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])
 +
#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"]
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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,  ''J. Chem. Theor. Comput.'' '''15''' 4660-4672 (2019)
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#:[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)
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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]
+
#:[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]
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# 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]
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# 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]
Line 97: Line 101:
 
# 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, ''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''', 12426–12435 (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.'' '''46''', 538-545 (2018)
+
# 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.'' '''46''', 1553-1561 (2018)
+
# 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)
−
#: [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/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]
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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''' in press (2018)
+
# B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, ''Nucleic Acids Res.'' '''46''', 538-545 (2018)
−
#: Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly ([http://arxiv.org/abs/1712.02161 arXiv])
+
#: [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])
−
# 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
+
# 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)
−
#: Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase ([https://www.biorxiv.org/content/early/2018/02/10/263038 bioRXiv])
+
#: [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)
 
# 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]
 
#: [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, E. Carlon, submitted
+
# 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 ([http://arxiv.org/abs/1801.10005 arXiv])
+
#: [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, submitted
+
# M.M.C. Tortora and J.P.K. Doye, ''Mol. Phys.'' '''116''', 2773-2791 (2018)
−
#: Introducing particle flexibility into a density functional description of nematics and cholesterics ([http://arxiv.org/abs/1801.10601 arXiv])
+
#: [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, submitted
+
# 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 ([http://arxiv.org/abs/1802.07145 arXiv])
+
#: [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, submitted
+
# 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
+
#: [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, ''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)
 +
#: [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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# W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, ''Nucleic Acids Res.'' '''50''', 2480–2492 (2022).
 +
#: [https://doi.org/10.1093/nar/gkac082 The interplay of supercoiling and thymine dimers in DNA] ([https://doi.org/10.1101/2021.09.27.461905 bioRxiv])
 +
# W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, ''ACS Nano'' '''16''', accepted (2022).
 +
#: [https://doi.org/10.1021/acsnano.1c08999 Probing the mechanical properties of DNA nanostructures with metadynamics] ([https://arxiv.org/abs/2110.01477 arXiv])
 +
# H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, ''J. Am. Chem. Soc.'' '''43''', 19466–19473 (2021).
 +
#: [https://doi.org/10.1021/jacs.1c08796 Massively parallelized molecular force manipulation with on demand thermal and optical control]
 +
# L. Yang, C. Cullin and J. Elezgaray, ''ChemPhysChem'' '''23''', e202200021 (2022).
 +
#: [https://doi.org/10.1002/cphc.202200021 Detection of short DNA sequences with DNA nanopores] ([https://arxiv.org/abs/2110.11642 arXiv])
 +
# Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, R. Liu, X. Dai, Y. Qian, X. Su, submitted.
 +
#: Intramolecular Orthogonal Reporters for Dissecting Oxidative Stress and Response ([https://doi.org/10.21203/rs.3.rs-917337/v1 Research Square])
 +
# X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, submitted.
 +
#: Planar 2D wireframe DNA origami
 +
# E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, ''Nucleic Acids Res.'' '''50''', D246–D252 (2022)
 +
#: [https://doi.org/10.1093/nar/gkab1000 Nanobase.org: a repository for DNA and RNA nanostructures]
 +
# R. Foffi, F. Sciortino, J. M. Tavares, P. I. C. Teixeira, ''Soft Matter'' '''17''', 10736-10743 (2021)
 +
#: [https://doi.org/10.1039/D1SM01130H Building up DNA, bit by bit: a simple description of chain assembly] ([https://arxiv.org/abs/2111.03978 arXiv])
 +
# J. Yoo, S. Park, C. Maffeo, T. Ha, A. Aksimentiev, ''Nucleic Acids Res.'' '''49''', 11459–11475 (2021).
 +
#: [https://doi.org/10.1093/nar/gkab967 DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles]
 +
# E. Lin-Shiao,  W.G. Pfeifer, B.R. Shy, M. Saffari Doost, E. Chen, V.S. Vykunta,  J.R. Hamilton,  E.C. Stahl, D.M. Lopez,  C.R. Sandoval Espinoza, A.E. Dejanov, R.J. Lew, M.G. Poirer, A. Marson,  C.E. Castro,  J.A. Doudna, ''Nucleic Acids Res.'' '''50''', 1256–1268 (2022)
 +
#: [https://doi.org/10.1093/nar/gkac049 CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells] ([https://doi.org/10.1101/2021.11.08.467750 bioRxiv])
 +
# J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, to appear in ''[https://www.elsevier.com/books/energy-landscapes-of-nanoscale-systems/wales/978-0-12-824406-7 Energy Landscapes of Nanoscale Systems]'', ed. D.J. Wales, ''Frontiers of Nanoscience'' Vol. 21 (Elsevier)
 +
#: Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling ([https://arxiv.org/abs/2111.10166 arXiv])
 +
# Y. Deng, Y. Tan, L. Zhang, C. Zhang, X. Su, submitted.
 +
#: Forecasting the reaction of DNA modifying enzymes on DNA nanostructures by coarse grained model for stimuli-responsive drug delivery ([https://doi.org/10.21203/rs.3.rs-1038517/v1 Research Square])
 +
# D. Smith and G. Tikhomirov, submitted.
 +
#: small: A programmatic nanostructure design and modelling environment ([https://arxiv.org/abs/2111.15184 arXiv])
 +
# S. Assenza and R. Pérez, ''J. Chem. Theory Comput'' '''18''', 3239–3256 (2022).
 +
#: [https://doi.org/10.1021/acs.jctc.2c00138 Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA] ([https://doi.org/10.1101/2021.12.02.470889  biorXiv])
 +
# D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, ''Molecules'' '''27''', 63 (2022)
 +
#: [https://doi.org/10.3390/molecules27010063 Unified Nanotechnology Format: One Way to Store Them All]
 +
# M. Centola,  E. Poppleton,  M. Centola,  J. Valero,  P. Šulc and  M. Famulok, submitted.
 +
#: A rhythmically pulsing leaf-spring nanoengine that drives a passive follower ([https://doi.org/10.1101/2021.12.22.473833 biorXiv])
 +
# C.K. Wong and J.P.K. Doye, submitted
 +
#: The free-energy landscape of a mechanically bistable DNA origami ([http://arxiv.org/abs/2201.08920 arXiv])
 +
# L. Zhang, J. Chen, M. He, X. Su, ''Exploration'' '''2''', 20210265 (2022)
 +
#: [https://doi.org/10.1002/EXP.20210265 Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection]
 +
# F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, ''Entropy'' '''24''', 458 (2022)
 +
#: [https://doi.org/10.3390/e24040458 OxDNA to study species interactions] ([https://arxiv.org/abs/2202.05653 arXiv])
 +
# Y.A.G. Fosado, submitted
 +
#: Nanostars planarity modulates the elasticity of DNA hydrogels ([https://arxiv.org/abs/2202.06331 arXiv])
 +
# X. Hu, L. Tang, M. Zheng, J. Liu, Z. Zhang, Z. Li, Q. Yang, S. Xiang, L. Fang, Q. Ren, X. Liu, C.Z. Huang, C. Mao and H. Zuo, ''J. Am. Chem. Soc.'' '''144''', 4507–4514 (2022)
 +
#: [https://doi.org/10.1021/jacs.1c12593 Structure-guided designing pre-organization in bivalent aptamers]
 +
# L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, ''Sci. Adv.'' '''8''', eabm9530 (2022)
 +
#: [https://doi.org/10.1126/sciadv.abm9530 A localized DNA finite-state machine with temporal resolution]
 +
# Y. Xin, P. Piskunen, A. Suma, C. Li, H. Ijäs, S. Ojasalo, I. Seitz, M.A. Kostiainen, G. Grundmeier, V. Linko and A. Keller, ''Small'' '''18''', 2107393 (2022)
 +
#: [https://doi.org/10.1002/smll.202107393 Environment-dependent stability and mechanical properties of DNA origami six-helix bundles with different crossover spacings]
 +
# R.L. Bender, H. Ogasawara, A.V. Kellner, A. Velusamy and K. Salaita, submitted
 +
#: Unbreakable DNA tension probes show that cell adhesion receptors detect the molecular force-extension curve of their ligands ([https://doi.org/10.1101/2022.04.04.487040 bioRxiv])
 +
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
 +
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
 +
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, submitted
 +
#: Weak tension accelerates hybridization and dehybridization of short oligonucleotides ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
 +
# S. Sensale, P. Sharma and G. Arya, ''Phys. Rev. E'' '''105''', 044136 (2022)
 +
#: [https://doi.org/10.1103/PhysRevE.105.044136 Binding kinetics of harmonically confined random walkers]
 +
# S. Dey, A. Dorey, L. Abraham, Y. Xing, I. Zhang, F. Zhang, S. Howorka and H. Yan, ''Nat. Commun.'' '''13''', 2271 (2022)
 +
#: [https://doi.org/10.1038/s41467-022-28522-2 A reversibly gated protein-transporting membrane channel made of DNA]
 +
# D. Luo, A. Kouyoumdjian, O. Strnad, H. Miao, I. Barišić and I. Viola, submitted (2022)
 +
#: SynopSet: Multiscale visual abstraction set for explanatory analysis of DNA nanotechnology simulations ([https://arxiv.org/abs/2205.01628 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 08:45, 18 May 2022

  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. R.V. Reshetnikov, A.V. Stolyarova, A.O. Zalevsky, D.Y. Panteleev, G.V. Pavlova, D.V. Klinov, A.V. Golovin, A.D. Protopopova, Nucleic Acids Res. 46, 1102–1112 (2018)
    A coarse-grained model for DNA origami
  58. 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)
  59. 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)
  60. 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)
  61. 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
  62. 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)
  63. 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)
  64. 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)
  65. 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
  66. 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
  67. 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
  68. 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)
  69. E. Spruijt, S.E. Tusk and H. Bayley, Nature Nanotechnology 13, 739-745 (2018)
    DNA scaffolds support stable and uniform peptide nanopores
  70. 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)
  71. 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
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    Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model(arxiv)
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    The temperature dependence of the helical twist of DNA
  74. 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
  75. 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)
  76. 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)
  77. N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, Nat. Commun 11, 2562 (2020)
    Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement (bioRXiv)
  78. 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
  79. 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)
  80. 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
  81. Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
    Design and Synthesis of a Reconfigurable DNA Accordion Rack
  82. M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, Sci. Adv. 6, eaaw8331 (2020)
    Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis (arXiv)
  83. 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
  84. 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
  85. M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
    Overtwisting induces polygonal shapes in bent DNA (arXiv)
  86. 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
  87. Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
    A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
  88. 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
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    Twist-bend coupling, twist waves and DNA loops (arXiv)
  90. A. Suma, A. Stopar, A.W. Nicholson, M. Castronovo, V. Carnevale, Nucleic Acids Res. 48, 4672–4680 (2020)
    Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure (bioRxiv)
  91. 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
  92. 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
  93. 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)
  94. K.G. Young, B. Najafi, W.M. Sant, S. Contera, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, Angew. Chem. Int. Ed. 59, 15942-15946 (2020)
    Reconfigurable T-junction DNA origami
  95. 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)
  96. 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
  97. 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
  98. Z. Shi and G. Arya, Nucleic Acids Research 48, 548-560 (2020)
    Free energy landscape of salt-actuated reconfigurable DNA nanodevices
  99. E. Torelli, J.W. Kozyra, B. Shirt-Ediss, L. Piantanida, K. Voïtchovsky, N. Krasnogor, ACS Synth. Biol. 9, 1682-1692 (2020)
    Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami (bioRxiv)
  100. P.R Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman, Nucleic Acids Res. 48, 10713–10725 (2020)
    Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches (bioRxiv)
  101. 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
  102. E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, Nucleic Acids Res. 48, e72 (2020)
    Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation (bioRxiv)
  103. M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, J. Chem. Theor. Comput. 16, 7764–7775 (2020).
    Measuring internal forces in single-stranded DNA: Application to a DNA force clamp (arXiv)
  104. 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
  105. A. Bader and S.L. Cockroft, Chem. Commun. 56, 5135-5138 (2020)
    Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices
  106. J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton and B.E.K. Snodin, Methods in Molecular Biology, submitted.
    The oxDNA coarse-grained model as a tool to simulate DNA origami (arXiv) (data)
  107. J. Lee, J.-H. Huh, S. Lee, Langmuir 36, 5118–5125 (2020)
    DNA Base Pair-Stacking Crystallization of Gold Colloids
  108. A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, Nat. Commun. 12, 501 (2021)
    Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy (bioRxiv)
  109. B. Najafi, K.G. Young, J. Bath, A.A. Louis, J.P.K. Doye and A.J. Turberfield, submitted
    Characterising DNA T-motifs by simulation and experiment (arXiv)
  110. C.M. Huang, A. Kucinic, J.A. Johnson, H.-J. Su, C.E. Castro, Nat. Mater. 20, 1264–1271 (2021)
    Integrating computer-aided engineering and design for DNA assemblies (bioRxiv)
  111. P. Irmisch, T.E. Ouldridge, and R. Seidel, J. Am. Chem. Soc 142, 11451–11463 (2020)
    Modelling DNA-strand displacement reactions in the presence of base-pair mismatches
  112. F. Hong, J.S. Schreck and P. Šulc, Nucleic Acids Res. 48, 10726–10738 (2020).
    Understanding DNA interactions in crowded environments with a coarse-grained model (bioRxiv)
  113. A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, J. Am. Chem. Soc. 142, 12069–12078 (2020)
    Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy (bioRxiv)
  114. H. Chhabra, G. Mishra, Y. Cao, D. Prešern, E. Skoruppa, M.M.C. Tortora and J.P.K. Doye, J. Chem. Theor. Comput. 16, 7748–7763 (2020).
    Computing the elastic mechanical properties of rod-like DNA nanostructures (arXiv)
  115. K. Tapio, A. Mostafa, Y. Kanehira, A. Suma, A. Dutta, I. Bald, ACS Nano 15, 7065–7077 (2021)
    A versatile DNA origami based plasmonic nanoantenna for label-free single-molecule SERS (Research Square)
  116. E.G. Noya, C.K. Wong, P. Llombart and J.P.K. Doye, Nature 596, 367–371 (2021)
    How to design an icosahedral quasicrystal through directional bonding
  117. Y.A.G. Fosado, F. Landuzzi and T. Sakaue, Soft Matter 17, 1530-1537 (2021)
    Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending (arXiv)
  118. F. Spinozzi, M.G. Ortore, G. Nava, F. Bomboi, F. Carducci, H. Amenitsch, T. Bellini, F. Sciortino, and P. Mariani, Langmuir 36, 10387–10396 (2020)
    Gelling without structuring: a SAXS study of the interactions among DNA nanostars
  119. J. Huang A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar and A. Keller, Small Str. 1, 2000038 (2020)
    Arranging small molecules with sub‐nanometer precision on DNA origami substrates for the single‐molecule investigation of protein‐ligand interactions
  120. G. Yao, F. Zhang, F. Wang, T. Peng, H. Liu, E. Poppleton, P. Šulc, S. Jiang, L. Liu, C. Gong, X. Jing, X. Liu, L. Wang, Y. Liu, C. Fan and H. Yan, Nat. Chem. 12, 1067–1075 (2020)
    Meta-DNA structures
  121. J.F. Berengut, C.K. Wong, J.C. Berengut, J.P.K. Doye, T.E. Ouldridge and L.K. Lee, ACS Nano 14, 17428–17441 (2020)
    Self-limiting polymerization of DNA origami subunits with strain accumulation
  122. J. Procyk, E. Poppleton and P. Šulc, Soft Matter 17, 3586-3593 (2021).
    Coarse-grained nucleic acid-protein model for hybrid nanotechnology (arXiv)
  123. Z. Sierzega, J. Wereszczynski and C. Prior, Sci. Rep. 11, 1527 (2021)
    WASP: A software package for correctly characterizing the topological development of ribbon structures (bioRXiv)
  124. E. Skoruppa, A. Voorspoels, J. Vreede and E. Carlon, Phys. Rev. E 103, 042408 (2021)
    Length scale dependent elasticity in DNA from coarse-grained and all-atom models (arXiv)
  125. C. Bores, M. Woodson, M.C. Morais, and B. Montgomery Pettitt, J. Phys. Chem. B 124, 10337–10344 (2020)
    Effects of model shape, volume, and softness of the capsid for DNA packaging of phi29
  126. E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, Nanoscale 12, 23003-23012 (2020)
    Hyperbranched DNA clusters (arXiv)
  127. B.J.H.M. Rosier, A.J. Markvoort, B. Gumí Audenis, J.A.L. Roodhuizen, A. den Hamer, L. Brunsveld and T.F.A. de Greef, Nat. Catal. 3, 295–306 (2020)
    Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome
  128. R. Li, H. Chen and J.H. Choi, Angew. Chem. Int. Ed. 60, 7165-7173 (2021)
    Auxetic Two‐Dimensional Nanostructures from DNA (bioRXiv)
  129. D. Wang, L. Yu, C.-M. Huang, G. Arya, S. Chang, and Y. Ke, J. Am. Chem. Soc. 143, 2256–2263 (2021)
    Programmable transformations of DNA origami made of small modular dynamic units
  130. R. Li, H. Chen, H. Lee, J. H. Choi, Appl. Sci. 11, 2357 (2021)
    Elucidating the mechanical energy for cyclization of a DNA origami tile (bioRxiv)
  131. G. Park, M. K. Cho, and Y. Jung, J. Chem. Theory Comput., 17 1308-1317 (2021)
    Sequence-dependent kink formation in short DNA loops: Theory and molecular dynamics simulations
  132. S. Jonchhe, S. Pandey, D. Karna, P. Pokhrel, Y. Cui, S. Mishra, H. Sugiyama, M. Endo and H. Mao, J. Am. Chem. Soc 142, 10042–10049 (2020)
    Duplex DNA Is Weakened in Nanoconfinement
  133. R. Li, H. Chen and J. H. Choi, Small 17, 2007069 (2021)
    Topological Assembly of a Deployable Hoberman Flight Ring from DNA
  134. S. Naskar, P. K. Maiti, J. Mater. Chem. B 9, 5102-5113
    Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA (arXiv)
  135. B. Babatunde, S. Arias, J. Cagan and R.E. Taylor, Appl. Sci. 11, 2950 (2021)
    Generating DNA origami nanostructures through shape annealing
  136. N.M. Gravina, J.C. Gumbart and H.D. Kim, J. Phys. Chem. B 125, 4016–4024 (2021)
    Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding
  137. A. Sengar, T.E. Ouldridge, O. Henrich, L. Rovigatti and P. Šulc, Front. Mol. Biosci. 8, 693710 (2021)
    A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results (arXiv) (data)
  138. E. Poppleton, R. Romero, A. Mallya, L. Rovigatti and P. Šulc, Nucl. Acids Res. 49 W491–W498 (2021)
    OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
  139. Y. Yamashita, K. Watanabe, S. Murata and I. Kawamata, Chem-Bio Informatics Journal 21, 28-38 (2021)
    Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures
  140. E. Benson, R. Carrascosa Marzo, J. Bath, A.J. Turberfield, Small 17, 2007704 (2021)
    Strategies for Constructing and Operating DNA Origami Linear Actuators
  141. Z. Qu, Y.N. Zhang, Z. Dai, Y. Zhang, Y. Hao, J. Shen, F. Wang, Q. Li, C. Fan, X. Liu, Angew. Chem. Int. Ed. 60, 16693-16699 (2021)
    DNA framework-engineered long-range electrostatic interactions for DNA hybridization reactions
  142. Y. Wang, I. Baars, F. Fördös and B. Högberg, ACS Nano 15 9614–9626 (2021)
    Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides
  143. Y. Wang, E. Benson, F. Fördős, M. Lolaico, I. Baars, T. Fang, A.I. Teixeira, B. Högberg, Adv. Mater. 33, 2008457 (2021)
    DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design
  144. L. Li, H. Wang, C. Xiong, D. Luo, H. Chen and Y. Liu, J. Phys.: Condens. Matter 33, 185102 (2021)
    Quantify the combined effects of temperature and force on the stability of DNA hairpin
  145. J. P. Mahalik and M. Muthukumar, submitted
    Nucleotide Dynamics During Flossing of Polycation-DNA-Polycation through a Nanopore using Molecular Dynamics (bioRxiv)
  146. N. Li, Y. Liu, Z. Yin, R. Liu, L. Zhang, Y. Zhao, L. Ma, X. Dai, D. Zhou, X. Su, Nano Today 41 101308 (2021)
    Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems (medRxiv)
  147. Y. Yang, Q. Lu, C.-M. Huang, H. Qian, Y. Zhang, S. Deshpande, G. Arya, Y. Ke, S. Zauscher, Angew. Chem. Int. Ed. 60, 3241-23247 (2021)
    Programmable site-specific functionalization of DNA origami with polynucleotide brushes
  148. Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, J. Am. Chem. Soc. 143, 13292–13298 (2021)
    A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy
  149. Y. Wang, J. V. Le, K. Crocker, M.A. Darcy, P.D. Halley, D. Zhao, N. Andrioff, C. Croy, M.G Poirier, R. Bundschuh, C.E Castro, Nucleic Acids Res. 49, 8987–8999 (2021)
    A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules
  150. F. Liu, X. Liu, Q. Shi, C. Maffeo, M. Kojima, L. Dong, A. Aksimentiev, Q. Huang, T. Fukuda and T. Arai, Nanoscale 13, 15552-15559 (2021)
    A tetrahedral DNA nanorobot with conformational change in response to molecular trigger
  151. J. Appeldorn, S. Lemcke, T. Speck and A. Nikoubashman, submitted.
    Employing artificial neural networks to find reaction coordinates and pathways for self-assembly (ChemRxiv)
  152. H. Jun, X. Wang, M.F. Parsons, W.P. Bricker, T. John, S. Li, S. Jackson, W. Chiu, M. Bathe, Nucleic Acids Res. 49, 10265–10274 (2021)
    Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
  153. C.K. Wong, C. Tang, J.S. Schreck and J.P.K. Doye, Nanoscale 14, 2638–2648 (2022).
    Characterizing the free-energy landscapes of DNA origamis (arXiv)
  154. W. Lim, F. Randisi, J.P.K. Doye and A.A. Louis, Nucleic Acids Res. 50, 2480–2492 (2022).
    The interplay of supercoiling and thymine dimers in DNA (bioRxiv)
  155. W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, ACS Nano 16, accepted (2022).
    Probing the mechanical properties of DNA nanostructures with metadynamics (arXiv)
  156. H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, J. Am. Chem. Soc. 43, 19466–19473 (2021).
    Massively parallelized molecular force manipulation with on demand thermal and optical control
  157. L. Yang, C. Cullin and J. Elezgaray, ChemPhysChem 23, e202200021 (2022).
    Detection of short DNA sequences with DNA nanopores (arXiv)
  158. Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, R. Liu, X. Dai, Y. Qian, X. Su, submitted.
    Intramolecular Orthogonal Reporters for Dissecting Oxidative Stress and Response (Research Square)
  159. X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, submitted.
    Planar 2D wireframe DNA origami
  160. E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, Nucleic Acids Res. 50, D246–D252 (2022)
    Nanobase.org: a repository for DNA and RNA nanostructures
  161. R. Foffi, F. Sciortino, J. M. Tavares, P. I. C. Teixeira, Soft Matter 17, 10736-10743 (2021)
    Building up DNA, bit by bit: a simple description of chain assembly (arXiv)
  162. J. Yoo, S. Park, C. Maffeo, T. Ha, A. Aksimentiev, Nucleic Acids Res. 49, 11459–11475 (2021).
    DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles
  163. E. Lin-Shiao, W.G. Pfeifer, B.R. Shy, M. Saffari Doost, E. Chen, V.S. Vykunta, J.R. Hamilton, E.C. Stahl, D.M. Lopez, C.R. Sandoval Espinoza, A.E. Dejanov, R.J. Lew, M.G. Poirer, A. Marson, C.E. Castro, J.A. Doudna, Nucleic Acids Res. 50, 1256–1268 (2022)
    CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells (bioRxiv)
  164. J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, to appear in Energy Landscapes of Nanoscale Systems, ed. D.J. Wales, Frontiers of Nanoscience Vol. 21 (Elsevier)
    Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling (arXiv)
  165. Y. Deng, Y. Tan, L. Zhang, C. Zhang, X. Su, submitted.
    Forecasting the reaction of DNA modifying enzymes on DNA nanostructures by coarse grained model for stimuli-responsive drug delivery (Research Square)
  166. D. Smith and G. Tikhomirov, submitted.
    small: A programmatic nanostructure design and modelling environment (arXiv)
  167. S. Assenza and R. Pérez, J. Chem. Theory Comput 18, 3239–3256 (2022).
    Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA (biorXiv)
  168. D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, Molecules 27, 63 (2022)
    Unified Nanotechnology Format: One Way to Store Them All
  169. M. Centola, E. Poppleton, M. Centola, J. Valero, P. Šulc and M. Famulok, submitted.
    A rhythmically pulsing leaf-spring nanoengine that drives a passive follower (biorXiv)
  170. C.K. Wong and J.P.K. Doye, submitted
    The free-energy landscape of a mechanically bistable DNA origami (arXiv)
  171. L. Zhang, J. Chen, M. He, X. Su, Exploration 2, 20210265 (2022)
    Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection
  172. F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, Entropy 24, 458 (2022)
    OxDNA to study species interactions (arXiv)
  173. Y.A.G. Fosado, submitted
    Nanostars planarity modulates the elasticity of DNA hydrogels (arXiv)
  174. X. Hu, L. Tang, M. Zheng, J. Liu, Z. Zhang, Z. Li, Q. Yang, S. Xiang, L. Fang, Q. Ren, X. Liu, C.Z. Huang, C. Mao and H. Zuo, J. Am. Chem. Soc. 144, 4507–4514 (2022)
    Structure-guided designing pre-organization in bivalent aptamers
  175. L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, Sci. Adv. 8, eabm9530 (2022)
    A localized DNA finite-state machine with temporal resolution
  176. Y. Xin, P. Piskunen, A. Suma, C. Li, H. Ijäs, S. Ojasalo, I. Seitz, M.A. Kostiainen, G. Grundmeier, V. Linko and A. Keller, Small 18, 2107393 (2022)
    Environment-dependent stability and mechanical properties of DNA origami six-helix bundles with different crossover spacings
  177. R.L. Bender, H. Ogasawara, A.V. Kellner, A. Velusamy and K. Salaita, submitted
    Unbreakable DNA tension probes show that cell adhesion receptors detect the molecular force-extension curve of their ligands (bioRxiv)
  178. E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, Sci. Robot. 7, eabn5459 (2022)
    A DNA molecular printer capable of programmable positioning and patterning in two dimensions
  179. D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, submitted
    Weak tension accelerates hybridization and dehybridization of short oligonucleotides (bioRxiv)
  180. S. Sensale, P. Sharma and G. Arya, Phys. Rev. E 105, 044136 (2022)
    Binding kinetics of harmonically confined random walkers
  181. S. Dey, A. Dorey, L. Abraham, Y. Xing, I. Zhang, F. Zhang, S. Howorka and H. Yan, Nat. Commun. 13, 2271 (2022)
    A reversibly gated protein-transporting membrane channel made of DNA
  182. D. Luo, A. Kouyoumdjian, O. Strnad, H. Miao, I. Barišić and I. Viola, submitted (2022)
    SynopSet: Multiscale visual abstraction set for explanatory analysis of DNA nanotechnology simulations (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=1652"