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# F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, ''Entropy'' '''24''', 458 (2022)
# F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, ''Entropy'' '''24''', 458 (2022)
#: [https://doi.org/10.3390/e24040458 OxDNA to study species interactions] ([https://arxiv.org/abs/2202.05653 arXiv])
#: [https://doi.org/10.3390/e24040458 OxDNA to study species interactions] ([https://arxiv.org/abs/2202.05653 arXiv])
# Y.A.G. Fosado, submitted
# Y.A.G. Fosado, ''Soft Matter'' '''19''', 4820-4828 (2023)
#: Nanostars planarity modulates the elasticity of DNA hydrogels ([https://arxiv.org/abs/2202.06331 arXiv])
#: [https://doi.org/10.1039/D2SM00221C Nanostars planarity modulates the elasticity of DNA hydrogels] ([https://arxiv.org/abs/2202.06331 arXiv])
# 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)
# 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)
#: [https://doi.org/10.1021/jacs.1c12593 Structure-guided designing pre-organization in bivalent aptamers]
#: [https://doi.org/10.1021/jacs.1c12593 Structure-guided designing pre-organization in bivalent aptamers]
Line 355: Line 355:
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
# E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, ''Sci. Robot.'' '''7''', eabn5459 (2022)
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
#: [https://doi.org/10.1126/scirobotics.abn5459 A DNA molecular printer capable of programmable positioning and patterning in two dimensions]
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, submitted
# 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 ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
#: [https://doi.org/10.1093/nar/gkad118 Weak tension accelerates hybridization and dehybridization of short oligonucleotides] ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
# S. Sensale, P. Sharma and G. Arya, ''Phys. Rev. E'' '''105''', 044136 (2022)
# S. Sensale, P. Sharma and G. Arya, ''Phys. Rev. E'' '''105''', 044136 (2022)
#: [https://doi.org/10.1103/PhysRevE.105.044136 Binding kinetics of harmonically confined random walkers]
#: [https://doi.org/10.1103/PhysRevE.105.044136 Binding kinetics of harmonically confined random walkers]
Line 367: Line 367:
# J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, ''Nat. Protoc.'' '''17''', 1762–1788 (2022)
# J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, ''Nat. Protoc.'' '''17''', 1762–1788 (2022)
#: [https://doi.org/10.1038/s41596-022-00688-5 Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView]
#: [https://doi.org/10.1038/s41596-022-00688-5 Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView]
# C. Zhou, D. Yang, S. Sensale, P. Sharma, D. Wang, L. Yu, G. Arya, Y. Ke and P. Wang, submitted (2022)
# 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 ([https://doi.org/10.21203/rs.3.rs-1706596/v1 Research Square])
#: [https://doi.org/10.1126/sciadv.ade3003 A bistable and reconfigurable molecular system with encodable bonds] ([https://doi.org/10.21203/rs.3.rs-1706596/v1 Research Square])
# R. Li, M. Zheng, A.S. Madhvacharyula, Y. Du, C. Mao and J.H. Choi, Biophys. J. accepted (2022)
# R. Li, M. Zheng, A.S. Madhvacharyula, Y. Du, C. Mao and J.H. Choi, Biophys. J. accepted (2022)
#: [https://doi.org/10.1016/j.bpj.2022.09.036 Mechanical deformation behaviors and structural properties of ligated DNA crystals] ([https://doi.org/10.1101/2022.06.13.495931 bioRxiv])
#: [https://doi.org/10.1016/j.bpj.2022.09.036 Mechanical deformation behaviors and structural properties of ligated DNA crystals] ([https://doi.org/10.1101/2022.06.13.495931 bioRxiv])
Line 375: Line 375:
# F. Fontana, T. Bellini and M. Todisco, ''Macromolecules'' '''55''', 5946–5953 (2022)
# F. Fontana, T. Bellini and M. Todisco, ''Macromolecules'' '''55''', 5946–5953 (2022)
#: [https://doi.org/10.1021/acs.macromol.2c00856 Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities]
#: [https://doi.org/10.1021/acs.macromol.2c00856 Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities]
# J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, submitted (2022)
# 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 ([https://arxiv.org/abs/2207.06954 arXiv])
#: [https://doi.org/10.1021/acsnano.2c09677 Designing the self-assembly of arbitrary shapes using minimal complexity building blocks] ([https://arxiv.org/abs/2207.06954 arXiv])
# Y. Deng, Y. Tan, Y. Zhang, L. Zhang, C. Zhang, Y. Ke and X. Su, ''ACS Appl. Mater. Interfaces'' '''14''', 34470–34479 (2022)
# Y. Deng, Y. Tan, Y. Zhang, L. Zhang, C. Zhang, Y. Ke and X. Su, ''ACS Appl. Mater. Interfaces'' '''14''', 34470–34479 (2022)
#: [https://doi.org/10.1021/acsami.2c09488 Design of uracil-modified DNA nanotubes for targeted drug release via DNA-modifying enzyme reactions]
#: [https://doi.org/10.1021/acsami.2c09488 Design of uracil-modified DNA nanotubes for targeted drug release via DNA-modifying enzyme reactions]
# J. G. Lee, K. S. Kim, J. Y. Lee and D.-N. Kim, ''ACS Nano'' '''16''', 4289–4297 (2022)
# J. G. Lee, K. S. Kim, J. Y. Lee and D.-N. Kim, ''ACS Nano'' '''16''', 4289–4297 (2022)
#: [https://doi.org/10.1021/acsnano.1c10347 Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint]
#: [https://doi.org/10.1021/acsnano.1c10347 Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint]
# M. Micheloni, L. Petrolli, G. Lattanzi and R. Potestio, submitted (2022)
# 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 ([https://doi.org/10.1101/2022.07.03.498607 bioRxiv])
#: [https://doi.org/10.1016/j.bpj.2023.07.008 Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations] ([https://doi.org/10.1101/2022.07.03.498607 bioRxiv])
# 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'' accepted (2022)
# 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'' accepted (2022)
#: [https://doi.org/10.1021/acsnano.2c06035 Algorithmic design of 3D wireframe RNA polyhedra] ([https://doi.org/10.1101/2022.04.27.489653 bioRxiv])
#: [https://doi.org/10.1021/acsnano.2c06035 Algorithmic design of 3D wireframe RNA polyhedra] ([https://doi.org/10.1101/2022.04.27.489653 bioRxiv])
Line 407: Line 407:
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' '''157''', 135101 (2022)
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' '''157''', 135101 (2022)
#: [https://doi.org/10.1063/5.0117047 Interpenetrating gels in binary suspensions of DNA nanostars]
#: [https://doi.org/10.1063/5.0117047 Interpenetrating gels in binary suspensions of DNA nanostars]
# P. E. Beshay, A. Kucinic, N. Wile, P. Halley, L. Des Rosiers, A. Chowdhury, J. L. Hall, C. E. Castro and M. W. Hudoba, submitted
# 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''', accepted (2023)
#: Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories ([https://doi.org/10.1101/2022.09.15.508130 bioRxiv])
#: [https://doi.org/10.35459/tbp.2022.000228 Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories] ([https://doi.org/10.1101/2022.09.15.508130 bioRxiv])
# A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' accepted (2022)
# A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' accepted (2022)
#: [https://doi.org/10.1016/j.bpj.2022.08.046 Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking]
#: [https://doi.org/10.1016/j.bpj.2022.08.046 Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking]


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

Revision as of 03:41, 14 September 2023

  1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
    DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)
  2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Phys. Condens. Matter. 22, 104102 (2010)
    Extracting bulk properties of self-assembling systems from small simulations (arXiv)
  3. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
    Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
  4. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
    Coarse-grained modelling of DNA and DNA self-assembly
  5. F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 136, 215102 (2012)
    The effect of topology on the structure and free energy landscape of DNA kissing complexes (arXiv)
  6. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)
    Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link (arXiv)
  7. C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, J. Phys. Chem. B 116, 1161-11625 (2012)
    DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism (arXiv)
  8. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)
    Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)
  9. T.E. Ouldridge, J. Chem. Phys. 137, 144105 (2012)
    Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble (arXiv)
  10. F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, J. Chem. Phys. 138, 085101 (2013)
    Coarse-grained simulations of DNA overstretching (arXiv)
  11. T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ACS Nano 7, 2479-2490 (2013)
    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker
  12. T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye, A. A. Louis, Nucleic Acids Res. 41, 8886-8895 (2013)
    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)
  13. J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith, Phys. Chem. Chem. Phys 15, 20395-20414 (2013)
    Coarse-graining DNA for simulations of DNA nanotechnology (arXiv)
  14. N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, Nucleic Acids Res. 41, 10641-10658 (2013)
    On the biophysics and kinetics of toehold-mediated DNA strand displacement
  15. P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, Natural Computing 13, 535 (2014)
    Simulating a burnt-bridges DNA motor with a coarse-grained DNA model (arXiv)
  16. L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)
    Accurate phase diagram of tetravalent DNA nanostars (arXiv)
  17. P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014)
    A nucleotide-level coarse-grained model of RNA (arXiv)
  18. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)
    Gels of DNA Nanostars Never Crystallise
  19. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
    Modeling DNA Thermodynamics under Torsional Stress
  20. J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, Nucleic Acids Res. 43, 6181-6190 (2014)
    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization (arXiv)
  21. R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, Nature Comm. 5, 5324 (2014)
    Programmable energy landscapes for kinetic control of DNA strand displacement
  22. M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, J. Phys. Chem. B 118, 14326-14335 (2014)
    The role of loop stacking in the dynamics of DNA hairpin formation (arXiv)
  23. I. Y. Loh, J.Cheng, S. R. Tee, A. Efremov, and Z. Wang, ACS Nano 8, 10293–10304 (2014)
    From bistate molecular switches to self-directed track-walking nanomotors
  24. C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, Sci. Rep., 5, 7655 (2015)
    Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA (arXiv)
  25. L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1-8 (2015)
    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
  26. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)
    Physical model for recognition tunneling
  27. F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)
    Switching Bonds in a DNA Gel: An All-DNA Vitrimer
  28. J. S. Schreck, T. E. Ouldridge, F. Romano, A. A. Louis, J.P.K. Doye, J. Chem. Phys. 142, 165101 (2015)
    Characterizing the bending and flexibility induced by bulges in DNA duplexes (arXiv)
  29. M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ACS Nano 9, 11993 (2015)
    Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors (arXiv)
  30. T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)
    DNA nanotechnology: understanding and optimisation through simulation (arXiv)
  31. P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, Biophys. J. 108, 1238-1247 (2015)
    Modelling toehold-mediated RNA strand displacement (arXiv)
  32. B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, J. Chem. Phys. 142, 234901 (2015)
    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
  33. C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, J. Chem. Phys. 143, 243122 (2015)
    Coarse-grained modelling of supercoiled RNA (arXiv)
  34. Q. Wang, C.G. Myers, and B.M. Pettitt, J. Phys. Chem. B 119, 4937–4943 (2015)
    Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density
  35. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, arXiv (2015)
    Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
  36. R. M. Harrison, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, J. Chem. Theor. Comput. 15 4660-4672 (2019)
    Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model (arXiv) (data)
  37. J. Y. Lee, T. Terakawa, Z. Qi, J. B. Steinfeld, S. Redding, Y. Kwon, W. A. Gaines, W. Zhao, P. Sung, E. C. Greene, Science 349, 977-981 (2015)
    Base triplet stepping by the Rad51/RecA family of recombinases
  38. B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ACS Nano 10, 1724-1737 (2016)
    Direct Simulation of the Self-Assembly of a Small DNA Origami (data)
  39. V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala, Nat. Commun. 7, 10803 (2016)
    Design principles for rapid folding of knotted DNA nanostructures
  40. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
    Characterizing DNA star-tile-based nanostructures using a coarse-grained model
  41. M. Liu, J. Cheng, S.R. Tee, S. Sreelatha, I.Y. Loh, and Z. Wang, ACS Nano, 10, 5882–5890 (2016)
    Biomimetic autonomous enzymatic nanowalker of high fuel efficiency
  42. J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini and F. Sciortino, J. Chem. Phys. 145, 084910 (2016)
    Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars
  43. T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, Nucleic Acids Res. 44, 9121-9130 (2016)
    Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
  44. Q. Wang and B.M. Pettitt, J. Phys. Chem. Lett 7, 1042–1046 (2016)
    Sequence affects the cyclization of DNA minicircles
  45. A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, J. Phys: Condens. Matter 29, 014006 (2017).
    Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal (arXiv) (data)
  46. E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino and L. Rovigatti, ACS Nano 11, 2094-2102 (2017)
    Condensation and demixing in solutions of DNA nanostars and their mixtures
  47. E. Skoruppa, M. Laleman, S. Nomidis, E. Carlon, J. Chem. Phys 146, 214902 (2017)
    DNA elasticity from coarse-grained simulations: the effect of groove asymmetry (arXiv)
  48. A. Suma and C. Micheletti, Proc. Natl. Acad. Sci. USA 114, E2991–E2997 (2017)
    Pore translocation of knotted DNA rings
  49. Z. Shi, C. E. Castro and G. Arya, ACS Nano 11, 4617–4630 (2017)
    Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations
  50. H. Yagyu, J.-Y. Lee, D.-N. Kim, and O. Tabata, J. Phys. Chem. B 121, 5033–5039 (2017)
    Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design
  51. S. Vangaveti, R. J. D'Esposito, J. L. Lippens, D. Fabris and S. V. Ranganathan, Phys. Chem. Chem. Phys. 19, 14937-14946 (2017)
    A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry–mass spectrometry
  52. A. Henning-Knechtel, J. Knechtel and M. Magzoub, Nucleic Acids Res. 45, 12057–12068 (2017)
    DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels
  53. R. Sharma, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ACS Nano 11, 12426–12435 (2017)
    Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
  54. Q.Y. Yeo, I.Y. Loh, S.R. Tee, Y.H. Chiang, J. Cheng, M.H. Liu and Z.S. Wang, Nanoscale 9, 12142-12149 (2017)
    A DNA bipedal nanowalker with a piston-like expulsion stroke
  55. Q. Wang, R.N. Irobalieva, W. Chiu, M.F. Schmid, J.M. Fogg, L. Zechiedrich, B.M. Pettitt, Nucleic Acids Res. 45 7633-7642 (2017)
    Influence of DNA sequence on the structure of minicircles under torsional stress
  56. B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucleic Acids Res. 46, 538-545 (2018)
    Rolling circle amplification shows a sinusoidal template length-dependent amplification bias (data)
  57. R.V. Reshetnikov, A.V. Stolyarova, A.O. Zalevsky, D.Y. Panteleev, G.V. Pavlova, D.V. Klinov, A.V. Golovin, A.D. Protopopova, Nucleic Acids Res. 46, 1102–1112 (2018)
    A coarse-grained model for DNA origami
  58. D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, Nucleic Acids Res. 46, 1553-1561 (2018)
    DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size (data)
  59. P. Fonseca, F. Romano, J. S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, J. Chem. Phys 148, 134910 (2018)
    Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly (arXiv)
  60. T.D. Craggs, M. Sustarsic, A. Plochowietz, M. Mosayebi, H. Kaju, A. Cuthbert, J. Hohlbein, L. Domicevica, P.C. Biggin, J.P.K. Doye and A.N. Kapanidis, Nucleic Acids Res. 47, 10788–10800 (2019)
    Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase (bioRXiv)
  61. S.R. Tee and Z. Wang, ACS Omega, 3, 292-301 (2018)
    How well can DNA rupture DNA? Shearing and unzipping forces inside DNA nanostructures
  62. E. Skoruppa, S.K. Nomidis, J.F. Marko and E. Carlon, Phys. Rev. Lett. 121, 088101 (2018)
    Bend-induced twist waves and the structure of nucleosomal DNA (arXiv)
  63. M.M.C. Tortora and J.P.K. Doye, Mol. Phys. 116, 2773-2791 (2018)
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    Nanostars planarity modulates the elasticity of DNA hydrogels (arXiv)
  174. X. Hu, L. Tang, M. Zheng, J. Liu, Z. Zhang, Z. Li, Q. Yang, S. Xiang, L. Fang, Q. Ren, X. Liu, C.Z. Huang, C. Mao and H. Zuo, J. Am. Chem. Soc. 144, 4507–4514 (2022)
    Structure-guided designing pre-organization in bivalent aptamers
  175. L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, Sci. Adv. 8, eabm9530 (2022)
    A localized DNA finite-state machine with temporal resolution
  176. Y. Xin, P. Piskunen, A. Suma, C. Li, H. Ijäs, S. Ojasalo, I. Seitz, M.A. Kostiainen, G. Grundmeier, V. Linko and A. Keller, Small 18, 2107393 (2022)
    Environment-dependent stability and mechanical properties of DNA origami six-helix bundles with different crossover spacings
  177. R.L. Bender, H. Ogasawara, A.V. Kellner, A. Velusamy and K. Salaita, submitted
    Unbreakable DNA tension probes show that cell adhesion receptors detect the molecular force-extension curve of their ligands (bioRxiv)
  178. E. Benson, R. Carrascosa Marzo, J. Bath and A.J. Turberfield, Sci. Robot. 7, eabn5459 (2022)
    A DNA molecular printer capable of programmable positioning and patterning in two dimensions
  179. D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, Nucleic Acids Res. 51, 3030–3040 (2023)
    Weak tension accelerates hybridization and dehybridization of short oligonucleotides (bioRxiv)
  180. S. Sensale, P. Sharma and G. Arya, Phys. Rev. E 105, 044136 (2022)
    Binding kinetics of harmonically confined random walkers
  181. S. Dey, A. Dorey, L. Abraham, Y. Xing, I. Zhang, F. Zhang, S. Howorka and H. Yan, Nat. Commun. 13, 2271 (2022)
    A reversibly gated protein-transporting membrane channel made of DNA
  182. D. Luo, A. Kouyoumdjian, O. Strnad, H. Miao, I. Barišić and I. Viola, submitted (2022)
    SynopSet: Multiscale visual abstraction set for explanatory analysis of DNA nanotechnology simulations (arXiv)
  183. L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, Nanoscale, accepted (2022)
    A simple solution to the problem of self-assembling cubic diamond crystals (arXIv)
  184. J. Bohlin, M. Matthies, E. Poppleton, J. Procyk, A. Mallya, H. Yan and P. Šulc, Nat. Protoc. 17, 1762–1788 (2022)
    Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView
  185. 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)
  186. R. Li, M. Zheng, A.S. Madhvacharyula, Y. Du, C. Mao and J.H. Choi, Biophys. J. accepted (2022)
    Mechanical deformation behaviors and structural properties of ligated DNA crystals (bioRxiv)
  187. 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
  188. F. Fontana, T. Bellini and M. Todisco, Macromolecules 55, 5946–5953 (2022)
    Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities
  189. 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)
  190. 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
  191. 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
  192. 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)
  193. 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 accepted (2022)
    Algorithmic design of 3D wireframe RNA polyhedra (bioRxiv)
  194. 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. 144, accepted (2022)
    Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus
  195. 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
  196. 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
  197. 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
  198. 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
  199. 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
  200. 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
  201. S. Bianco, T. Hu, O. Henrich and S. W.Magennis, Biophysical Reports 2, 100070 (2022)
    Heterogeneous migration routes of DNA triplet repeat slip-outs
  202. 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
  203. G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, Nano Lett. accepted (2022)
    Far-field electrostatic signatures of macromolecular 3D conformation
  204. E. Lattuada, T. Pietrangeli and F. Sciortino, J. Chem. Phys. 157, 135101 (2022)
    Interpenetrating gels in binary suspensions of DNA nanostars
  205. 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', accepted (2023)
    Translating DNA origami nanotechnology to middle school, high school, and undergraduate laboratories (bioRxiv)
  206. A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, Biophys. J. accepted (2022)
    Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking

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

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