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, arXiv (2015)

    Coarse-grained modelling of strong DNA bending II: Cyclization (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. accepted (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 accepted (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, submitted

    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. accepted

    tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami