Difference between revisions of "Publications"

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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])
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#T.E. Ouldridge, ''J. Chem. Phys.'' '''137''', 144105 (2012)
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#:[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)
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# 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]
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#:[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]
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# 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)
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# 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])
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#:[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)
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# 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]
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# 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]
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# R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''ACS Nano'' '''11''', 12426–12435 (2017)
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#:[http://dx.doi.org/10.1021/acsnano.7b06470 Characterizing the motion of jointed DNA nanostructures using a coarse-grained model]
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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)
 +
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
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# 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]
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# B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, ''Nucleic Acids Res.'' '''46''', 538-545 (2018)
 +
#: [http://dx.doi.org/10.1093/nar/gkx1238 Rolling circle amplification shows a sinusoidal template length-dependent amplification bias] ([http://dx.doi.org/10.5287/bodleian:VJJYJXOrg data])
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# 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])
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# 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])
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# 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)
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#: [http://dx.doi.org/10.1021/acsomega.7b01692 How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures]
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# 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])
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# M.M.C. Tortora and J.P.K. Doye, ''Mol. Phys.'' '''116''', 2773-2791 (2018)
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#: [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]
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# 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]
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# 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])
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# E. Spruijt, S.E. Tusk and H. Bayley, ''Nature Nanotechnology'' '''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)
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#: [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]
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# E. Benson, A. Mohammed, D. Rayneau-Kirkhope, A. Gådin, P. Orponen, and B. Högberg, ''ACS Nano'' '''12''', 9291-9299 (2018)
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#: [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])
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# N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, submitted
 +
#: Rational design of hidden thermodynamic driving through DNA mismatch repair ([https://doi.org/10.1101/426668 bioRXiv])
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# L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, ''Small'' '''14''', 1802580 (2018)
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#: [https://doi.org/10.1002/smll.201802580 Paper origami‐inspired design and actuation of DNA nanomachines with complex motions]
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# R. A. Brady, W.T. Kaufhold, N.J. Brooks, V. Foderà and L. Di Michele, ''J. Phys. Condens. Matter'' '''31''', 074003 (2019)
 +
#: [https://doi.org/10.1088/1361-648X/aaf4a1 Flexibility defines structure in crystals of amphiphilic DNA nanostars] ([https://arxiv.org/abs/1810.05761 arXiv])
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# 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)
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#: [https://doi.org/10.1021/jacs.8b07180 Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering]
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# Y. Choi, H. Choi, A.C. Lee, S. Kwon, ''J. Vis. Exp.'', e58364 (2018)
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#: [https://doi.org/10.3791/58364 Design and Synthesis of a Reconfigurable DNA Accordion Rack]
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# M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, submitted
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#: Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis ([https://arxiv.org/abs/1811.12331 arXiv])
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#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, ''Nanoscale'' '''11''', 1647-1660 (2019)
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#: [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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# I.T. Hoffecker, S. Chen, A. Gådin, A. Bosco, A.I. Teixeira and B. Högberg, ''Small'' '''15''', 1803628 (2019)
 +
#: [https://doi.org/10.1002/smll.201803628 Solution‐controlled conformational switching of an anchored wireframe DNA nanostructure]
 +
# M. Coraglio, E. Skoruppa and E. Carlon, ''J. Chem. Phys.'' '''150''', 135101 (2019)
 +
#: [https://doi.org/10.1063/1.5084950 Overtwisting induces polygonal shapes in bent DNA] ([https://arxiv.org/abs/1812.03701 arXiv])
 +
# M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Šulc, and T.L. Schmidt, ''ACS Nano'' '''13''' 1839-1848 (2019)
 +
#: [https://doi.org/10.1021/acsnano.8b08009 Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles]
 +
# Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
 +
#: A Numerical Study of Three-Armed DNA Hydrogel Structures ([https://arxiv.org/abs/1903.04186 arXiv])
 +
# W.T. Kaufhold, R.A. Brady, J.M. Tuffnell, P. Cicuta, and L. Di Michele, ''Bioconjugate Chem'' '''30''', 1850-1859 (2019)
 +
#: [https://doi.org/10.1021/acs.bioconjchem.9b00080 Membrane scaffolds enhance the responsiveness and stability of DNA-based sensing circuits]
 +
# 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])
 +
# A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, ''Nucleic Acids Res.'' Advance Article (2020)
 +
#: [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)
 +
#: [https://doi.org/10.3390/biom9050199 Computational simulation of adapter length-dependent LASSO probe capture efficiency]
 +
# 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)
 +
#: [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)
 +
#: [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
 +
#: 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, ''Soft Matter'' '''16''', 990-1001 (2020)
 +
#: [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)
 +
#: [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)
 +
#: [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'' '''48''', 548-560 (2020)
 +
#: [https://doi.org/10.1093/nar/gkz1137 Free energy landscape of salt-actuated reconfigurable DNA nanodevices]
 +
# E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, submitted
 +
#: Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami ([https://doi.org/10.1101/864678 bioRxiv])
 +
# P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, submitted
 +
#: 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, submitted
 +
#: 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, submitted
 +
#: Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
 +
# 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. Accepted Manuscript (2020)
 +
#: [https://doi.org/10.1039/D0CC00882F Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices]
 +
 +
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 20:29, 3 April 2020

  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. 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
  56. 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)
  57. 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)
  58. 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)
  59. 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)
  60. 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
  61. 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)
  62. 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)
  63. 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)
  64. 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
  65. 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
  66. 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
  67. 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)
  68. E. Spruijt, S.E. Tusk and H. Bayley, Nature Nanotechnology 13, 739-745 (2018)
    DNA scaffolds support stable and uniform peptide nanopores
  69. 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)
  70. 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
  71. 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)
  72. 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
  73. 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
  74. 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)
  75. 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)
  76. N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, submitted
    Rational design of hidden thermodynamic driving through DNA mismatch repair (bioRXiv)
  77. 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
  78. 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)
  79. 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
  80. Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
    Design and Synthesis of a Reconfigurable DNA Accordion Rack
  81. M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, submitted
    Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis (arXiv)
  82. 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
  83. 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
  84. M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
    Overtwisting induces polygonal shapes in bent DNA (arXiv)
  85. 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
  86. Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
    A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
  87. 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
  88. 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)
  89. A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, Nucleic Acids Res. Advance Article (2020)
    Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure (bioRxiv)
  90. 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
  91. 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
  92. 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)
  93. K.G. Young, B. Najafi, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, submitted
    Reconfigurable T-junction DNA origami
  94. 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)
  95. E. Benson, M. Lolaico, Y. Tarasov, A. Gådin and B. Högberg, ACS Nano 13, 12591-12598 (2019)
    Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations
  96. S.W. Shin, S.Y. Ahn, Y.T. Lim and S.H. Um, Anal. Chem. 91, 14808-14811 (2019)
    Improved Sensitivity of Intramolecular Strand Displacement Based on Localization of Probes
  97. Z. Shi and G. Arya, Nucleic Acids Research 48, 548-560 (2020)
    Free energy landscape of salt-actuated reconfigurable DNA nanodevices
  98. E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, submitted
    Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami (bioRxiv)
  99. P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, submitted
    Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches (bioRxiv)
  100. K. Bartnik, A. Barth, M. Pilo-Pais, A.H. Crevenna, T. Liedl and D.C. Lamb, J. Am. Chem. Soc 142, 815-825 (2020).
    A DNA origami platform for single-pair Förster resonance energy transfer investigation of DNA–DNA interactions and ligation
  101. E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, submitted
    Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation (bioRxiv)
  102. M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, submitted
    Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
  103. C. Bores and B.M. Pettitt, Phys. Rev. E 101, 012406 (2020)
    Structure and the role of filling rate on model dsDNA packed in a phage capsid
  104. A. Bader and S.L. Cockroft, Chem. Commun. Accepted Manuscript (2020)
    Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices

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