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# 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.  
# 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 ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
#: The oxDNA coarse-grained model as a tool to simulate DNA origami ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''' 5118–5125 (2020)
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''', 5118–5125 (2020)
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, submitted
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, submitted
Line 219: Line 219:
# C.M. Huang, A. Kucinic, J.A. Johnson, H.-J. Su, C.E. Castro, submitted
# C.M. Huang, A. Kucinic, J.A. Johnson, H.-J. Su, C.E. Castro, submitted
#: Integrating computer-aided engineering and computer-aided design for DNA assemblies ([https://doi.org/10.1101/2020.05.28.119701 bioRxiv])
#: Integrating computer-aided engineering and computer-aided design for DNA assemblies ([https://doi.org/10.1101/2020.05.28.119701 bioRxiv])
# P. Irmisch, T.E. Ouldridge, and R. Seidel, ''J. Am. Chem. Soc'', '''142''', 11451–11463 (2020)
# P. Irmisch, T.E. Ouldridge, and R. Seidel, ''J. Am. Chem. Soc'' '''142''', 11451–11463 (2020)
#: [https://doi.org/10.1021/jacs.0c03105 Modelling DNA-strand displacement reactions in the presence of base-pair mismatches]
#: [https://doi.org/10.1021/jacs.0c03105 Modelling DNA-strand displacement reactions in the presence of base-pair mismatches]
# F. Hong, J.S. Schreck and P. Šulc, submitted
# F. Hong, J.S. Schreck and P. Šulc, submitted
#: Understanding DNA interactions in crowded environments with a coarse-grained model ([https://doi.org/10.1101/2020.06.08.140434 bioRxiv])
#: Understanding DNA interactions in crowded environments with a coarse-grained model ([https://doi.org/10.1101/2020.06.08.140434 bioRxiv])
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, ''J. Am. Chem. Soc.'', '''142''', 12069–12078 (2020)
# A.H. Clowsley, W.T. Kaufhold, T. Lutz, A. Meletiou, L. Di Michele, C. Soeller, ''J. Am. Chem. Soc.'' '''142''', 12069–12078 (2020)
#: [https://doi.org/10.1021/jacs.9b03418 Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy] ([https://doi.org/10.1101/591081 bioRxiv])
#: [https://doi.org/10.1021/jacs.9b03418 Detecting nanoscale distribution of protein pairs by proximity dependent super-resolution microscopy] ([https://doi.org/10.1101/591081 bioRxiv])
# H. Chhabra, G. Mishra, Y. Cao, D. Prešern, E. Skoruppa, M.M.C. Tortora and J.P.K. Doye, submitted
# H. Chhabra, G. Mishra, Y. Cao, D. Prešern, E. Skoruppa, M.M.C. Tortora and J.P.K. Doye, submitted
Line 233: Line 233:
# Y.A.G. Fosado, F. Landuzzi and T. Sakaue, submitted
# Y.A.G. Fosado, F. Landuzzi and T. Sakaue, submitted
#: Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending ([https://arxiv.org/abs/2008.05686 arXiv]
#: Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending ([https://arxiv.org/abs/2008.05686 arXiv]
# F. Spinozzi, M.G. Ortore, G. Nava, F. Bomboi, F. Carducci, H. Amenitsch, T. Bellini, F. Sciortino, and P. Mariani, ''Langmuir'' '''36''', accepted (2020)
#: [https://doi.org/10.1021/acs.langmuir.0c01520 Gelling without structuring: a SAXS study of the interactions among DNA nanostars]


We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].
We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Revision as of 05:35, 19 August 2020

  1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
    DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)
  2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Phys. Condens. Matter. 22, 104102 (2010)
    Extracting bulk properties of self-assembling systems from small simulations (arXiv)
  3. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
  4. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
    Coarse-grained modelling of DNA and DNA self-assembly
  5. F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 136, 215102 (2012)
    The effect of topology on the structure and free energy landscape of DNA kissing complexes (arXiv)
  6. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)
    Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link (arXiv)
  7. C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, J. Phys. Chem. B 116, 1161-11625 (2012)
    DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arXiv)
  8. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)
    Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)
  9. T.E. Ouldridge, J. Chem. Phys. 137, 144105 (2012)
    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
  10. F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 138, 085101 (2013)
    Coarse-grained simulations of DNA overstretching (arXiv)
  11. T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ACS Nano 7, 2479-2490 (2013)
    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker
  12. T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye, A. A. Louis, Nucleic Acids Res. 41, 8886-8895 (2013)
    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)
  13. J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, Phys. Chem. Chem. Phys 15, 20395-20414 (2013)
    Coarse-graining DNA for simulations of DNA nanotechnology (arXiv)
  14. N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, Nucleic Acids Res. 41, 10641-10658 (2013)
    On the biophysics and kinetics of toehold-mediated DNA strand displacement
  15. P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, Natural Computing 13, 535 (2014)
    Simulating a burnt-bridges DNA motor with a coarse-grained DNA model (arXiv)
  16. L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)
    Accurate phase diagram of tetravalent DNA nanostars (arXiv)
  17. P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014)
    A nucleotide-level coarse-grained model of RNA (arXiv)
  18. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)
    Gels of DNA Nanostars Never Crystallise
  19. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
    Modeling DNA Thermodynamics under Torsional Stress
  20. J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, Nucleic Acids Res. 43, 6181-6190 (2014)
    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization (arXiv)
  21. R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, Nature Comm. 5, 5324 (2014)
    Programmable energy landscapes for kinetic control of DNA strand displacement
  22. M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, J. Phys. Chem. B 118, 14326-14335 (2014)
    The role of loop stacking in the dynamics of DNA hairpin formation (arXiv)
  23. I. Y. Loh, J.Cheng, S. R. Tee, A. Efremov, and Z. Wang, ACS Nano 8, 10293–10304 (2014)
    From bistate molecular switches to self-directed track-walking nanomotors
  24. C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, Sci. Rep., 5, 7655 (2015)
    Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA (arXiv)
  25. L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1-8 (2015)
    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
  26. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)
    Physical model for recognition tunneling
  27. F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)
    Switching Bonds in a DNA Gel: An All-DNA Vitrimer
  28. J. S. Schreck, T. E. Ouldridge, F. Romano, A. A. Louis, J.P.K. Doye, J. Chem. Phys. 142, 165101 (2015)
    Characterizing the bending and flexibility induced by bulges in DNA duplexes (arXiv)
  29. M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ACS Nano 9, 11993 (2015)
    Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors (arXiv)
  30. T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)
    DNA nanotechnology: understanding and optimisation through simulation (arXiv)
  31. P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, Biophys. J. 108, 1238-1247 (2015)
    Modelling toehold-mediated RNA strand displacement (arXiv)
  32. B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, J. Chem. Phys. 142, 234901 (2015)
    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
  33. C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, J. Chem. Phys. 143, 243122 (2015)
    Coarse-grained modelling of supercoiled RNA (arXiv)
  34. Q. Wang, C.G. Myers, and B.M. Pettitt, J. Phys. Chem. B 119, 4937–4943 (2015)
    Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density
  35. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, arXiv (2015)
    Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
  36. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, J. Chem. Theor. Comput. 15 4660-4672 (2019)
    Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model (arXiv) (data)
  37. J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, Science 349, 977-981 (2015)
    Base triplet stepping by the Rad51/RecA family of recombinases
  38. B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ACS Nano 10, 1724-1737 (2016)
    Direct Simulation of the Self-Assembly of a Small DNA Origami (data)
  39. V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, Nat. Commun. 7, 10803 (2016)
    Design principles for rapid folding of knotted DNA nanostructures
  40. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
    Characterizing DNA star-tile-based nanostructures using a coarse-grained model
  41. M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ACS Nano, 10, 5882–5890 (2016)
    Biomimetic autonomous enzymatic nanowalker of high fuel efficiency
  42. J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, J. Chem. Phys. 145, 084910 (2016)
    Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars
  43. T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, Nucleic Acids Res. 44, 9121-9130 (2016)
    Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
  44. Q. Wang and B.M. Pettitt, J. Phys. Chem. Lett 7, 1042–1046 (2016)
    Sequence affects the cyclization of DNA minicircles
  45. A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, J. Phys: Condens. Matter 29, 014006 (2017).
    Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal (arXiv) (data)
  46. E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ACS Nano 11, 2094-2102 (2017)
    Condensation and demixing in solutions of DNA nanostars and their mixtures
  47. E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, J. Chem. Phys 146, 214902 (2017)
    DNA elasticity from coarse-grained simulations: the effect of groove asymmetry (arXiv)
  48. A. Suma and C. Micheletti, Proc. Natl. Acad. Sci. USA 114, E2991–E2997 (2017)
    Pore translocation of knotted DNA rings
  49. Z. Shi, C. E. Castro and G. Arya, ACS Nano 11, 4617–4630 (2017)
    Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations
  50. H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, J. Phys. Chem. B 121, 5033–5039 (2017)
    Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design
  51. S. Vangaveti, R. J. D'Esposito, J. L. Lippens, D. Fabris and S. V. Ranganathan, Phys. Chem. Chem. Phys. 19, 14937-14946 (2017)
    A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry
  52. A. Henning-Knechtel, J. Knechtel and M. Magzoub, Nucleic Acids Res. 45, 12057–12068 (2017)
    DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels
  53. R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ACS Nano 11, 12426–12435 (2017)
    Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
  54. Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, Nanoscale 9, 12142-12149 (2017)
    A DNA bipedal nanowalker with a piston-like expulsion stroke
  55. Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, Nucleic Acids Res. 45 7633-7642 (2017)
    Influence of DNA sequence on the structure of minicircles under torsional stress
  56. B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucleic Acids Res. 46, 538-545 (2018)
    Rolling circle amplification shows a sinusoidal template length-dependent amplification bias (data)
  57. 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
  72. 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)
  73. 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
  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
  89. 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)
  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, accepted (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, submitted
    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, submitted
    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, submitted
    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, submitted
    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, submitted
    Integrating computer-aided engineering and computer-aided 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, submitted
    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, submitted
    Computing the elastic mechanical properties of rod-like DNA nanostructures (arXiv)
  115. K. Tapio, A. Mostafa, Y. Kanehira, A. Suma, A. Dutta, I. Bald, submitted
    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, submitted
    How to design an icosahedral quasicrystal through directional bonding
  117. Y.A.G. Fosado, F. Landuzzi and T. Sakaue, submitted
    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, accepted (2020)
    Gelling without structuring: a SAXS study of the interactions among DNA nanostars

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=1458"