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# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''arXiv'' (2015)
# R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye,  ''J. Chem. Theor. Comput.'' '''15''' 4660-4672 (2019)
#:[http://arxiv.org/abs/1506.09008 Coarse-grained modelling of strong DNA bending II: Cyclization] ([http://dx.doi.org/10.5281/zenodo.1753767 data])
#: [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]
Line 115: Line 115:
# P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys'' '''148''', 134910 (2018)
# 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])
#: [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, submitted
# 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 ([https://www.biorxiv.org/content/early/2018/02/10/263038 bioRXiv])
#: [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]
Line 139: Line 139:
# E. Torelli, J.W. Kozyra, J.-Y. Gu, U. Stimming, L. Piantanida. K. Voitchovsky and N. Krasnogor, ''Scientific Reports'' '''8''', 6989 (2018)
# 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 ]
#: [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, submitted
# R. Jin and L. Maibaum, ''J. Chem. Phys.'' '''150''', 105103 (2019)
#: Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model ([https://arxiv.org/abs/1807.04258 arxiv])
#: [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)
# 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]
#: [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)
# 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]
#: [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, submitted.
# 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 DNA: Perturbation theory and beyond ([https://doi.org/10.1101/422683 bioRXiv],[https://arxiv.org/abs/1809.07050 arXiv])
#: [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.'' accepted.
# B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ''Nucleic Acids Res.'' '''47''', 1585–1597 (2019).
#: [http://dx.doi.org/10.1093/nar/gky1304 Coarse-grained modelling of the structural properties of DNA origami] ([https://arxiv.org/abs/1809.08430 arXiv]) ([http://dx.doi.org/10.5287/bodleian:8gY5EnYYO data])
#: [http://dx.doi.org/10.1093/nar/gky1304 Coarse-grained modelling of the structural properties of DNA origami] ([https://arxiv.org/abs/1809.08430 arXiv]) ([http://dx.doi.org/10.5287/bodleian:8gY5EnYYO data])
# N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, submitted
# N. E. C. Haley, T. E. Ouldridge, A. Geraldini, A. A. Louis, J. Bath and A. J. Turberfield, submitted
#: Rational design of hidden thermodynamic driving through DNA mismatch repair ([https://doi.org/10.1101/426668 bioRXiv])
#: Rational design of hidden thermodynamic driving through DNA mismatch repair ([https://doi.org/10.1101/426668 bioRXiv])
# L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, ''Small'', 14, 1802580 (2018)
# L. Zhou, A.E. Marras, C.-M. Huang, C.E. Castro and H.-J Su, ''Small'' '''14''', 1802580 (2018)
#: [https://doi.org/10.1002/smll.201802580 Paper origami‐inspired design and actuation of DNA nanomachines with complex motions]
#: [https://doi.org/10.1002/smll.201802580 Paper origami‐inspired design and actuation of DNA nanomachines with complex motions]
# R. A. Brady, W.T. Kaufhold, N.J. Brooks, V. Foderà and L. Di Michele, ''J. Phys. Condens. Matter'', accepted.
# 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])
#: [https://doi.org/10.1088/1361-648X/aaf4a1 Flexibility defines structure in crystals of amphiphilic DNA nanostars] ([https://arxiv.org/abs/1810.05761 arXiv])
# 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)
# 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)
#: [https://doi.org/10.1021/jacs.8b07180 Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering]
#: [https://doi.org/10.1021/jacs.8b07180 Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering]
# Y. Choi, H. Choi, A.C. Lee, S. Kwon, ''J. Vis. Exp.'', e58364 (2018)
#: [https://doi.org/10.3791/58364 Design and Synthesis of a Reconfigurable DNA Accordion Rack]
# M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, submitted
# M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, submitted
#: Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis ([https://arxiv.org/abs/1811.12331 arXiv])
#: Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis ([https://arxiv.org/abs/1811.12331 arXiv])
#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, Nanoscale, Advance Article (2019)  
#  C.-M. Huang,  A. Kucinic, J.V. Le, C.E. Castro and H.-J. Su, ''Nanoscale'' '''11''', 1647-1660 (2019)  
#: [https://dx.doi.org/10.1039/C8NR06377J Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis]
#: [https://dx.doi.org/10.1039/C8NR06377J Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis]
# I.T. Hoffecker, S. Chen, A. Gådin, A. Bosco, A.I. Teixeira and B. Högberg, Small, Early View.
# 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]
#: [https://doi.org/10.1002/smll.201803628 Solution‐controlled conformational switching of an anchored wireframe DNA nanostructure]
# M. Coraglio, E. Skoruppa and E. Carlon, submitted.
# M. Coraglio, E. Skoruppa and E. Carlon, ''J. Chem. Phys.'' '''150''', 135101 (2019)
#: DNA polygons ([https://arxiv.org/abs/1812.03701 arXiv])
#: [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, submitted
#: Allosteric modulation of local reactivity in DNA origami ([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.'' Advance Article
#: [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, submitted
#: 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'' Article ASAP (2019)
#: [https://doi.org/10.1021/acsnano.9b03473 Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations]
 
We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Revision as of 08:45, 20 November 2019

  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, submitted
    Allosteric modulation of local reactivity in DNA origami (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. Advance Article
    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, submitted
    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 Article ASAP (2019)
    Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations

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