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# 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)
# 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]
#:[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)
# 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]  
#: [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)
# 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])
#: [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])
# 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)
#: [https://doi.org/10.1093/nar/gkx1262 A coarse-grained model for DNA origami]
# 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)
# 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)
#: [http://dx.doi.org/10.1093/nar/gkx1282 DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size] ([https://doi.org/10.5287/bodleian:w4ZwVr6Jg data])
#: [http://dx.doi.org/10.1093/nar/gkx1282 DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size] ([https://doi.org/10.5287/bodleian:w4ZwVr6Jg data])
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# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nature Nanotechnology'' '''13''', 739-745 (2018)
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nat. Nanotechnol.'' '''13''', 739-745 (2018)
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
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# B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''Nucleic Acids Res.'' '''47''', 1585–1597 (2019).
# B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''Nucleic Acids Res.'' '''47''', 1585–1597 (2019).
#: [http://dx.doi.org/10.1093/nar/gky1304 Coarse-grained modelling of the structural properties of DNA origami] ([https://arxiv.org/abs/1809.08430 arXiv]) ([http://dx.doi.org/10.5287/bodleian:8gY5EnYYO data])
#: [http://dx.doi.org/10.1093/nar/gky1304 Coarse-grained modelling of the structural properties of DNA origami] ([https://arxiv.org/abs/1809.08430 arXiv]) ([http://dx.doi.org/10.5287/bodleian:8gY5EnYYO data])
# N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, submitted
# N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, ''Nat. Commun'' '''11''', 2562 (2020)
#: Rational design of hidden thermodynamic driving through DNA mismatch repair ([https://doi.org/10.1101/426668 bioRXiv])
#: [https://doi.org/10.1038/s41467-020-16353-y Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement] ([https://doi.org/10.1101/426668 bioRXiv])
# L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, ''Small'' '''14''', 1802580 (2018)
# L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, ''Small'' '''14''', 1802580 (2018)
#: [https://doi.org/10.1002/smll.201802580 Paper origami‐inspired design and actuation of DNA nanomachines with complex motions]
#: [https://doi.org/10.1002/smll.201802580 Paper origami‐inspired design and actuation of DNA nanomachines with complex motions]
Line 159: Line 163:
# Y. Choi, H. Choi, A.C. Lee, S. Kwon, ''J. Vis. Exp.'', e58364 (2018)
# Y. Choi, H. Choi, A.C. Lee, S. Kwon, ''J. Vis. Exp.'', e58364 (2018)
#: [https://doi.org/10.3791/58364 Design and Synthesis of a Reconfigurable DNA Accordion Rack]
#: [https://doi.org/10.3791/58364 Design and Synthesis of a Reconfigurable DNA Accordion Rack]
# M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, submitted
# 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 ([https://arxiv.org/abs/1811.12331 arXiv])
#: [https://dx.doi.org/10.1126/sciadv.aaw8331 Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis] ([https://arxiv.org/abs/1811.12331 arXiv])
#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, ''Nanoscale'' '''11''', 1647-1660 (2019)  
#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, ''Nanoscale'' '''11''', 1647-1660 (2019)  
#: [https://dx.doi.org/10.1039/C8NR06377J Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis]
#: [https://dx.doi.org/10.1039/C8NR06377J Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis]
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# S.K. Nomidis, M. Coraglio, M. Laleman, K. Phillips, E. Skoruppa and E. Carlon, ''Phys. Rev. E'' '''100''', 022402 (2019)
# S.K. Nomidis, M. Coraglio, M. Laleman, K. Phillips, E. Skoruppa and E. Carlon, ''Phys. Rev. E'' '''100''', 022402 (2019)
#: [https://doi.org/10.1103/PhysRevE.100.022402 Twist-bend coupling, twist waves and DNA loops] ([https://arxiv.org/abs/1904.04677 arXiv])
#: [https://doi.org/10.1103/PhysRevE.100.022402 Twist-bend coupling, twist waves and DNA loops] ([https://arxiv.org/abs/1904.04677 arXiv])
# A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, submitted
# A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, ''Nucleic Acids Res.'' '''48''', 4672–4680 (2020)
#: Allosteric modulation of local reactivity in DNA origami ([https://doi.org/10.1101/640847 bioRxiv])
#: [https://doi.org/10.1093/nar/gkaa080 Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure] ([https://doi.org/10.1101/640847 bioRxiv])
# J. Liu, S. Shukor, S. Li, A. Tamayo, L. Tosi, B. Larman, V. Nanda, W.K. Olson and B. Parekkadan, ''Biomolecules'' '''9''', 199 (2019)
# J. Liu, S. Shukor, S. Li, A. Tamayo, L. Tosi, B. Larman, V. Nanda, W.K. Olson and B. Parekkadan, ''Biomolecules'' '''9''', 199 (2019)
#: [https://doi.org/10.3390/biom9050199 Computational simulation of adapter length-dependent LASSO probe capture efficiency]
#: [https://doi.org/10.3390/biom9050199 Computational simulation of adapter length-dependent LASSO probe capture efficiency]
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# J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee,, ''Nucleic Acids Res.'' '''47''', 11963–11975(2019)
# J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee,, ''Nucleic Acids Res.'' '''47''', 11963–11975(2019)
#: [https://doi.org/10.1093/nar/gkz1056 Design and synthesis of pleated DNA origami nanotubes with adjustable diameters] ([http://dx.doi.org/10.1101/534792 bioRxiv])
#: [https://doi.org/10.1093/nar/gkz1056 Design and synthesis of pleated DNA origami nanotubes with adjustable diameters] ([http://dx.doi.org/10.1101/534792 bioRxiv])
# K.G. Young, B. Najafi, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, submitted
# K.G. Young, B. Najafi, W.M. Sant, S. Contera, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, ''Angew. Chem. Int. Ed.'' '''59''', 15942-15946 (2020)
#: Reconfigurable T-junction DNA origami
#: [https://doi.org/10.1002/anie.202006281 Reconfigurable T-junction DNA origami]
# I.D. Stoev, T. Cao, A. Caciagli, J. Yu, C. Ness, R. Liu, R. Ghosh, T. O'Neill, D. Liu and E. Eiser, submitted
# I.D. Stoev, T. Cao, A. Caciagli, J. Yu, C. Ness, R. Liu, R. Ghosh, T. O'Neill, D. Liu and E. Eiser, ''Soft Matter'' '''16''', 990-1001 (2020)
#: On the Role of Flexibility in Linker-Mediated DNA Hydrogels ([https://arxiv.org/abs/1909.05611 arXiv])
#: [http://dx.doi.org/10.1039/C9SM01398A On the Role of Flexibility in Linker-Mediated DNA Hydrogels] ([https://arxiv.org/abs/1909.05611 arXiv])
# E. Benson, M. Lolaico, Y. Tarasov, A. Gådin and B. Högberg, ''ACS Nano'' '''13''', 12591-12598 (2019)
# E. Benson, M. Lolaico, Y. Tarasov, A. Gådin and B. Högberg, ''ACS Nano'' '''13''', 12591-12598 (2019)
#: [https://doi.org/10.1021/acsnano.9b03473 Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations]
#: [https://doi.org/10.1021/acsnano.9b03473 Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations]
# S.W. Shin, S.Y. Ahn, Y.T. Lim and S.H. Um, ''Anal. Chem.'' '''91''',  14808-14811 (2019)
# S.W. Shin, S.Y. Ahn, Y.T. Lim and S.H. Um, ''Anal. Chem.'' '''91''',  14808-14811 (2019)
#: [https://doi.org/10.1021/acs.analchem.9b03173 Improved Sensitivity of Intramolecular Strand Displacement Based on Localization of Probes]
#: [https://doi.org/10.1021/acs.analchem.9b03173 Improved Sensitivity of Intramolecular Strand Displacement Based on Localization of Probes]
# Z. Shi and G. Arya, ''Nucleic Acids Research'' Advance Article.
# Z. Shi and G. Arya, ''Nucleic Acids Research'' '''48''', 548-560 (2020)
#: [https://doi.org/10.1093/nar/gkz1137 Free energy landscape of salt-actuated reconfigurable DNA nanodevices]
#: [https://doi.org/10.1093/nar/gkz1137 Free energy landscape of salt-actuated reconfigurable DNA nanodevices]
# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, submitted
# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ''ACS Synth. Biol.'' '''9''', 1682-1692 (2020)
#: Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami ([https://doi.org/10.1101/864678 bioRxiv])
#: [https://doi.org/10.1021/acssynbio.0c00009 Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami] ([https://doi.org/10.1101/864678 bioRxiv])
# P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, submitted
# P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, ''Nucleic Acids Res.'' '''48''', 10713–10725 (2020)
#: Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches ([https://doi.org/10.1101/2019.12.20.885533 bioRxiv])
#: Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches ([https://doi.org/10.1101/2019.12.20.885533 bioRxiv])
# K. Bartnik, A. Barth, M. Pilo-Pais, A.H. Crevenna, T. Liedl and D.C. Lamb, ''J. Am. Chem. Soc'' '''142''', 815-825 (2020).
#:[https://doi.org/10.1021/jacs.9b09093 A DNA origami platform for single-pair Förster resonance energy transfer investigation of DNA–DNA interactions and ligation]
# E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, ''Nucleic Acids Res.'' '''48''', e72 (2020)
#: [https://doi.org/10.1093/nar/gkaa417 Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation] ([https://doi.org/10.1101/2020.01.24.917419 bioRxiv])
# M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, ''J. Chem. Theor. Comput.'' '''16''', 7764–7775 (2020).
#: [https://doi.org/10.1021/acs.jctc.0c00286 Measuring internal forces in single-stranded DNA: Application to a DNA force clamp] ([http://arxiv.org/abs/arXiv:2007.13865 arXiv])
# C. Bores and B.M. Pettitt, ''Phys. Rev. E'' '''101''', 012406 (2020)
#: [https://doi.org/10.1103/PhysRevE.101.012406 Structure and the role of filling rate on model dsDNA packed in a phage capsid]
# A. Bader and S.L. Cockroft, ''Chem. Commun.'' '''56''', 5135-5138 (2020)
#: [https://doi.org/10.1039/D0CC00882F Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices]
# J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton and B.E.K. Snodin, ''Methods in Molecular Biology'' ''2639'', 93-112 (2023).
#: [https://doi.org/10.1007/978-1-0716-3028-0_6 The oxDNA coarse-grained model as a tool to simulate DNA origami] ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''', 5118–5125 (2020)
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, ''Nat. Commun.'' '''12''', 501 (2021)
#: [https://doi.org/10.1038/s41467-020-20686-z Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy] ([https://doi.org/10.1101/2020.04.24.059410 bioRxiv])
# B. Najafi, K.G. Young, J. Bath, A.A. Louis, J.P.K. Doye and A.J. Turberfield, submitted
#: Characterising DNA T-motifs by simulation and experiment ([https://arxiv.org/abs/2005.11545 arXiv])
# C.M. Huang, A. Kucinic, J.A. Johnson, H.-J. Su, C.E. Castro, ''Nat. Mater.'' '''20''', 1264–1271 (2021)
#: [https://doi.org/10.1038/s41563-021-00978-5 Integrating computer-aided engineering and design for DNA assemblies] ([https://doi.org/10.1101/2020.05.28.119701 bioRxiv])
# P. Irmisch, T.E. Ouldridge, and R. Seidel, ''J. Am. Chem. Soc'' '''142''', 11451–11463 (2020)
#: [https://doi.org/10.1021/jacs.0c03105 Modelling DNA-strand displacement reactions in the presence of base-pair mismatches]
# F. Hong, J.S. Schreck and P. Šulc, ''Nucleic Acids Res.'' '''48''', 10726–10738 (2020).
#: [https://doi.org/10.1093/nar/gkaa854 Understanding DNA interactions in crowded environments with a coarse-grained model] ([https://doi.org/10.1101/2020.06.08.140434 bioRxiv])
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, ''J. Am. Chem. Soc.'' '''142''', 12069–12078 (2020)
#: [https://doi.org/10.1021/jacs.9b03418 Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy] ([https://doi.org/10.1101/591081 bioRxiv])
# H. Chhabra, G. Mishra, Y. Cao, D. Prešern, E. Skoruppa, M.M.C. Tortora and J.P.K. Doye, ''J. Chem. Theor. Comput.'' '''16''', 7748–7763 (2020).
#: [https://dx.doi.org/10.1021/acs.jctc.0c00661 Computing the elastic mechanical properties of rod-like DNA nanostructures] ([http://arXiv.org arXiv])
# K. Tapio, A. Mostafa, Y. Kanehira, A. Suma, A. Dutta, I. Bald, ''ACS Nano'' '''15''', 7065–7077 (2021)
#: [https://doi.org/10.1021/acsnano.1c00188 A versatile DNA origami based plasmonic nanoantenna for label-free single-molecule SERS] ([https://doi.org/10.21203/rs.3.rs-47458/v1 Research Square])
# E.G. Noya, C.K. Wong, P. Llombart and J.P.K. Doye, ''Nature'' 596, 367–371 (2021)
#: [https://doi.org/10.1038/s41586-021-03700-2 How to design an icosahedral quasicrystal through directional bonding]
# Y.A.G. Fosado, F. Landuzzi and T. Sakaue, ''Soft Matter'' '''17''', 1530-1537 (2021)
#: [https://doi.org/10.1039/D0SM01812K Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending] ([https://arxiv.org/abs/2008.05686 arXiv])
# F. Spinozzi, M.G. Ortore, G. Nava, F. Bomboi, F. Carducci, H. Amenitsch, T. Bellini, F. Sciortino, and P. Mariani, ''Langmuir'' '''36''', 10387–10396 (2020)
#: [https://doi.org/10.1021/acs.langmuir.0c01520 Gelling without structuring: a SAXS study of the interactions among DNA nanostars]
# J. Huang  A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar and A. Keller, ''Small Str.'' '''1''', 2000038 (2020)
#: [https://doi.org/10.1002/sstr.202000038 Arranging small molecules with sub‐nanometer precision on DNA origami substrates for the single‐molecule investigation of protein‐ligand interactions]
# G. Yao, F. Zhang, F. Wang, T. Peng, H. Liu, E. Poppleton, P. Šulc, S. Jiang, L. Liu, C. Gong, X. Jing, X. Liu, L. Wang, Y. Liu, C. Fan and H. Yan, ''Nat. Chem.'' '''12''', 1067–1075 (2020)
#: [https://doi.org/10.1038/s41557-020-0539-8 Meta-DNA structures]
# J.F. Berengut, C.K. Wong, J.C. Berengut, J.P.K. Doye, T.E. Ouldridge and L.K. Lee, ''ACS Nano'' '''14''', 17428–17441 (2020)
#: [http://dx.doi.org/10.1021/acsnano.0c07696 Self-limiting polymerization of DNA origami subunits with strain accumulation]
# J. Procyk, E. Poppleton and  P. Šulc, ''Soft Matter'' '''17''', 3586-3593 (2021).
#: [https://doi.org/10.1039/D0SM01639J Coarse-grained nucleic acid-protein model for hybrid nanotechnology] ([https://arxiv.org/abs/2009.09589 arXiv])
# Z. Sierzega, J. Wereszczynski and C. Prior, ''Sci. Rep.'' '''11''', 1527 (2021)
#: [https://doi.org/10.1038/s41598-020-80851-8 WASP: A software package for correctly characterizing the topological development of ribbon structures] ([https://doi.org/10.1101/2020.09.17.301309 bioRXiv])
# E. Skoruppa, A. Voorspoels, J. Vreede and E. Carlon, ''Phys. Rev. E'' '''103''', 042408 (2021)
#: [https://doi.org/10.1103/PhysRevE.103.042408 Length scale dependent elasticity in DNA from coarse-grained and all-atom models] ([https://arxiv.org/abs/2010.01302 arXiv])
# C. Bores, M. Woodson, M.C. Morais, and B. Montgomery Pettitt, ''J. Phys. Chem. B'' '''124''', 10337–10344 (2020)
#: [https://doi.org/10.1021/acs.jpcb.0c07478 Effects of model shape, volume, and softness of the capsid for DNA packaging of phi29]
# E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, ''Nanoscale'' '''12''', 23003-23012 (2020)
#: [https://doi.org/10.1039/D0NR04840B Hyperbranched DNA clusters] ([https://arxiv.org/abs/2011.07854 arXiv])
# B.J.H.M. Rosier, A.J. Markvoort, B. Gumí Audenis, J.A.L. Roodhuizen, A. den Hamer, L. Brunsveld and T.F.A. de Greef, ''Nat. Catal.'' '''3''', 295–306 (2020)
#: [https://doi.org/10.1038/s41929-019-0403-7 Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome]
# R. Li, H. Chen and J.H. Choi, ''Angew. Chem. Int. Ed.'' '''60''', 7165-7173 (2021)
#: [https://doi.org/10.1002/anie.202014729 Auxetic Two‐Dimensional Nanostructures from DNA] ([https://doi.org/10.1101/2020.08.21.262139 bioRXiv])
# D. Wang, L. Yu, C.-M. Huang, G. Arya, S. Chang, and Y. Ke, ''J. Am. Chem. Soc.'' '''143''', 2256–2263 (2021)
#: [https://doi.org/10.1021/jacs.0c10576 Programmable transformations of DNA origami made of small modular dynamic units]
# R. Li, H. Chen, H. Lee, J. H. Choi, ''Appl. Sci.'' '''11''', 2357 (2021)
#: [https://doi.org/10.3390/app11052357 Elucidating the mechanical energy for cyclization of a DNA origami tile] ([https://doi.org/10.1101/2021.02.07.430115 bioRxiv])
# G. Park, M. K. Cho, and Y. Jung, ''J. Chem. Theory Comput.'', '''17''' 1308-1317 (2021)
#: [https://doi.org/10.1021/acs.jctc.0c01116 Sequence-dependent kink formation in short DNA loops: Theory and molecular dynamics simulations]
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# X. Chen, Y. Wang, X. Dai, L. Ding, J. Chen, G. Yao, X. Liu, S. Luo, J. Shi, L. Wang, R. Nechushtai, E. Pikarsky, I. Willner, C. Fan, and J. Li, ''J. Am. Chem. Soc.'' '''144''', 6311–6320 (2022)
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# Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, ''Small'' '''18''', 2205191 (2022)
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# P. E. Beshay, A. Kucinic, N. Wile, P. Halley, L. Des Rosiers, A. Chowdhury, J. L. Hall, C. E. Castro and M. W. Hudoba, ''The Biophysicist'' '''4''', 68–81 (2023)
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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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# E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti,  ''J. Open Source Softw.'' '''8''', 4693 (2023)
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# A. Suma, V. Carnevale and C. Micheletti, ''Phys. Rev. Lett.'' '''130''', 048101 (2023)
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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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# M. DeLuca, W.G. Pfeifer, B. Randoing,  C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, ''Nanoscale'' '''15''', 8356-8365 (2023)
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# T. Liang, C. Yang, X. Song, Y. Feng, Y. Liu and H. Chen, ''Phys. Rev. E'' '''108''', 014406 (2023)
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# D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard ''J. Am. Chem. Soc.'' '''145''', 16691–16703 (2023) 
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# A. Kucinic, C.-M. Huang, J. Wang, H.-J. Su and  C.E. Castro, ''Nanoscale'', '''15''' 562-572 (2023)
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# Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, ''Sci. Adv.''  '''9''', adf8263 (2023)
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# M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ''ACS Nano'' '''17''', 6565–6574 (2023)
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# Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, ''Appl. Sci.'' '''13''', 3208 (2023)
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# D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, ''Nanoscale'' '''15''', 2849-2859 (2023)
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# L. Zhang, H. Zhao, H. Yang and X. Su, ''Biosens. Bioelectron.'' '''239''', 115622 (2023)
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# Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma ''J. Phys. Chem. B'' '''127''', 4015–4021 (2023)
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# K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, ''Molecules'' '''28''', 3686 (2023)
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# H.L. Too and Z. Wang, ''Nanoscale'' '''15''', 11915-11926 (2023)
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# D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, ''Nanoscale'' '''15''', 5403-5413 (2023)
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# J. Lee and S. Lee, ''Anal. Chem.'' '''95''', 1856–1866 (2023) 
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# X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, ''Anal. Chem.'' '''95''', 5903–5910 (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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# Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''Chem. Sci.'' '''14''', 3652-3660 (2023)
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# M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, ''Nature Physics'' '''19''', 741–751 (2023)
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# C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, ''Commun. Comput. Inf. Sci.'', '''1801''', 647–654 (2023)
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# S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, ''Entropy'' '''25''', 796 (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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# Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, ''Nat. Biotechnol.'' (2023)
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# X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, ''Angew. Chem. Int. Ed.'' '''62''' e202309869 (2023)
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# Y. Zhao, S. Cao, Y. Wang, F. Li, L. Lin, L. Guo, F. Wang, J. Chao, X. Zuo, Y. Zhu, L. Wang, J. Li and C. Fan, ''Nat. Mach. Intell.'' '''5''', 980–990 (2023)
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# X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, ''Nanoscale Horiz.'', '''8''', 827-841 (2023)
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# H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang and C. Fan, ''Nature'' '''622''', 292–300(2023). 
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# C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, ''J. Phys.: Condens. Matter'' '''35''', 265101 (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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# R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, ''Nat. Methods'' '''20''', 1666–1671 (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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# J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, ''Anal. Chem.'' '''95''', 16089–16097 (2023)
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# J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. '''14''', 7079 (2023)
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# Y.-P. Qiao and C.-L. Ren, ''Langmuir'' '''40''', 109–117 (2024)
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# L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024)
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# N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, ''Small'', '''20''', 2308763 (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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# Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ''ACS Appl. Bio Mater.'' '''7''', 1311–1316 (2024)
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# S. He, H. Deng, P. Li, Q. Tian, Y. Yang, J. Hu, H. Li, T. Zhao, H. Ling, Y. Liu, S. Liu and Q. Guo, ''J. Nanobiotechnol.'' '''22''', 39 (2024)
#: 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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# A.S.G. Martins, S.D. Reis, E. Benson, M.M. Domingues, J. Cortinhas, J.A. Vidal Silva, S.D. Santos, N.C. Santos, A.P. Pêgo, P.M.D. Moreno, ''Small'' '''20''', 2309140 (2024)
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# S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, ''Nanoscale'' '''16''', 4872-4879 (2024)
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# T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, ''Angew. Chem. Int. Ed'' '''63''', e202319117 (2024)
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# Y. Liu, Z. Dai, X. Xie, B. Li, S. Jia, Q. Li, M. Li, C. Fan and X. Liu, ''J. Am. Chem. Soc.'' '''146''', 8, 5461–5469 (2024)
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# Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''J. Am. Chem. Soc.'' '''146''', 9, 6094–6103 (2024)
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# M. Sample, M. Matthies and P. Šulc, ''ACS Nano'' accepted (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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# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
#: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv])
# 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
#: Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds ([https://doi.org/10.1101/2023.05.15.540824 bioRxiv])
# 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
#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])
# 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, submitted
#: Engineering modular and tunable single Molecule sensors by decoupling sensing from signal output ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])
# 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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# F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, ''J. Chem. Phys.'' '''160''', 205102 (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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# M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, ''Nat. Chem.'' accepted (2024)
#: [https://doi.org/10.1038/s41557-024-01571-4 De novo DNA-based catch bonds]
# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' accepted (2024)
#: [https://doi.org/10.1038/s41565-024-01723-0 Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors]
# D. Svenšek, J. Sočan and M. Praprotnik, ''Macromol. Rapid Commun.'' accepted 2400382 (2024)
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# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024)
#: [https://doi.org/10.1063/5.0214313 Design and simulation of a wireframe DNA origami nanoactuator]
# S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, ''Nano Lett.'' '''24''', 11210–11216 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02564 Modulating the DNA/lipid interface through multivalent hydrophobicity]
# 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])
# 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])


We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].
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 16:19, 19 October 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
  86. M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
    Overtwisting induces polygonal shapes in bent DNA (arXiv)
  87. M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Šulc, and T.L. Schmidt, ACS Nano 13 1839-1848 (2019)
    Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles
  88. Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
    A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
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  305. 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
  306. 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)
  307. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  308. 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)
  309. S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
    How we simulate DNA origami (arXiv)
  310. 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)


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

Retrieved from "https://dna.physics.ox.ac.uk/index.php?title=Publications&oldid=1861"