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. 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)

112. 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

113. 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)

114. 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)

115. 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)

116. 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)

117. 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

118. 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)

119. 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

120. 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

121. 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

122. 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

123. J. Procyk, E. Poppleton and P. Šulc, Soft Matter 17, 3586-3593 (2021).

     Coarse-grained nucleic acid-protein model for hybrid nanotechnology (arXiv)

124. 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)

125. 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)

126. 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

127. E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, Nanoscale 12, 23003-23012 (2020)

     Hyperbranched DNA clusters (arXiv)

128. 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

129. R. Li, H. Chen and J.H. Choi, Angew. Chem. Int. Ed. 60, 7165-7173 (2021)

     Auxetic Two‐Dimensional Nanostructures from DNA (bioRXiv)

130. 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

131. 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)

132. 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

133. 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

134. R. Li, H. Chen and J. H. Choi, Small 17, 2007069 (2021)

     Topological Assembly of a Deployable Hoberman Flight Ring from DNA

135. 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)

136. B. Babatunde, S. Arias, J. Cagan and R.E. Taylor, Appl. Sci. 11, 2950 (2021)

     Generating DNA origami nanostructures through shape annealing

137. 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

138. 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)

139. 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

140. 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

141. E. Benson, R. Carrascosa Marzo, J. Bath, A.J. Turberfield, Small 17, 2007704 (2021)

     Strategies for Constructing and Operating DNA Origami Linear Actuators

142. 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

143. 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

144. 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

145. 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

146. J. P. Mahalik and M. Muthukumar, submitted

     Nucleotide Dynamics During Flossing of Polycation-DNA-Polycation through a Nanopore using Molecular Dynamics (bioRxiv)

147. 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)

148. 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

149. 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

150. T. Lee, S. Do, J.G. Lee, D.-N. Kim and Y. Shin, Nanoscale 13, 17638-17647 (2021)

     The flexibility-based modulation of DNA nanostar phase separation

151. 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

152. 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

153. J. Appeldorn, S. Lemcke, T. Speck and A. Nikoubashman, J. Phys. Chem. B 126, 5007–5016 (2022).

     Employing artificial neural networks to find reaction coordinates and pathways for self-assembly (ChemRxiv)

154. 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

155. 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)

156. 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)

157. W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, ACS Nano 16, 8784–8797 (2022).

     Probing the mechanical properties of DNA nanostructures with metadynamics (arXiv)

158. 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

159. L. Yang, C. Cullin and J. Elezgaray, ChemPhysChem 23, e202200021 (2022).

     Detection of short DNA sequences with DNA nanopores (arXiv)

160. Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, L. Zhang, H. Xiao, Y. Qian, X. Su, Nano Today 46 101573 (2022).

     Simulation guided intramolecular orthogonal reporters for dissecting cellular oxidative stress and response (Research Square)

161. 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

162. 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

163. 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)

164. 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

165. 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)

166. J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, 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)

167. 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)

168. D. Smith and G. Tikhomirov, submitted.

     small: A programmatic nanostructure design and modelling environment (arXiv)

169. 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)

170. D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, Molecules 27, 63 (2022)

     Unified Nanotechnology Format: One Way to Store Them All

171. M. Centola, E. Poppleton, M. Centola, J. Valero, P. Šulc and M. Famulok, Nat. Nanotechnol. 19, 226–236 (2024)

     A rhythmically pulsing leaf-spring nanoengine that drives a passive follower (biorXiv)

172. C.K. Wong and J.P.K. Doye, Appl. Sci. 12, 5875 (2022)

     The free-energy landscape of a mechanically bistable DNA origami (arXiv)

173. 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

174. F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, Entropy 24, 458 (2022)

     OxDNA to study species interactions (arXiv)

175. Y.A.G. Fosado, Soft Matter 19, 4820-4828 (2023)

     Nanostars planarity modulates the elasticity of DNA hydrogels (arXiv)

176. 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

177. 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

178. 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

179. 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)

180. 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

181. A. Dutta, K. Tapio, A. Suma, A. Mostafa, Y. Kanehira, V. Carnevale, G. Bussi and I. Bald, Nanoscale 14, 16467-16478 (2022)

     Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering

182. D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, Nucleic Acids Res. 51, 3030–3040 (2023)

     Weak tension accelerates hybridization and dehybridization of short oligonucleotides (bioRxiv)

183. S. Sensale, P. Sharma and G. Arya, Phys. Rev. E 105, 044136 (2022)

     Binding kinetics of harmonically confined random walkers

184. 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

185. 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)

186. L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, Nanoscale 14, 14268-14275 (2022)

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

187. J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, Nat. Protoc. 17, 1762–1788 (2022)

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

188. C. Zhou, D. Yang, S. Sensale, P. Sharma, D. Wang, L. Yu, G. Arya, Y. Ke and P. Wang, Sci. Adv 8, eade3003 (2022)

     A bistable and reconfigurable molecular system with encodable bonds (Research Square)

189. R. Li, M. Zheng, A.S. Madhvacharyula, Y. Du, C. Mao and J.H. Choi, Biophys. J. 121, 4078-4090 (2022)

     Mechanical deformation behaviors and structural properties of ligated DNA crystals (bioRxiv)

190. C. Xie, Y. Hu, Z. Chen, K. Chen and L. Pan, Nanotechnology 33, 405603 (2022)

     Tuning curved DNA origami structures through mechanical design and chemical adducts

191. F. Fontana, T. Bellini and M. Todisco, Macromolecules 55, 5946–5953 (2022)

     Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities

192. Z. Weng, H. Yu, W. Luo, L. Zhang, Z. Zhang, T. Wang, Q. Liu, Y. Guo, Y. Yang, J. Li, L. Yang, L. Dai, Q. Pu, X. Zhou and G. Xie, Anal. Chim. Acta 1199, 339568 (2022)

     Specific and robust hybridization based on double-stranded nucleic acids with single-base resolution

193. J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, ACS Nano 17, 5387–5398 (2023)

     Designing the self-assembly of arbitrary shapes using minimal complexity building blocks (arXiv)

194. Y. Deng, Y. Tan, Y. Zhang, L. Zhang, C. Zhang, Y. Ke and X. Su, ACS Appl. Mater. Interfaces 14, 34470–34479 (2022)

     Design of uracil-modified DNA nanotubes for targeted drug release via DNA-modifying enzyme reactions

195. J. G. Lee, K. S. Kim, J. Y. Lee and D.-N. Kim, ACS Nano 16, 4289–4297 (2022)

     Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint

196. M. Micheloni, L. Petrolli, G. Lattanzi and R. Potestio, Biophys. J. 122, 3314-3322 (2023)

     Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations (bioRxiv)

197. A. Elonen, A.K. Natarajan, I. Kawamata, L. Oesinghaus, A. Mohammed, J. Seitsonen, Y. Suzuki, F. C. Simmel, A. Kuzyk and P. Orponen, ACS Nano 16, 16608–16616 (2022)

     Algorithmic design of 3D wireframe RNA polyhedra (bioRxiv)

198. D. Fu, R.P. Narayanan, A. Prasad, F. Zhang, D. Williams, J.S. Schreck, H. Yan and J. Reif, Sci. Adv. 8, ade4455 (2022)

     Automated design of 3D DNA origami with non-rasterized 2D curvature

199. N. Chauhan, Y. Xiong, S. Ren, A. Dwivedy, N. Magazine, L. Zhou, X. Jin, T. Zhang, B.T. Cunningham, S. Yao, W. Huang and X. Wang, J. Am. Chem. Soc. 145, 20214–20228 (2023)

     Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus

200. A. Mills, N. Aissaoui, D. Maurel, J. Elezgaray, F. Morvan, J. J. Vasseur, E. Margeat, R.B. Quast, J. Lai Kee-Him, N. Saint, C. Benistant, A. Nord, F. Pedaci and G. Bellot, Nat. Commun. 13, 3182 (2022)

     A modular spring-loaded actuator for mechanical activation of membrane proteins

201. T. Panczyk, K. Nieszporek and P. Wolski, Molecules 27, 4915 (2022)

     Stability and existence of noncanonical i-motif DNA structures in computer simulations based on atomistic and coarse-grained force fields

202. E.E. Kurisinkal, V. Caroprese, M.M. Koga, D. Morzy and M.M.C. Bastings, Molecules 27 4968 (2022)

     Selective integrin α5β1 targeting through spatially constrained multivalent DNA-based nanoparticles

203. R.P. Narayanan, J. Procyk, P. Nandi, A. Prasad, Y. Xu, E. Poppleton, D. Williams, F. Zhang, H. Yan, P.-L. Chiu, N. Stephanopoulos and P. Šulc, ACS Nano 16, 14086–14096 (2022)

     Coarse-grained simulations for the characterization and optimization of hybrid protein–DNA nanostructures

204. J. Wang, Y. Wei, P. Zhang, Y. Wang, Q. Xia, X. Liu, S. Luo, J. Shi, J. Hu, C. Fan, B. Li, L. Wang, X. Zhou and J. Li, Nano Lett. 22, 7173–7179 (2022)

     Probing heterogeneous folding pathways of DNA origami self-assembly at the molecular level with atomic force microscopy

205. S. Li, Y. Coffinier, C. Lagadec, F. Cleri, K. Nishiguchi, A. Fujiwara, T. Fujii, S.-H. Kim and N.Clément, Biosens. Bioelectron. 216, 114643 (2022)

     Redox-labelled electrochemical aptasensors with nanosupported cancer cells

206. S. Bianco, T. Hu, O. Henrich and S. W.Magennis, Biophysical Reports 2, 100070 (2022)

     Heterogeneous migration routes of DNA triplet repeat slip-outs

207. Y. Li, C. Maffeo, H. Joshi, A. Aksimentiev, B. Ménard and R. Schulman, Sci. Adv. 8, eabq4834 (2022)

     Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

208. G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, Nano Lett. 22, 7834–7840 (2022)

     Far-field electrostatic signatures of macromolecular 3D conformation

209. L. Guo, Y. Zhang, Y. Wang, M. Xie, J. Dai, Z. Qu, M. Zhou, S. Cao, J. Shi, L. Wang, X. Zuo, C. Fan and J. Li, Angew. Chem. Int. Ed. 61, e202117168 (2022)

     Directing multivalent aptamer-receptor binding on the cell surface with programmable atom-like nanoparticles

210. N. Xie, M. Li, Y. Wang, H. Lv, J. Shi, J. Li, Q. Li, F. Wang and C. Fan, J. Am. Chem. Soc. 144, 9479–9488 (2022)

     Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions

211. E. Lattuada, T. Pietrangeli and F. Sciortino, J. Chem. Phys. 157, 135101 (2022)

     Interpenetrating gels in binary suspensions of DNA nanostars

212. X. Chen, Y. Wang, X. Dai, L. Ding, J. Chen, G. Yao, X. Liu, S. Luo, J. Shi, L. Wang, R. Nechushtai, E. Pikarsky, I. Willner, C. Fan, and J. Li, J. Am. Chem. Soc. 144, 6311–6320 (2022)

     Single-Stranded DNA-Encoded Gold Nanoparticle Clusters as Programmable Enzyme Equivalents

213. Q. Kou, L. Wang, L. Zhang, L. Ma, S. Fu and X. Su, Small 18, 2205191 (2022)

     Simulation-assisted localized DNA logical circuits for cancer biomarkers detection and imaging

214. P. E. Beshay, A. Kucinic, N. Wile, P. Halley, L. Des Rosiers, A. Chowdhury, J. L. Hall, C. E. Castro and M. W. Hudoba, The Biophysicist 4, 68–81 (2023)

     Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories (bioRxiv)

215. A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, Biophys. J. 121, 4849-4859 (2022)

     Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking

216. E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti, J. Open Source Softw. 8, 4693 (2023)

     oxDNA: coarse-grained simulations of nucleic acids made simple

217. A. Suma, V. Carnevale and C. Micheletti, Phys. Rev. Lett. 130, 048101 (2023)

     Nonequilibrium Thermodynamics of DNA Nanopore Unzipping (arXiv)

218. Y. Tang, H. Liu, Q. Wang, X. Qi, L. Yu, P. Šulc, F. Zhang, H. Yan and S. Jiang, J. Am. Chem. Soc. 145, 25, 13858–13868 (2023)

     DNA Origami Tessellations

219. M. DeLuca, W.G. Pfeifer, B. Randoing, C.-M. Huang, M.G. Poirier, C.E. Castro and G. Arya, Nanoscale 15, 8356-8365 (2023)

     Thermally reversible pattern formation in arrays of molecular rotors

220. T. Liang, C. Yang, X. Song, Y. Feng, Y. Liu and H. Chen, Phys. Rev. E 108, 014406 (2023)

     Quantification of macromolecule crowding at single-molecule level

221. D. Lysne, T. Hachigian, C. Thachuk, J. Lee and E. Graugnard J. Am. Chem. Soc. 145, 16691–16703 (2023)

     Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions

222. A. Kucinic, C.-M. Huang, J. Wang, H.-J. Su and C.E. Castro, Nanoscale, 15 562-572 (2023)

     DNA origami tubes with reconfigurable cross-sections

223. Y. Zhang, X. Yin, C. Cui, K. He, F. Wang, J. Chao, T. Li, X. Zuo, A. Li, L. Wang, N. Wang, X. Bo and C. Fan, Sci. Adv. 9, adf8263 (2023)

     Prime factorization via localized tile assembly in a DNA origami framework

224. W.G. Pfeifer, C.-M. Huang, M. G. Poirier, G. Arya and C. E. Castro, Sci. Adv. 9, adi0697 (2023)

     Versatile computer-aided design of free-form DNA nanostructures and assemblies (bioRxiv)

225. M. Lolaico, S. Blokhuizen, B. Shen, Y. Wang, and B. Högberg, ACS Nano 17, 6565–6574 (2023)

     Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges

226. Y. Wang, A. Kucinic, L. Des Rosiers, P.E. Beshay, N. Wile, M.W. Hudoba and C.E. Castro, Appl. Sci. 13, 3208 (2023)

     Mechanical Design of DNA Origami in the Classroom

227. D. Morzy, C. Tekin, V. Caroprese, R. Rubio-Sánchez, L. Di Michele and M.M.C. Bastings, Nanoscale 15, 2849-2859 (2023)

     Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes

228. L. Zhang, H. Zhao, H. Yang and X. Su, Biosens. Bioelectron. 239, 115622 (2023)

     Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection

229. Y.-P. Qiao, C.-L. Ren and Y.-Q. Ma J. Phys. Chem. B 127, 4015–4021 (2023)

     Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick

230. K. Cervantes-Salguero, Y.A. Gutiérrez Fosado, W. Megone, J.E. Gautrot and M. Palma, Molecules 28, 3686 (2023)

     Programmed self-assembly of DNA nanosheets with discrete single-molecule thickness and interfacial mechanics: Design, simulation, and characterization

231. H.L. Too and Z. Wang, Nanoscale 15, 11915-11926 (2023)

     Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration

232. D. Saliba, X. Luo, F.J. Rizzuto and H.F. Sleiman, Nanoscale 15, 5403-5413 (2023)

     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

234. X. Shen, Q. Ouyang, H. Tan, J. Ouyang and N. Na, Anal. Chem. 95, 5903–5910 (2023)

     Computation-assisted design of ssDNA framework nanorobots for cancer logical recognition, toehold disintegration, visual dual-diagnosis, and synergistic therapy

235. L. Tang, M. Huang, M. Zhang, Y. Pei, Y. Liu, Y. Wei, C. Yang, T. Xie, D. Zhang, R. Zhou, Y. Song, J. Song, Small Methods 7, 2300327 (2023)

     De novo evolution of an antibody-mimicking multivalent aptamer via a DNA framework

236. Z. Zheng, S.H. Kim, A. Chovin, N. Clement and C. Demaille, Chem. Sci. 14, 3652-3660 (2023)

     Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics

237. M. Vogt, M. Langecker, M. Gouder, E. Kopperger, F. Rothfischer, F.C. Simmel and J. List, Nature Physics 19, 741–751 (2023)

     Storage of mechanical energy in DNA nanorobotics using molecular torsion springs

238. C. Xie, Y. Hu, K. Chen, Z. Chen and L. Pan, Commun. Comput. Inf. Sci., 1801, 647–654 (2023)

     Tuning Geometric Conformations of Curved DNA Structures by Controlling Positions of Nicks

239. S. Yu, J. Zhao, R. Chu, X. Li, G. Wu and X. Meng, Entropy 25, 796 (2023)

     Anomalous diffusion of polyelectrolyte segments on supported charged lipid bilayers

240. I. Madrid, Z. Zheng, C. Gerbelot, A. Fujiwara, S. Li, S. Grall, K. Nishiguchi, S.H. Kim, A. Chovin, C. Demaille and N. Clement, ACS Nano 17, 17031–17040 (2023)

     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

251. J. Fu, L. Zhang, Y. Long, Z. Liu, G. Meng, H. Zhao, X. Su and S. Shi, Anal. Chem. 95, 16089–16097 (2023)

     Multiplexed CRISPR-based nucleic acid detection using a single Cas protein

252. Y. Yang, Q. Lu, Y. Chen, M. DeLuca, G. Arya, Y. Ke and S. Zauscher, Angew. Chem. Int. Ed. 62, e202311727 (2023)

     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, 20, 2308763 (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

260. Y. Liu, B. Li, F. Wang, Q. Li, S. Jia, X. Liu, and M. Li, ACS Appl. Bio Mater. 7, 1311–1316 (2024)

     Quantitative analysis of resistance to deformation of the DNA origami framework supported by struts

261. S. He, H. Deng, P. Li, Q. Tian, Y. Yang, J. Hu, H. Li, T. Zhao, H. Ling, Y. Liu, S. Liu and Q. Guo, J. Nanobiotechnol. 22, 39 (2024)

     Bimodal DNA self-origami material with nucleic acid function enhancement

262. B. Babatunde, J. Cagan, R.E. Taylor, J. Mech. Des. 146, 051708 (2024)

     An improved shape annealing algorithm for the generation of coated deoxyribonucleic acid origami nanostructures

263. A.S.G. Martins, S.D. Reis, E. Benson, M.M. Domingues, J. Cortinhas, J.A. Vidal Silva, S.D. Santos, N.C. Santos, A.P. Pêgo, P.M.D. Moreno, Small 20, 2309140 (2024)

     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

265. T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, Angew. Chem. Int. Ed 63, e202319117 (2024)

     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

267. Z. Zheng, S. Grall, S.H. Kim, A. Chovin, N. Clement and C. Demaille, J. Am. Chem. Soc. 146, 9, 6094–6103 (2024)

     Activationless electron transfer of redox-DNA in electrochemical nanogaps

268. M. Sample, M. Matthies and P. Šulc, ACS Nano 18, 30004–30016 (2024)

     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. 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)

271. C. Shi, D. Yang, X.Ma, L. Pan, Y. Shao, G. Arya, Y. Ke, C. Zhang, F. Wang, X. Zuo, M. Li and P. Wang, Angew. Chem. Int. Ed. 63 e202320179 (2024)

     A programmable DNAzyme for the sensitive detection of nucleic acids (medRxiv)

272. 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)

273. K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, APL Mater. 11, 061129 (2023)

     Towards new liquid crystal phases of DNA mesogens (arXiv)

274. 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)

275. H. Koh, J.Y. Lee, J.G. Lee, submitted

     Forming superhelix of double stranded DNA from local deformation (arXiv)

276. N.P. Agarwal and A. Gopinath, submited

     DNA origami 2.0 (bioRxiv)

277. J.M. Weck and A. Heuer-Jungemann, submitted

     Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)

278. 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)

279. 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, Science 384, 776-781 (2024)

     Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments (arXiv)

280. L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, Nat. Nanotechnol. accepted (2024)

     Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output (bioRxiv)

281. F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted

     nNxB: a new coarse-grained model for RNA and DNA nanotechnology (arXiv)

282. 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)

283. M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, Nat. Commun. 15, 3015 (2024)

     Mechanism of DNA origami folding elucidated by mesoscopic simulations (bioRxiv)

284. S. Cristofaro, L. Querciagrossa, L. Soprani, T.P. Fraccia, T. Bellini, R. Berardi, A. Arcioni, C. Zannoni, L. Muccioli, and S. Orlandi, Biomacromolecules 25, 3920–3929 (2024)

     Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer

285. 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

286. A. Voorspoels, J. Gevers, S. Santermans, N. Akkan, K. Martens, K. Willems, P. Van Dorpe, and A.S. Verhulst, J. Phys. Chem. A 128, 3926–3933 (2024)

     Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations

287. F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, J. Chem. Phys. 160, 205102 (2024)

     ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems (arXiv)

288. Y. Wang, I. Baars, I. Berzina, I. Rocamonde-Lago, B. Shen, Y. Yang, M. Lolaico, J. Waldvogel, I. Smyrlaki, K. Zhu, R.A. Harris and B. Högberg, Nat. Nanotechnol. 19, 1366–137 (2024)

     A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns

289. W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, Nat. Chem. 16, 1408–1417 (2024)

     Encoding signal propagation on topology-programmed DNA origami

290. M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, Nat. Chem. accepted (2024)

     De novo DNA-based catch bonds

291. Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, Nat. Nanotechnol. 19, 1674–1685 (2024)

     Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors

292. D. Svenšek, J. Sočan and M. Praprotnik, Macromol. Rapid Commun. accepted 2400382 (2024)

     Density–nematic coupling in isotropic solution of DNA: Multiscale model

293. M. Mogheiseh and R.H. Ghasemi, J. Chem. Phys. 161, 045101 (2024)

     Design and simulation of a wireframe DNA origami nanoactuator

294. S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, Nano Lett. 24, 11210–11216 (2024)

     Modulating the DNA/lipid interface through multivalent hydrophobicity

295. G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, Nucl. Acids Res. 52, 8661–8674 (2024)

     Weak-cooperative binding of a long single-stranded DNA chain on a surface

296. Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted

     DNA nanostar structures with tunable auxetic properties (bioRxiv)

297. 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)

298. A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, Nat. Commun. 15, 7564 (2024)

     Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement (bioRxiv)

299. S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted

     Bending Unwinds DNA (bioRxiv)

300. X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, Nat. Commun. 15, 7210 (2024)

     A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport (ResearchSquare)

301. L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, Nano Lett. 24, 13481–13486 (2024)

     Driving DNA nanopore membrane insertion through dipolar coupling

302. J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ACM Trans. Evol. Learn. Optim. accepted (2024)

     Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications

303. C. Karfusehr, M. Eder, F.C. Simmel

     Self-assembled cell-scale containers made from DNA origami membranes (bioRxiv)

304. 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)

305. M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, submitted

     Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells (bioRxiv)

306. V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)

     Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA (bioRxiv)

307. R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)

     Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations

308. E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted

     Controlling DNA-RNA strand displacement kinetics with base distribution (bioRxiv)

309. A. Suma and C. Micheletti, submitted

     Unzipping of knotted DNA via nanopore translocation (arXiv)

310. G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.

     Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model (arXiv)

311. S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.

     How we simulate DNA origami (arXiv)

312. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted

     Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)

313. R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)

     A Differentiable Model of Nucleic Acid Dynamics (arXiv)

314. Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted

     Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells (ResearchSquare)

315. K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.

     DNA nanodevice for analysis of force-activated protein extension and interactions (bioRxiv)

316. W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted

     Economical and versatile subunit design principles for self-assembled DNA origami structures (arXiv)

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