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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]
Line 182: Line 186:
#: [http://dx.doi.org/10.1002/jcc.26029 tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami]
#: [http://dx.doi.org/10.1002/jcc.26029 tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami]
# 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, ''ACS Synth. Biol.'' '''9''', 1682-1692 (2020)
#: [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, ''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])
# 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]
# S. Jonchhe, S. Pandey, D. Karna, P. Pokhrel, Y. Cui, S. Mishra, H. Sugiyama, M. Endo and H. Mao, ''J. Am. Chem. Soc'' '''142''', 10042–10049 (2020)
#:[https://doi.org/10.1021/jacs.0c01978 Duplex DNA Is Weakened in Nanoconfinement]
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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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# 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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# 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
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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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# 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.'' accepted (2024)
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# 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, submitted
#: 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, submitted
#: A dynamically gated 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, submitted
#: Context-dependent structure formation of RNA hairpin motifs ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
# 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])


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].

Revision as of 14:08, 4 September 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)
  89. W.T. Kaufhold, R.A. Brady, J.M. Tuffnell, P. Cicuta, and L. Di Michele, Bioconjugate Chem 30, 1850-1859 (2019)
    Membrane scaffolds enhance the responsiveness and stability of DNA-based sensing circuits
  90. S.K. Nomidis, M. Coraglio, M. Laleman, K. Phillips, E. Skoruppa and E. Carlon, Phys. Rev. E 100, 022402 (2019)
    Twist-bend coupling, twist waves and DNA loops (arXiv)
  91. A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, Nucleic Acids Res. 48, 4672–4680 (2020)
    Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure (bioRxiv)
  92. J. Liu, S. Shukor, S. Li, A. Tamayo, L. Tosi, B. Larman, V. Nanda, W.K. Olson and B. Parekkadan, Biomolecules 9, 199 (2019)
    Computational simulation of adapter length-dependent LASSO probe capture efficiency
  93. A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A.A. Louis, J.P.K. Doye, C. Micheletti, and L. Rovigatti, J. Comput. Chem. 40, 2586-2595 (2019)
    tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami
  94. 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)
    Design and synthesis of pleated DNA origami nanotubes with adjustable diameters (bioRxiv)
  95. 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
  96. 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 (arXiv)
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    Leakless end-to-end transport of small molecules through micron-length DNA nanochannels
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    Far-field electrostatic signatures of macromolecular 3D conformation
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    Directing multivalent aptamer-receptor binding on the cell surface with programmable atom-like nanoparticles
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    Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions
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    Single-Stranded DNA-Encoded Gold Nanoparticle Clusters as Programmable Enzyme Equivalents
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    Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging
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    Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories (bioRxiv)
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    Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking
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    oxDNA: coarse-grained simulations of nucleic acids made simple
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    Nonequilibrium Thermodynamics of DNA Nanopore Unzipping (arXiv)
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    DNA Origami Tessellations
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    Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions
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    DNA origami tubes with reconfigurable cross-sections
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    Prime factorization via localized tile assembly in a DNA origami framework
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    Ballistic Brownian Motion of Nanoconfined DNA
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    Spatial imaging of glycoRNA in single cells with ARPLA
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    Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics
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    A temporally resolved DNA framework state machine in living cells
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    A light-operated integrated DNA walker–origami system beyond bridge burning
  245. 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).
    DNA-based programmable gate arrays for general-purpose DNA computing
  246. C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, J. Phys.: Condens. Matter 35, 265101 (2023)
    Stability of DNA and RNA hairpins: a comparative study based on ox-DNA
  247. Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, Commun. Theor. Phys. 75, 055601 (2023)
    A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments
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    Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
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    Molecular mechanocytometry using tension-activated cell tagging (bioRxiv)
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    Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
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    Multiplexed CRISPR-based nucleic acid detection using a single Cas protein
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    Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures
  253. J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. 14, 7079 (2023)
    A computational model for structural dynamics and reconfiguration of DNA assemblies
  254. M.C. Engel, J.A. Smith and M.P. Brenner, Phys. Rev. X 13, 041032 (2023)
    Optimal control of nonequilibrium systems through automatic differentiation
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    CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm
  256. Y.-P. Qiao and C.-L. Ren, Langmuir 40, 109–117 (2024)
    Correlated hybrid DNA structures explored by the oxDNA Model
  257. L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ACS Nano 18, 885–893 (2024)
    Multilayer DNA origami with terminal interfaces that are flat and wide-area
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    Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility
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    DNA mechanocapsules for programmable piconewton responsive drug delivery
  260. Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ACS Appl. Bio Mater. 7, 1311–1316 (2024)
    Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts
  261. 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
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    An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures
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    Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures
  264. S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, Nanoscale 16, 4872-4879 (2024)
    Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective
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    Proximity-enhanced functional imaging analysis of engineered tumors
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    Spacer-programmed two-dimensional DNA origami assembly
  267. Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, J. Am. Chem. Soc. 146, 9, 6094–6103 (2024)
    Activationless electron transfer of redox-DNA in electrochemical nanogaps
  268. M. Sample, M. Matthies and P. Šulc, submitted
    Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs (arXiv)
  269. M. Sample, M. Matthies and P. Šulc, 2023 Winter Simulation Conference (WSC), San Antonio, TX, USA, pp. 91-105 (2023)
    Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial (arXiv)
  270. 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 (bioRxiv)
  271. 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)
    A programmable DNAzyme for the sensitive detection of nucleic acids (medRxiv)
  272. 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 (bioRxiv)
  273. K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, APL Mater. 11, 061129 (2023)
    Towards new liquid crystal phases of DNA mesogens (arXiv)
  274. 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 (bioRxiv)
  275. H. Koh, J.Y. Lee, J.G. Lee, submitted
    Forming superhelix of double stranded DNA from local deformation (arXiv)
  276. N.P. Agarwal and A. Gopinath, submited
    DNA origami 2.0 (bioRxiv)
  277. J.M. Weck and A. Heuer-Jungemann, submitted
    Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)
  278. 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 (bioRxiv)
  279. 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)
    Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments (arXiv)
  280. 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 (bioRxiv)
  281. F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
    nNxB: a new coarse-grained model for RNA and DNA nanotechnology (arXiv)
  282. E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 160, 115101 (2024)
    Coarse-grained modelling of DNA-RNA hybrids (arXiv)
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    Mechanism of DNA origami folding elucidated by mesoscopic simulations (bioRxiv)
  284. 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)
    Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer
  285. A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, Nat. Commun. 15, 704 (2024)
    DNA mechanocapsules for programmable piconewton responsive drug delivery
  286. 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)
    Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations
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    ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems (arXiv)
  288. 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. accepted (2024)
    A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns
  289. W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, Nat. Chem. accepted (2024)
    Encoding signal propagation on topology-programmed DNA origami
  290. M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, Nat. Chem. accepted (2024)
    De novo DNA-based catch bonds
  291. Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, Nat. Nanotechnol. accepted (2024)
    Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors
  292. D. Svenšek, J. Sočan and M. Praprotnik, Macromol. Rapid Commun. accepted 2400382 (2024)
    Density–nematic coupling in isotropic solution of DNA: Multiscale model
  293. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
    DNA nanostar structures with tunable auxetic properties (bioRxiv)
  294. 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 (bioRxiv)
  295. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, submitted
    Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)
  296. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
    Bending Unwinds DNA (bioRxiv)
  297. X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, submitted
    A dynamically gated triangular DNA nanopore for molecular sensing and cross-membrane transport (ResearchSquare)
  298. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  299. 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)
  300. 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)
  301. V. Bukina and A. Božič, submitted
    Context-dependent structure formation of RNA hairpin motifs (bioRxiv)
  302. 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)
  303. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  304. 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)


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=1845"