8984/29/1/014006 Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal] ([http://arxiv.org/abs/1607.06626 arXiv]) ([http://dx.doi.org/10.17863/cam.4904 data])
# E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ''ACS Nano'' '''11''', 2094-2102 (2017)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b08287 Condensation and demixing in solutions of DNA nanostars and their mixtures]
# E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, ''J. Chem. Phys'' '''146''', 214902 (2017)
#:[http://dx.doi.org/10.1063/1.4984039 DNA elasticity from coarse-grained simulations: the effect of groove asymmetry] [https://arxiv.org/abs/1703.02598 (arXiv)]
# A. Suma and C. Micheletti, ''Proc. Natl. Acad. Sci. USA'' '''114''', E2991–E2997 (2017)
#:[http://dx.doi.org/10.1073/pnas.1701321114 Pore translocation of knotted DNA rings]
# Z. Shi, C. E. Castro and G. Arya, ''ACS Nano'' '''11''', 4617–4630 (2017)
#:[http://dx.doi.org/10.1021/acsnano.7b00242 Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations]
# H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, ''J. Phys. Chem. B'' '''121''', 5033–5039 (2017)
#:[http://dx.doi.org/10.1021/acs.jpcb.7b03931 Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design]
# S. Vangaveti,  R. J. D'Esposito,  J. L. Lippens,  D. Fabris  and  S. V. Ranganathan, ''Phys. Chem. Chem. Phys.'' '''19''', 14937-14946 (2017)
#:[http://pubs.rsc.org/en/content/articlehtml/2017/cp/c7cp00717e A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry]
# A. Henning-Knechtel, J. Knechtel and M. Magzoub, ''Nucleic Acids Res.'' '''45''', 12057–12068 (2017)
#: [https://doi.org/10.1093/nar/gkx990 DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels]
# R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''ACS Nano'' '''11''', 12426–12435 (2017)
#:[http://dx.doi.org/10.1021/acsnano.7b06470 Characterizing the motion of jointed DNA nanostructures using a coarse-grained model]
# Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, ''Nanoscale'' '''9''', 12142-12149 (2017)
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
# G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, ''Nat. Nanotechnol.'' '''12''', 920–927 (2017)
#: [https://doi.org/10.1038/nnano.2017.127 A spatially localized architecture for fast and modular DNA computing]
# Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, ''Nucleic Acids Res.'' '''45''' 7633-7642 (2017)
#: [https://doi.org/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]
# B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, ''Nucleic Acids Res.'' '''46''', 538-545 (2018)
#: [http://dx.doi.org/10.1093/nar/gkx1238 Rolling circle amplification shows a sinusoidal template length-dependent amplification bias] ([http://dx.doi.org/10.5287/bodleian:VJJYJXOrg data])
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# A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' '''121''', 4849-4859 (2022)
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# Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, ''J. Am. Chem. Soc.'' 145, 25, 13858–13868 (2023)
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# H.L. Too and Z. Wang, ''Nanoscale'' '''15''', 11915-11926 (2023)
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# J. Lee and S. Lee, ''Anal. Chem.'' '''95''', 1856–1866 (2023) 
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# L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, ''Small Methods'' '''7''', 2300327 (2023)
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# I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ''ACS Nano'' '''17''', 17031–17040 (2023)
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# Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, ''Commun. Theor. Phys.'' '''75''', 055601 (2023)
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# D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, ''Nat. Commun.'' '''14''', 6459 (2023)
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#: Bimodal DNA self-origami material with nucleic acid function enhancement
# B. Babatunde, J. Cagan, R.E. Taylor, ''J. Mech. Des.'' '''146''', 051708 (2024)
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# M. Sample, M. Matthies and P. Šulc, ''ACS Nano'' '''18''', 30004–30016 (2024)
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# M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023)
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# C. Shi, D. Yang, X.Ma, L. Pan, Y. Shao, G. Arya, Y. Ke, C. Zhang, F. Wang, X. Zuo, M. Li and P. Wang, ''Angew. Chem. Int. Ed.'' '''63''' e202320179 (2024)
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# F. Smith, A. Sengar, G.‐B.V. Stan, T.E. Ouldridge, M. Stevens, J. Goertz and W. Bae, submitted
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# K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, ''APL Mater.'' '''11''', 061129 (2023)
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# G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted
#: High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv])
# H. Koh, J.Y. Lee, J.G. Lee, submitted
#: Forming superhelix of double stranded DNA from local deformation ([https://doi.org/10.48550/arXiv.2307.04597 arXiv])
# N.P. Agarwal and A. Gopinath, submited
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# J.M. Weck and A. Heuer-Jungemann, submitted
#: Fully addressable, designer superstructures assembled from a single modular DNA origami ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])
# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li,  S. Wang, H. Yan, P. Sulc,  N. Stephanopoulos, submitted
#: High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv])
# H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, ''Science'' '''384''', 776-781 (2024)
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# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' accepted (2024)
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# F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
#: nNxB: a new coarse-grained model for RNA and DNA nanotechnology ([https://doi.org/10.48550/arXiv.2311.03317 arXiv])
# E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys.'' '''160''', 115101 (2024)
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# M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, ''Nat. Commun.'' '''15''', 3015 (2024)
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# S. Cristofaro, L. Querciagrossa, L. Soprani, T.P. Fraccia, T. Bellini, R. Berardi, A. Arcioni, C. Zannoni, L. Muccioli, and S. Orlandi, ''Biomacromolecules'' '''25''', 3920–3929 (2024)
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# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
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# A. Voorspoels, J. Gevers, S. Santermans, N. Akkan, K. Martens, K. Willems, P. Van Dorpe, and A.S. Verhulst, ''J. Phys. Chem. A'' '''128''', 3926–3933 (2024)
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# Y. Wang, I. Baars, I. Berzina, I. Rocamonde-Lago, B. Shen, Y. Yang, M. Lolaico, J. Waldvogel, I. Smyrlaki, K. Zhu, R.A. Harris and B. Högberg, ''Nat. Nanotechnol.'' '''19''', 1366–137 (2024)
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# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''',  1408–1417 (2024)
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# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' '''19''', 1674–1685 (2024)
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# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024)
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# S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, ''Nano Lett.'' '''24''', 11210–11216 (2024)
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# G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, ''Nucl. Acids Res.'' '''52''', 8661–8674 (2024)
#: [https://doi.org/10.1093/nar/gkae576 Weak-cooperative binding of a long single-stranded DNA chain on a surface]
# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109  bioRxiv])
# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro
#: Piggybacking functionalized DNA nanostructures into live cell nuclei ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])
# A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, ''Nat. Commun.'' '''15''', 7564 (2024)
#: [https://doi.org/10.1038/s41467-024-51813-9 Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement] ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv])
# S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
#: Bending Unwinds DNA ([https://doi.org/10.1101/2024.02.14.579968 bioRxiv])
# X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, ''Nat. Commun.'' '''15''', 7210 (2024)
#: [https://doi.org/10.1038/s41467-024-51630-0 A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport] ([https://doi.org/10.21203/rs.3.rs-3878148/v1  ResearchSquare])
# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling]
# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' accepted (2024)
#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications]
# C. Karfusehr, M. Eder, F.C. Simmel
#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])
# M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
#: Reconfigurable multi-component nanostructures built from DNA origami voxels ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv])
# M.P. Tran,  T. Chakraborty,  E. Poppleton,  L. Monari,  F. Giessler and  K. Göpfrich, submitted
#: Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv])
# V. Bukina and A. Božič,  ''Biophys. J.'' '''123''', 3397-3407 (2024)
#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
# R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
#: [https://doi.org/10.1038/s41598-024-70641-x Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations]
# E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
#: Controlling DNA-RNA strand displacement kinetics with base distribution ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv])
# A. Suma and C. Micheletti, submitted
#: Unzipping of knotted DNA via nanopore translocation ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
#: DNA nanodevice for analysis of force-activated protein extension and interactions ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv])
# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])
We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Latest revision as of 13:12, 23 November 2024

  1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
    DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)
  2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Phys. Condens. Matter. 22, 104102 (2010)
    Extracting bulk properties of self-assembling systems from small simulations (arXiv)
  3. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
  4. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
    Coarse-grained modelling of DNA and DNA self-assembly
  5. F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 136, 215102 (2012)
    The effect of topology on the structure and free energy landscape of DNA kissing complexes (arXiv)
  6. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)
    Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link (arXiv)
  7. C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, J. Phys. Chem. B 116, 1161-11625 (2012)
    DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arXiv)
  8. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)
    Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)
  9. T.E. Ouldridge, J. Chem. Phys. 137, 144105 (2012)
    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
  10. F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 138, 085101 (2013)
    Coarse-grained simulations of DNA overstretching (arXiv)
  11. T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ACS Nano 7, 2479-2490 (2013)
    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker
  12. T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye, A. A. Louis, Nucleic Acids Res. 41, 8886-8895 (2013)
    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)
  13. J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, Phys. Chem. Chem. Phys 15, 20395-20414 (2013)
    Coarse-graining DNA for simulations of DNA nanotechnology (arXiv)
  14. N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, Nucleic Acids Res. 41, 10641-10658 (2013)
    On the biophysics and kinetics of toehold-mediated DNA strand displacement
  15. P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, Natural Computing 13, 535 (2014)
    Simulating a burnt-bridges DNA motor with a coarse-grained DNA model (arXiv)
  16. L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)
    Accurate phase diagram of tetravalent DNA nanostars (arXiv)
  17. P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014)
    A nucleotide-level coarse-grained model of RNA (arXiv)
  18. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)
    Gels of DNA Nanostars Never Crystallise
  19. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
    Modeling DNA Thermodynamics under Torsional Stress
  20. J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, Nucleic Acids Res. 43, 6181-6190 (2014)
    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization (arXiv)
  21. R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, Nature Comm. 5, 5324 (2014)
    Programmable energy landscapes for kinetic control of DNA strand displacement
  22. M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, J. Phys. Chem. B 118, 14326-14335 (2014)
    The role of loop stacking in the dynamics of DNA hairpin formation (arXiv)
  23. I. Y. Loh, J.Cheng, S. R. Tee, A. Efremov, and Z. Wang, ACS Nano 8, 10293–10304 (2014)
    From bistate molecular switches to self-directed track-walking nanomotors
  24. C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, Sci. Rep., 5, 7655 (2015)
    Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA (arXiv)
  25. L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1-8 (2015)
    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
  26. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)
    Physical model for recognition tunneling
  27. F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)
    Switching Bonds in a DNA Gel: An All-DNA Vitrimer
  28. J. S. Schreck, T. E. Ouldridge, F. Romano, A. A. Louis, J.P.K. Doye, J. Chem. Phys. 142, 165101 (2015)
    Characterizing the bending and flexibility induced by bulges in DNA duplexes (arXiv)
  29. M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ACS Nano 9, 11993 (2015)
    Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors (arXiv)
  30. T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)
    DNA nanotechnology: understanding and optimisation through simulation (arXiv)
  31. P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, Biophys. J. 108, 1238-1247 (2015)
    Modelling toehold-mediated RNA strand displacement (arXiv)
  32. B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, J. Chem. Phys. 142, 234901 (2015)
    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
  33. C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, J. Chem. Phys. 143, 243122 (2015)
    Coarse-grained modelling of supercoiled RNA (arXiv)
  34. Q. Wang, C.G. Myers, and B.M. Pettitt, J. Phys. Chem. B 119, 4937–4943 (2015)
    Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density
  35. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, arXiv (2015)
    Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
  36. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, J. Chem. Theor. Comput. 15 4660-4672 (2019)
    Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model (arXiv) (data)
  37. J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, Science 349, 977-981 (2015)
    Base triplet stepping by the Rad51/RecA family of recombinases
  38. B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ACS Nano 10, 1724-1737 (2016)
    Direct Simulation of the Self-Assembly of a Small DNA Origami (data)
  39. V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, Nat. Commun. 7, 10803 (2016)
    Design principles for rapid folding of knotted DNA nanostructures
  40. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
    Characterizing DNA star-tile-based nanostructures using a coarse-grained model
  41. M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ACS Nano, 10, 5882–5890 (2016)
    Biomimetic autonomous enzymatic nanowalker of high fuel efficiency
  42. J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, J. Chem. Phys. 145, 084910 (2016)
    Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars
  43. T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, Nucleic Acids Res. 44, 9121-9130 (2016)
    Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
  44. Q. Wang and B.M. Pettitt, J. Phys. Chem. Lett 7, 1042–1046 (2016)
    Sequence affects the cyclization of DNA minicircles
  45. A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, J. Phys: Condens. Matter 29, 014006 (2017).
    Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal (arXiv) (data)
  46. E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ACS Nano 11, 2094-2102 (2017)
    Condensation and demixing in solutions of DNA nanostars and their mixtures
  47. E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, J. Chem. Phys 146, 214902 (2017)
    DNA elasticity from coarse-grained simulations: the effect of groove asymmetry (arXiv)
  48. A. Suma and C. Micheletti, Proc. Natl. Acad. Sci. USA 114, E2991–E2997 (2017)
    Pore translocation of knotted DNA rings
  49. Z. Shi, C. E. Castro and G. Arya, ACS Nano 11, 4617–4630 (2017)
    Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations
  50. H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, J. Phys. Chem. B 121, 5033–5039 (2017)
    Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design
  51. S. Vangaveti, R. J. D'Esposito, J. L. Lippens, D. Fabris and S. V. Ranganathan, Phys. Chem. Chem. Phys. 19, 14937-14946 (2017)
    A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry
  52. A. Henning-Knechtel, J. Knechtel and M. Magzoub, Nucleic Acids Res. 45, 12057–12068 (2017)
    DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels
  53. R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ACS Nano 11, 12426–12435 (2017)
    Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
  54. Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, Nanoscale 9, 12142-12149 (2017)
    A DNA bipedal nanowalker with a piston-like expulsion stroke
  55. G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, Nat. Nanotechnol. 12, 920–927 (2017)
    A spatially localized architecture for fast and modular DNA computing
  56. Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, Nucleic Acids Res. 45 7633-7642 (2017)
    Influence of DNA sequence on the structure of minicircles under torsional stress
  57. B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucleic Acids Res. 46, 538-545 (2018)
    Rolling circle amplification shows a sinusoidal template length-dependent amplification bias (data)
  58. R.V. Reshetnikov, A.V. Stolyarova, A.O. Zalevsky, D.Y. Panteleev, G.V. Pavlova, D.V. Klinov, A.V. Golovin, A.D. Protopopova, Nucleic Acids Res. 46, 1102–1112 (2018)
    A coarse-grained model for DNA origami
  59. D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, Nucleic Acids Res. 46, 1553-1561 (2018)
    DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size (data)
  60. P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, J. Chem. Phys 148, 134910 (2018)
    Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly (arXiv)
  61. T.D. Craggs, M. Sustarsic, A. Plochowietz, M. Mosayebi, H. Kaju, A. Cuthbert, J. Hohlbein, L. Domicevica, P.C. Biggin, J.P.K. Doye and A.N. Kapanidis, Nucleic Acids Res. 47, 10788–10800 (2019)
    Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase (bioRXiv)
  62. S.R. Tee and Z. Wang, ACS Omega, 3, 292-301 (2018)
    How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures
  63. E. Skoruppa, S.K. Nomidis, J.F. Marko and E. Carlon, Phys. Rev. Lett. 121, 088101 (2018)
    Bend-induced twist waves and the structure of nucleosomal DNA (arXiv)
  64. M.M.C. Tortora and J.P.K. Doye, Mol. Phys. 116, 2773-2791 (2018)
    Incorporating particle flexibility in a density functional description of nematics and cholesterics (arXiv)
  65. O. Henrich, Y.A. Gutierrez-Fosado, T. Curk, T.E. Ouldridge, Eur. Phys. J. E 41, 57 (2018)
    Coarse-Grained Simulation of DNA using LAMMPS (arXiv)
  66. M.C. Engel, D. M. Smith, M.A. Jobst, M. Sajfutdinow, T. Liedl, F. Romano, L. Rovigatti, A.A. Louis and J.P.K. Doye, ACS Nano 12, 6734-6747 (2018)
    Force-induced unravelling of DNA Origami
  67. F. Romano and L. Rovigatti, in Design of Self-Assembling Materials (Springer, ed. I. Coluzza) pp 71-90 (2017)
    A Nucleotide-Level Computational Approach to DNA-Based Materials
  68. S.R. Tee, X. Hu, I.Y. Loh and Z. Wang, Phys. Rev. Applied 9, 034025 (2018)
    Mechanosensing potentials gate fuel consumption in a bipedal DNA nanowalker
  69. E. Locatelli and L. Rovigatti, Polymers 10, 447 (2018)
    An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids (preprints)
  70. E. Spruijt, S.E. Tusk and H. Bayley, Nat. Nanotechnol. 13, 739-745 (2018)
    DNA scaffolds support stable and uniform peptide nanopores
  71. L. Coronel, A. Suma and C. Micheletti, Nucleic Acids Res. 46,7522–7532 (2018)
    Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking (bioRXiv)
  72. E. Torelli, J.W. Kozyra, J.-Y. Gu, U. Stimming, L. Piantanida. K. Voitchovsky and N. Krasnogor, Scientific Reports 8, 6989 (2018)
    Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
  73. R. Jin and L. Maibaum, J. Chem. Phys. 150, 105103 (2019)
    Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model(arxiv)
  74. F. Kriegel, C. Matek, T. Dršata, K. Kulenkampff, S. Tschirpke, M. Zacharias, F. Lankas and J. Lipfert, Nucleic Acids Res. 46, 7998–8009 (2018)
    The temperature dependence of the helical twist of DNA
  75. E. Benson, A. Mohammed, D. Rayneau-Kirkhope, A. Gådin, P. Orponen, and B. Högberg, ACS Nano 12, 9291-9299 (2018)
    Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures
  76. S.K. Nomidis, E. Skoruppa, E. Carlon and J.F. Marko, Phys. Rev. E 99 032414 (2019).
    Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: Perturbation theory and beyond (bioRXiv,arXiv)
  77. B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, Nucleic Acids Res. 47, 1585–1597 (2019).
    Coarse-grained modelling of the structural properties of DNA origami (arXiv) (data)
  78. N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, Nat. Commun 11, 2562 (2020)
    Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement (bioRXiv)
  79. L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, Small 14, 1802580 (2018)
    Paper origami‐inspired design and actuation of DNA nanomachines with complex motions
  80. R. A. Brady, W.T. Kaufhold, N.J. Brooks, V. Foderà and L. Di Michele, J. Phys. Condens. Matter 31, 074003 (2019)
    Flexibility defines structure in crystals of amphiphilic DNA nanostars (arXiv)
  81. F. Hong, S. Jiang, X. Lan, R.P. Narayanan, P. Šulc, F. Zhang, Y. Liu, and H. Yan, J. Am. Chem. Soc. 140, 14670–14676 (2018)
    Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering
  82. Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
    Design and Synthesis of a Reconfigurable DNA Accordion Rack
  83. M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, Sci. Adv. 6, eaaw8331 (2020)
    Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis (arXiv)
  84. C.-M. Huang, A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, Nanoscale 11, 1647-1660 (2019)
    Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis
  85. I.T. Hoffecker, S. Chen, A. Gådin, A. Bosco, A.I. Teixeira and B. Högberg, Small 15, 1803628 (2019)
    Solution‐controlled conformational switching of an anchored wireframe DNA nanostructure
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  302. J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ACM Trans. Evol. Learn. Optim. accepted (2024)
    Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications
  303. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  304. M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
    Reconfigurable multi-component nanostructures built from DNA origami voxels (bioRxiv)
  305. M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, submitted
    Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells (bioRxiv)
  306. V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)
    Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA (bioRxiv)
  307. R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
    Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations
  308. E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
    Controlling DNA-RNA strand displacement kinetics with base distribution (bioRxiv)
  309. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  310. G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
    Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model (arXiv)
  311. S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
    How we simulate DNA origami (arXiv)
  312. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
    Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
  313. R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
    A Differentiable Model of Nucleic Acid Dynamics (arXiv)
  314. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
    Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
  315. K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
    DNA nanodevice for analysis of force-activated protein extension and interactions (bioRxiv)
  316. W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
    Economical and versatile subunit design principles for self-assembled DNA origami structures (arXiv)

We are also maintaining a list of all published papers using oxDNA at publons.

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