Publications

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  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. G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, Nat. Nanotechnol. 12, 920–927 (2017)
    A spatially localized architecture for fast and modular DNA computing
  56. 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
  57. 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)
  58. 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
  59. 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)
  60. 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)
  61. 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)
  62. 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
  63. 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)
  64. 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)
  65. 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)
  66. 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
  67. 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
  68. 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
  69. 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)
  70. E. Spruijt, S.E. Tusk and H. Bayley, Nat. Nanotechnol. 13, 739-745 (2018)
    DNA scaffolds support stable and uniform peptide nanopores
  71. 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)
  72. 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
  73. 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)
  74. 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
  75. 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
  76. 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)
  77. 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)
  78. 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)
  79. 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
  80. 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)
  81. 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
  82. Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
    Design and Synthesis of a Reconfigurable DNA Accordion Rack
  83. 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)
  84. 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
  85. 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
  86. M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
    Overtwisting induces polygonal shapes in bent DNA (arXiv)
  87. 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
  88. Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
    A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
  89. 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
  90. 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)
  91. 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)
  92. 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
  93. 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
  94. 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)
  95. 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
  96. 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)
  97. 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
  98. 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
  99. Z. Shi and G. Arya, Nucleic Acids Research 48, 548-560 (2020)
    Free energy landscape of salt-actuated reconfigurable DNA nanodevices
  100. 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)
  101. 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)
  102. 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
  103. 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)
  104. 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)
  105. 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
  106. A. Bader and S.L. Cockroft, Chem. Commun. 56, 5135-5138 (2020)
    Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices
  107. 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 2639, 93-112 (2023).
    The oxDNA coarse-grained model as a tool to simulate DNA origami (arXiv) (data)
  108. J. Lee, J.-H. Huh, S. Lee, Langmuir 36, 5118–5125 (2020)
    DNA Base Pair-Stacking Crystallization of Gold Colloids
  109. 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)
  110. 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)
  111. 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)
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  228. L. Zhang, H. Zhao, H. Yang and X. Su, Biosens. Bioelectron. 239, 115622 (2023)
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    Programming rigidity into size-defined wireframe DNA nanotubes
  233. J. Lee and S. Lee, Anal. Chem. 95, 1856–1866 (2023)
    Non-invasive, reliable, and fast quantification of DNA loading on gold nanoparticles by a one-step optical measurement
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    Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy
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    Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics
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    Ballistic Brownian Motion of Nanoconfined DNA
  241. Y. Ma, W. Guo, Q. Mou, X. Shao, M. Lyu, V. Garcia, L. Kong, W. Lewis, C. Ward, Z. Yang, X. Pan, S.S. Yi and Y. Lu, Nat. Biotechnol. (2023)
    Spatial imaging of glycoRNA in single cells with ARPLA
  242. X. Luo, D. Saliba, T. Yang, S. Gentile, K. Mori, P.I. Garcia, T. Das, N. Bagheri, A. Porchetta, A. Guarne, G. Cosa, H.F. Sleiman, Angew. Chem. Int. Ed. 62 e202309869 (2023)
    Minimalist design of wireframe DNA nanotubes: Tunable geometry, size, chirality, and dynamics
  243. Y. Zhao, S. Cao, Y. Wang, F. Li, L. Lin, L. Guo, F. Wang, J. Chao, X. Zuo, Y. Zhu, L. Wang, J. Li and C. Fan, Nat. Mach. Intell. 5, 980–990 (2023)
    A temporally resolved DNA framework state machine in living cells
  244. X.R. Liu, I.Y. Loh, W. Siti, H.L. Too, T. Anderson and Z. Wang, Nanoscale Horiz., 8, 827-841 (2023)
    A light-operated integrated DNA walker–origami system beyond bridge burning
  245. H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang and C. Fan, Nature 622, 292–300(2023).
    DNA-based programmable gate arrays for general-purpose DNA computing
  246. C. Yang, X. Song, Y. Feng, G. Zhao, and Y. Liu, J. Phys.: Condens. Matter 35, 265101 (2023)
    Stability of DNA and RNA hairpins: a comparative study based on ox-DNA
  247. Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, and Yanhui Liu, Commun. Theor. Phys. 75, 055601 (2023)
    A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments
  248. W. Siti, H.L. Too, T. Anderson, X.R. Liu, I.Y. Loh and Z. Wang, Sci. Adv. 9, adi8444 (2023)
    Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics
  249. R. Ma, A. Velusamy, S.A. Rashid, B.R. Deal, W. Chen, B. Petrich, R. Li, K. Salaita, Nat. Methods 20, 1666–1671 (2023)
    Molecular mechanocytometry using tension-activated cell tagging (bioRxiv)
  250. D. Karna, E. Mano, J. Ji, I. Kawamata, Y. Suzuki and H. Mao, Nat. Commun. 14, 6459 (2023)
    Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
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    Multiplexed CRISPR-based nucleic acid detection using a single Cas protein
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    Spatiotemporal control over polynucleotide brush growth on DNA origami nanostructures
  253. J.Y. Lee, H. Koh and D.-N. Kim, Nat. Commun. 14, 7079 (2023)
    A computational model for structural dynamics and reconfiguration of DNA assemblies
  254. M.C. Engel, J.A. Smith and M.P. Brenner, Phys. Rev. X 13, 041032 (2023)
    Optimal control of nonequilibrium systems through automatic differentiation
  255. L. Yu, Y. Xu, M. Al-Amin, S. Jiang, M. Sample, A. Prasad, N. Stephanopoulos, P. Šulc, and H. Yan, J. Am. Chem. Soc. 145, 27336–27347 (2023)
    CytoDirect: A nucleic acid nanodevice for specific and efficient delivery of functional payloads to the cytoplasm
  256. Y.-P. Qiao and C.-L. Ren, Langmuir 40, 109–117 (2024)
    Correlated hybrid DNA structures explored by the oxDNA Model
  257. L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ACS Nano 18, 885–893 (2024)
    Multilayer DNA origami with terminal interfaces that are flat and wide-area
  258. N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, Small, accepted (2024)
    Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility
  259. A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, Nat. Commun. 15, 704 (2024)
    DNA mechanocapsules for programmable piconewton responsive drug delivery
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    Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts
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    Bimodal DNA self-origami material with nucleic acid function enhancement
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    An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures
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    Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures
  264. S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, Nanoscale 16, 4872-4879 (2024)
    Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective
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    Proximity-enhanced functional imaging analysis of engineered tumors
  266. Y. Liu, Z. Dai, X. Xie, B. Li, S. Jia, Q. Li, M. Li, C. Fan and X. Liu, J. Am. Chem. Soc. 146, 8, 5461–5469 (2024)
    Spacer-programmed two-dimensional DNA origami assembly
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    Activationless electron transfer of redox-DNA in electrochemical nanogaps
  268. M. Sample, M. Matthies and P. Šulc, submitted
    Hairygami: Analysis of DNA nanostructure's conformational change driven by functionalizable overhangs (arXiv)
  269. M. Sample, M. Matthies and P. Šulc, 2023 Winter Simulation Conference (WSC), San Antonio, TX, USA, pp. 91-105 (2023)
    Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial (arXiv)
  270. M. DeLuca, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, submitted
    Mechanism of DNA origami folding elucidated by mesoscopic simulations (bioRxiv)
  271. V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted
    Structural flexibility dominates over binding strength for supramolecular crystallinity (bioRxiv)
  272. C. Shi, P. Wang, submitted
    Allosteric DNAzyme for sensitive detection of nucleic acids for molecular diagnosis (medRxiv)
  273. F. Smith, A. Sengar, G.‐B.V. Stan, T.E. Ouldridge, M. Stevens, J. Goertz and W. Bae, submitted
    Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds (bioRxiv)
  274. K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, submitted
    Towards New Liquid Crystal Phases of DNA mesogens (arXiv)
  275. G.B.M. Wisna, D. Sukhareva, J. Zhao, D. Satyabola, M. Matthies, S. Roy, P. Šulc, H. Yan and R.F. Hariadia, submitted
    High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography (bioRxiv)
  276. H. Koh, J.Y. Lee, J.G. Lee, submitted
    Forming superhelix of double stranded DNA from local deformation (arXiv)
  277. N.P. Agarwal and A. Gopinath, submited
    DNA origami 2.0 (bioRxiv)
  278. J.M. Weck and A. Heuer-Jungemann, submitted
    Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)
  279. Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li, S. Wang, H. Yan, P. Sulc, N. Stephanopoulos, submitted
    High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody (bioRxiv)
  280. H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, submitted
    Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments (arXiv)
  281. L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, submitted
    Engineering modular and tunable single Molecule sensors by decoupling sensing from signal output (bioRxiv)
  282. F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
    nNxB: a new coarse-grained model for RNA and DNA nanotechnology (arXiv)
  283. E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 160, 115101 (2024)
    Coarse-grained modelling of DNA-RNA hybrids (arXiv)
  284. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
    DNA nanostar structures with tunable auxetic properties (bioRxiv)
  285. G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro
    Piggybacking functionalized DNA nanostructures into live cell nuclei (bioRxiv)
  286. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, submitted
    Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)
  287. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
    Bending Unwinds DNA (bioRxiv)
  288. X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, submitted
    A dynamically gated triangular DNA nanopore for molecular sensing and cross-membrane transport (ResearchSquare)
  289. C. Karfusehr, M. Eder, F.C. Simmel
    Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)
  290. M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, submitted
    Reconfigurable multi-component nanostructures built from DNA origami voxels (bioRxiv)

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