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#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Phys. Condens. Matter''. '''22''', 104102 (2010)
#:[http://dx.doi.org/10.1088/0953-8984/22/10/104102 Extracting bulk properties of self-assembling systems from small simulations] ([https://arxiv.org/abs/0910.1201 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#:[http://aip.scitation.org/doi/abs/10.1063/1.3552946?journalCode=jcp Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
#:[http://aip.scitation.org/doi/abs/10.1063/1.3552946?journalCode=jcp Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
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#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#:[http://dx.doi.org/10.1063/1.4754132 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])  
#:[http://dx.doi.org/10.1063/1.4754132 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])
#T.E. Ouldridge, ''J. Chem. Phys.'' '''137''', 144105 (2012)
#:[https://doi.org/10.1063/1.4757267 Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble] ([https://arxiv.org/abs/1204.5716 arXiv])
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#:[http://dx.doi.org/10.1063/1.4792252 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
#:[http://dx.doi.org/10.1063/1.4792252 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
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# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''J. Chem. Theor. Comput.'' '''15''' 4660-4672 (2019)
#:[http://arxiv.org/abs/1506.09008 Coarse-grained modelling of strong DNA bending II: Cyclization]
#: [https://doi.org/10.1021/acs.jctc.9b00112 Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model] ([http://arxiv.org/abs/1506.09008 arXiv]) ([http://dx.doi.org/10.5281/zenodo.1753767 data])
# J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, ''Science'' '''349''', 977-981 (2015)
# J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, ''Science'' '''349''', 977-981 (2015)
#:[http://dx.doi.org/10.1126/science.aab2666  Base triplet stepping by the Rad51/RecA family of recombinases]
#:[http://dx.doi.org/10.1126/science.aab2666  Base triplet stepping by the Rad51/RecA family of recombinases]
# B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ''ACS Nano'' '''10''', 1724-1737 (2016)
# B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ''ACS Nano'' '''10''', 1724-1737 (2016)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.5b05865 Direct Simulation of the Self-Assembly of a Small DNA Origami]
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.5b05865 Direct Simulation of the Self-Assembly of a Small DNA Origami] ([https://ora.ox.ac.uk/objects/uuid:e71db18a-71f2-4806-9200-dc4cdc283ec8 data])
# V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, ''Nat. Commun.'' '''7''', 10803 (2016)
# V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, ''Nat. Commun.'' '''7''', 10803 (2016)
#:[http://dx.doi.org/10.1038/ncomms10803 Design principles for rapid folding of knotted DNA nanostructures]
#:[http://dx.doi.org/10.1038/ncomms10803 Design principles for rapid folding of knotted DNA nanostructures]
Line 77: Line 81:
# M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ''ACS Nano'', '''10''', 5882–5890 (2016)
# M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ''ACS Nano'', '''10''', 5882–5890 (2016)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b01035 Biomimetic autonomous enzymatic nanowalker of high fuel efficiency]
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b01035 Biomimetic autonomous enzymatic nanowalker of high fuel efficiency]
# J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, ''J. Chem. Phys.'' '''145''', 084910 (2016)
# J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, ''J. Chem. Phys.'' '''145''', 084910 (2016)
#:[http://dx.doi.org/10.1063/1.4961398 Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars]
#:[http://dx.doi.org/10.1063/1.4961398 Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars]
# T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, ''Nucl. Acids Res.'' '''44''', 9121-9130 (2016)
# T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, ''Nucleic Acids Res.'' '''44''', 9121-9130 (2016)
#:[http://dx.doi.org/10.1093/nar/gkw815 Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation]
#:[http://dx.doi.org/10.1093/nar/gkw815 Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation]
# Q. Wang and B.M. Pettitt, ''J. Phys. Chem. Lett'' '''7''', 1042–1046 (2016)
# Q. Wang and B.M. Pettitt, ''J. Phys. Chem. Lett'' '''7''', 1042–1046 (2016)
#:[http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b00246 Sequence affects the cyclization of DNA minicircles]
#:[http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b00246 Sequence affects the cyclization of DNA minicircles]
# A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, ''J. Phys: Condens. Matter'', '''29''', 014006 (2017).
# A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, ''J. Phys: Condens. Matter'' '''29''', 014006 (2017).
#:[http://iopscience.iop.org/article/10.1088/0953-8984/29/1/014006 Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal] ([http://arxiv.org/abs/1607.06626 arXiv])
#:[http://iopscience.iop.org/article/10.1088/0953-8984/29/1/014006 Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal] ([http://arxiv.org/abs/1607.06626 arXiv]) ([http://dx.doi.org/10.17863/cam.4904 data])
# E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ''ACS Nano'', '''11''', 2094-2102 (2017)
# E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ''ACS Nano'' '''11''', 2094-2102 (2017)
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b08287 Condensation and demixing in solutions of DNA nanostars and their mixtures]
#:[http://pubs.acs.org/doi/abs/10.1021/acsnano.6b08287 Condensation and demixing in solutions of DNA nanostars and their mixtures]
# E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, ''J. Chem. Phys'', '''146''', 214902 (2017)
# E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, ''J. Chem. Phys'' '''146''', 214902 (2017)
#:[http://dx.doi.org/10.1063/1.4984039 DNA elasticity from coarse-grained simulations: the effect of groove asymmetry] [https://arxiv.org/abs/1703.02598 (arXiv)]
#:[http://dx.doi.org/10.1063/1.4984039 DNA elasticity from coarse-grained simulations: the effect of groove asymmetry] [https://arxiv.org/abs/1703.02598 (arXiv)]
# A. Suma and C. Micheletti, ''Proc. Natl. Acad. Sci. USA'', '''114''', E2991–E2997 (2017)
# A. Suma and C. Micheletti, ''Proc. Natl. Acad. Sci. USA'' '''114''', E2991–E2997 (2017)
#:[http://dx.doi.org/10.1073/pnas.1701321114 Pore translocation of knotted DNA rings]
#:[http://dx.doi.org/10.1073/pnas.1701321114 Pore translocation of knotted DNA rings]
# Z. Shi, C. E. Castro and G. Arya, ''ACS Nano'', '''11''', 4617–4630 (2017)
# Z. Shi, C. E. Castro and G. Arya, ''ACS Nano'' '''11''', 4617–4630 (2017)
#:[http://dx.doi.org/10.1021/acsnano.7b00242 Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations]
#:[http://dx.doi.org/10.1021/acsnano.7b00242 Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations]
# H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, ''J. Phys. Chem. B'', '''121''', 5033–5039 (2017)
# H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, ''J. Phys. Chem. B'' '''121''', 5033–5039 (2017)
#:[http://dx.doi.org/10.1021/acs.jpcb.7b03931 Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design]
#:[http://dx.doi.org/10.1021/acs.jpcb.7b03931 Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design]
# S. Vangaveti,  R. J. D'Esposito,  J. L. Lippens,  D. Fabris  and  S. V. Ranganathan, ''Phys. Chem. Chem Phys'', '''19''', 14937-14946 (2017)
# S. Vangaveti,  R. J. D'Esposito,  J. L. Lippens,  D. Fabris  and  S. V. Ranganathan, ''Phys. Chem. Chem. Phys.'' '''19''', 14937-14946 (2017)
#:[http://pubs.rsc.org/en/content/articlehtml/2017/cp/c7cp00717e A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry]
#:[http://pubs.rsc.org/en/content/articlehtml/2017/cp/c7cp00717e A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry]
# A. Henning-Knechtel, J. Knechtel and M. Magzoub, ''Nucl. Acids Res.'', '''45''', 12057–12068 (2017)
# A. Henning-Knechtel, J. Knechtel and M. Magzoub, ''Nucleic Acids Res.'' '''45''', 12057–12068 (2017)
#: [https://doi.org/10.1093/nar/gkx990 DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels]
#: [https://doi.org/10.1093/nar/gkx990 DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels]
# R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''ACS Nano'', '''11''', article ASAP (2017)
# R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''ACS Nano'' '''11''', 12426–12435 (2017)
#:[http://dx.doi.org/10.1021/acsnano.7b06470 Characterizing the motion of jointed DNA nanostructures using a coarse-grained model]
#:[http://dx.doi.org/10.1021/acsnano.7b06470 Characterizing the motion of jointed DNA nanostructures using a coarse-grained model]
# B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, ''Nucl. Acids Res.'' Advance Article
# 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)
#: [http://dx.doi.org/10.1093/nar/gkx1238 Rolling circle amplification shows a sinusoidal template length-dependent amplification bias]
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
# D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, ''Nucl. Acids Res.'' accepted
# G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, ''Nat. Nanotechnol.'' '''12''', 920–927 (2017)
#: [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/10.1038/nnano.2017.127 A spatially localized architecture for fast and modular DNA computing]
# P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, submitted
# 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)
#: Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly ([http://arxiv.org/abs/1712.02161 arXiv])
#: [https://doi.org/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]  
# 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, submitted
# B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, ''Nucleic Acids Res.'' '''46''', 538-545 (2018)
#: Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase
#: [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)
#: [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])
# P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys'' '''148''', 134910 (2018)
#: [https://doi.org/10.1063/1.5019344 Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly] ([http://arxiv.org/abs/1712.02161 arXiv])
# 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)
#: [http://dx.doi.org/10.1093/nar/gkz797 Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase] ([https://www.biorxiv.org/content/early/2018/02/10/263038 bioRXiv])
# S.R. Tee and Z. Wang, ''ACS Omega'', '''3''', 292-301 (2018)
#: [http://dx.doi.org/10.1021/acsomega.7b01692 How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures]
# E. Skoruppa, S.K. Nomidis, J.F. Marko and E. Carlon, ''Phys. Rev. Lett.'' '''121''', 088101 (2018)
#: [https://doi.org/10.1103/PhysRevLett.121.088101 Bend-induced twist waves and the structure of nucleosomal DNA] ([http://arxiv.org/abs/1801.10005 arXiv])
# M.M.C. Tortora and J.P.K. Doye, ''Mol. Phys.'' '''116''', 2773-2791 (2018)
#: [http://dx.doi.org/10.1080/00268976.2018.1464226 Incorporating particle flexibility in a density functional description of nematics and cholesterics] ([http://arxiv.org/abs/1801.10601 arXiv])
# O. Henrich, Y.A. Gutierrez-Fosado, T. Curk, T.E. Ouldridge, ''Eur. Phys. J. E'' '''41''', 57 (2018)
#: [http://dx.doi.org/10.1140/epje/i2018-11669-8 Coarse-Grained Simulation of DNA using LAMMPS] ([http://arxiv.org/abs/1802.07145 arXiv])
# 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)
#: [http://dx.doi.org/10.1021/acsnano.8b01844 Force-induced unravelling of DNA Origami]
# F. Romano and L. Rovigatti, in ''Design of Self-Assembling Materials'' (Springer, ed. I. Coluzza) pp 71-90 (2017)
#: [http://dx.doi.org/10.1007/978-3-319-71578-0_3 A Nucleotide-Level Computational Approach to DNA-Based Materials]
# S.R. Tee, X. Hu, I.Y. Loh and Z. Wang, ''Phys. Rev. Applied'' '''9''', 034025 (2018)
#: [https://doi.org/10.1103/PhysRevApplied.9.034025 Mechanosensing potentials gate fuel consumption in a bipedal DNA nanowalker]
# 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])
# 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]
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
#: [https://doi.org/10.1093/nar/gky523 Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking] ([https://doi.org/10.1101/331314 bioRXiv])
# E. Torelli, J.W. Kozyra, J.-Y. Gu, U. Stimming, L. Piantanida. K. Voitchovsky and N. Krasnogor, ''Scientific Reports'' '''8''', 6989 (2018)
#: [http://dx.doi.org/10.1038/s41598-018-25270-6 Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon ]
# R. Jin and L. Maibaum, ''J. Chem. Phys.'' '''150''', 105103 (2019)
#: [https://doi.org/10.1063/1.5054593 Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model]([https://arxiv.org/abs/1807.04258 arxiv])
# F. Kriegel, C. Matek, T. Dršata, K. Kulenkampff, S. Tschirpke, M. Zacharias, F. Lankas and J. Lipfert, ''Nucleic Acids Res.'' '''46''', 7998–8009 (2018)
#: [https://doi.org/10.1093/nar/gky599 The temperature dependence of the helical twist of DNA]
# E. Benson, A. Mohammed, D. Rayneau-Kirkhope, A. Gådin, P. Orponen, and B. Högberg, ''ACS Nano'' '''12''', 9291-9299 (2018)
#: [http://dx.doi.org/10.1021/acsnano.8b04148 Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures]
# S.K. Nomidis, E. Skoruppa,  E. Carlon and J.F. Marko, ''Phys. Rev. E'' '''99''' 032414 (2019).
#: [https://doi.org/10.1103/PhysRevE.99.032414 Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: Perturbation theory and beyond] ([https://doi.org/10.1101/422683 bioRXiv],[https://arxiv.org/abs/1809.07050 arXiv])
# 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])
# N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, ''Nat. Commun'' '''11''', 2562 (2020)
#: [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)
#: [https://doi.org/10.1002/smll.201802580 Paper origami‐inspired design and actuation of DNA nanomachines with complex motions]
# R. A. Brady, W.T. Kaufhold, N.J. Brooks, V. Foderà and L. Di Michele, ''J. Phys. Condens. Matter'' '''31''', 074003 (2019)
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#: [https://doi.org/10.3390/e25050796 Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers]
# 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)
#: [https://doi.org/10.1021/acsnano.3c04349 Ballistic Brownian Motion of Nanoconfined DNA]
# 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)
#: [https://doi.org/10.1038/s41587-023-01801-z Spatial imaging of glycoRNA in single cells with ARPLA]
# 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)
#: [https://doi.org/10.1002/anie.202309869 Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics]
# 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)
#: [https://doi.org/10.1038/s42256-023-00707-4 A temporally resolved DNA framework state machine in living cells]
# X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, ''Nanoscale Horiz.'', '''8''', 827-841 (2023)
#: [https://doi.org/10.1039/D2NH00565D A light-operated integrated DNA walker–origami system beyond bridge burning]
# 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). 
#: [https://doi.org/10.1038/s41586-023-06484-9 DNA-based programmable gate arrays for general-purpose DNA computing]
# C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, ''J. Phys.: Condens. Matter'' '''35''', 265101 (2023)
#: [https://doi.org/10.1088/1361-648X/acc7eb Stability of DNA and RNA hairpins: a comparative study based on ox-DNA]
# Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, ''Commun. Theor. Phys.'' '''75''', 055601 (2023)
#: [https://doi.org/10.1088/1572-9494/acc64c A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments]
# W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, ''Sci. Adv.'' '''9''', adi8444 (2023)
#: [https://dx.doi.org/10.1126/sciadv.adi8444 Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics]
# R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, ''Nat. Methods'' '''20''', 1666–1671 (2023)
#: [https://doi.org/10.1038/s41592-023-02030-7 Molecular mechanocytometry using tension-activated cell tagging] ([https://doi.org/10.1101/2023.01.10.523449 bioRxiv])
# D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, ''Nat. Commun.'' '''14''', 6459 (2023)
#: [https://doi.org/10.1038/s41467-023-41604-z Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies]
# J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, ''Anal. Chem.'' '''95''', 16089–16097 (2023)
#: [https://doi.org/10.1021/acs.analchem.3c01861 Multiplexed CRISPR-based nucleic acid detection using a single Cas protein]
# Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, ''Angew. Chem. Int. Ed.'' '''62''', e202311727 (2023)
#: [https://doi.org/10.1002/anie.202311727 Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures]
# J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. '''14''', 7079 (2023)
#: [https://doi.org/10.1038/s41467-023-42873-4 A computational model for structural dynamics and reconfiguration of DNA assemblies]
# M.C. Engel, J.A. Smith and M.P. Brenner, ''Phys. Rev. X'' '''13''', 041032 (2023)
#: [https://doi.org/10.1103/PhysRevX.13.041032 Optimal control of nonequilibrium systems through automatic differentiation]
# L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, ''J. Am. Chem. Soc.'' '''145''', 27336–27347 (2023)
#: [https://doi.org/10.1021/jacs.3c07491 CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm]
# Y.-P. Qiao and C.-L. Ren, ''Langmuir'' '''40''', 109–117 (2024)
#: [https://doi.org/10.1021/acs.langmuir.3c02231 Correlated hybrid DNA structures explored by the oxDNA Model]
# L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024)
#: [https://doi.org/10.1021/acsnano.3c09522 Multilayer DNA origami with terminal interfaces that are flat and wide-area]
# N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, ''Small'', '''20''', 2308763 (2024)
#: [https://doi.org/10.1002/smll.202308763 Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility]
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and  K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery]
# Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ''ACS Appl. Bio Mater.'' '''7''', 1311–1316 (2024)
#: [https://doi.org/10.1021/acsabm.3c01270 Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts]
# 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)
#: [https://doi.org/10.1115/1.4064242 An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures]
# 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)
#: [https://doi.org/10.1002/smll.202309140 Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures]
# S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, ''Nanoscale'' '''16''', 4872-4879 (2024)
#: [https://doi.org/10.1039/D3NR06140J Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective]
# T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, ''Angew. Chem. Int. Ed'' '''63''', e202319117 (2024)
#: [https://doi.org/10.1002/anie.202319117 Proximity-enhanced functional imaging analysis of engineered tumors]
# 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)
#: [https://doi.org/10.1021/jacs.3c13180 Spacer-programmed two-dimensional DNA origami assembly]
# Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, ''J. Am. Chem. Soc.'' '''146''', 9, 6094–6103 (2024)
#: [https://doi.org/10.1021/jacs.3c13532 Activationless electron transfer of redox-DNA in electrochemical nanogaps]
# M. Sample, M. Matthies and P. Šulc, ''ACS Nano'' '''18''', 30004–30016 (2024)
#: [https://doi.org/10.1021/acsnano.4c10796 Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs] ([https://doi.org/10.48550/arXiv.2302.09109 arXiv])
# M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023)
#: [https://doi.org/10.1109/WSC60868.2023.10407580 Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial] ([https://doi.org/10.48550/arXiv.2308.01455 arXiv])
# 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)
#: [https://doi.org/10.1002/anie.202320179 A programmable DNAzyme for the sensitive detection of nucleic acids] ([https://doi.org/10.1101/2023.08.20.23294196 medRxiv])
# 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)
#: [https://doi.org/10.1063/5.0145570 Towards new liquid crystal phases of DNA mesogens] ([https://doi.org/10.48550/arXiv.2302.03501 arXiv])
# 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)
#: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv])
# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' accepted (2024)
#: [https://doi.org/10.1038/s41565-024-01804-0 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)
#: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv])
# M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, ''Nat. Commun.'' '''15''', 3015 (2024)
#: [https://doi.org/10.1038/s41467-024-46998-y Mechanism of DNA origami folding elucidated by mesoscopic simulations] ([https://doi.org/10.1101/2023.06.20.545758 bioRxiv])
# 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)
#: [https://doi.org/10.1021/acs.biomac.3c01435 Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer]
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery]
# 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)
#: [https://doi.org/10.1021/acs.jpca.4c01772 Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations]
# F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, ''J. Chem. Phys.'' '''160''', 205102 (2024)
#: [https://doi.org/10.1063/5.0202829 ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems] ([https://doi.org/10.48550/arXiv.2311.03317 arXiv])
# 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)
#: [https://doi.org/10.1038/s41565-024-01676-4 A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns]
# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''',  1408–1417 (2024)
#: [https://doi.org/10.1038/s41557-024-01565-2 Encoding signal propagation on topology-programmed DNA origami]
# 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.'' '''19''', 1674–1685 (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)
#: [https://doi.org/10.1002/marc.202400382 Density–nematic coupling in isotropic solution of DNA: Multiscale model]
# 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])
# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling]
# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' accepted (2024)
#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications]
# C. Karfusehr, M. Eder, F.C. Simmel
#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])
# M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
#: Reconfigurable multi-component nanostructures built from DNA origami voxels ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv])
# M.P. Tran,  T. Chakraborty,  E. Poppleton,  L. Monari,  F. Giessler and  K. Göpfrich, submitted
#: Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv])
# V. Bukina and A. Božič,  ''Biophys. J.'' '''123''', 3397-3407 (2024)
#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
# R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
#: [https://doi.org/10.1038/s41598-024-70641-x Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations]
# E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
#: Controlling DNA-RNA strand displacement kinetics with base distribution ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv])
# A. Suma and C. Micheletti, submitted
#: Unzipping of knotted DNA via nanopore translocation ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])
# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
#: DNA nanodevice for analysis of force-activated protein extension and interactions ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv])
# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])
 
We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Latest revision as of 13:12, 23 November 2024

  1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
    DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)
  2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Phys. Condens. Matter. 22, 104102 (2010)
    Extracting bulk properties of self-assembling systems from small simulations (arXiv)
  3. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
  4. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
    Coarse-grained modelling of DNA and DNA self-assembly
  5. F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 136, 215102 (2012)
    The effect of topology on the structure and free energy landscape of DNA kissing complexes (arXiv)
  6. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)
    Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link (arXiv)
  7. C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, J. Phys. Chem. B 116, 1161-11625 (2012)
    DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arXiv)
  8. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)
    Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)
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    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
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    Coarse-grained simulations of DNA overstretching (arXiv)
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    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization (arXiv)
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    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
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    Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes
  228. L. Zhang, H. Zhao, H. Yang and X. Su, Biosens. Bioelectron. 239, 115622 (2023)
    Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection
  229. Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma J. Phys. Chem. B 127, 4015–4021 (2023)
    Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick
  230. K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, Molecules 28, 3686 (2023)
    Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization
  231. H.L. Too and Z. Wang, Nanoscale 15, 11915-11926 (2023)
    Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration
  232. D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, Nanoscale 15, 5403-5413 (2023)
    Programming rigidity into size-defined wireframe DNA nanotubes
  233. J. Lee and S. Lee, Anal. Chem. 95, 1856–1866 (2023)
    Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement
  234. X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, Anal. Chem. 95, 5903–5910 (2023)
    Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy
  235. 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)
    De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework
  236. Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, Chem. Sci. 14, 3652-3660 (2023)
    Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics
  237. M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, Nature Physics 19, 741–751 (2023)
    Storage of mechanical energy in DNA nanorobotics using molecular torsion springs
  238. C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, Commun. Comput. Inf. Sci., 1801, 647–654 (2023)
    Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks
  239. S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, Entropy 25, 796 (2023)
    Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers
  240. 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)
    Ballistic Brownian Motion of Nanoconfined DNA
  241. 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)
    Spatial imaging of glycoRNA in single cells with ARPLA
  242. 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)
    Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics
  243. 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)
    A temporally resolved DNA framework state machine in living cells
  244. X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, Nanoscale Horiz., 8, 827-841 (2023)
    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
  248. W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, Sci. Adv. 9, adi8444 (2023)
    Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
  249. R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, Nat. Methods 20, 1666–1671 (2023)
    Molecular mechanocytometry using tension-activated cell tagging (bioRxiv)
  250. D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, Nat. Commun. 14, 6459 (2023)
    Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
  251. J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, Anal. Chem. 95, 16089–16097 (2023)
    Multiplexed CRISPR-based nucleic acid detection using a single Cas protein
  252. Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, Angew. Chem. Int. Ed. 62, e202311727 (2023)
    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
  255. L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, J. Am. Chem. Soc. 145, 27336–27347 (2023)
    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
  258. N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, Small, 20, 2308763 (2024)
    Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility
  259. 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
  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
  262. B. Babatunde, J. Cagan, R.E. Taylor, J. Mech. Des. 146, 051708 (2024)
    An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures
  263. 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)
    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
  265. T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, Angew. Chem. Int. Ed 63, e202319117 (2024)
    Proximity-enhanced functional imaging analysis of engineered tumors
  266. 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)
    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, ACS Nano 18, 30004–30016 (2024)
    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, Nat. Nanotechnol. accepted (2024)
    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)
  283. M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, Nat. Commun. 15, 3015 (2024)
    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
  287. F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, J. Chem. Phys. 160, 205102 (2024)
    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. 19, 1366–137 (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. 16, 1408–1417 (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. 19, 1674–1685 (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. M. Mogheiseh and R.H. Ghasemi, J. Chem. Phys. 161, 045101 (2024)
    Design and simulation of a wireframe DNA origami nanoactuator
  294. S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, Nano Lett. 24, 11210–11216 (2024)
    Modulating the DNA/lipid interface through multivalent hydrophobicity
  295. 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)
    Weak-cooperative binding of a long single-stranded DNA chain on a surface
  296. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
    DNA nanostar structures with tunable auxetic properties (bioRxiv)
  297. 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)
  298. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, Nat. Commun. 15, 7564 (2024)
    Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)
  299. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
    Bending Unwinds DNA (bioRxiv)
  300. X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, Nat. Commun. 15, 7210 (2024)
    A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport (ResearchSquare)
  301. L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, Nano Lett. 24, 13481–13486 (2024)
    Driving DNA nanopore membrane insertion through dipolar coupling
  302. J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ACM Trans. Evol. Learn. Optim. accepted (2024)
    Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications
  303. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  304. M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
    Reconfigurable multi-component nanostructures built from DNA origami voxels (bioRxiv)
  305. M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, submitted
    Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells (bioRxiv)
  306. V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)
    Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA (bioRxiv)
  307. R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
    Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations
  308. E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
    Controlling DNA-RNA strand displacement kinetics with base distribution (bioRxiv)
  309. A. Suma and C. Micheletti, submitted
    Unzipping of knotted DNA via nanopore translocation (arXiv)
  310. G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
    Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model (arXiv)
  311. S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
    How we simulate DNA origami (arXiv)
  312. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
    Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
  313. R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
    A Differentiable Model of Nucleic Acid Dynamics (arXiv)
  314. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted
    Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)
  315. K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
    DNA nanodevice for analysis of force-activated protein extension and interactions (bioRxiv)
  316. W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
    Economical and versatile subunit design principles for self-assembled DNA origami structures (arXiv)

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

Retrieved from "https://dna.physics.ox.ac.uk/index.php?title=Publications&oldid=1870"