Publications

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, 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, Sci. Adv. 8, eabn0039 (2022).

     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 (Elsevier) Vol. 21, Chapter 9, pp 195-210 (2022)

     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, Appl. Sci. 12, 5875 (2022)

     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)

183. L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, submitted (2022)

     A simple solution to the problem of self-assembling cubic diamond crystals (arXIv)

184. J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, Nat. Protoc. 17, accepted (2022)

     Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView

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