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# 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)
# 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)
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
#:[https://doi.org/10.1039/C7NR03809G A DNA bipedal nanowalker with a piston-like expulsion stroke]
# G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips and G. Seelig, ''Nat. Nanotechnol.'' '''12''', 920–927 (2017)
#: [https://doi.org/10.1038/nnano.2017.127 A spatially localized architecture for fast and modular DNA computing]
# 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)
# 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)
#: [https://doi.org/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]  
#: [https://doi.org/10.1093/nar/gkx516 Influence of DNA sequence on the structure of minicircles under torsional stress]  
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# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
# E. Locatelli and L. Rovigatti, ''Polymers'' '''10''', 447 (2018)
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
#: [https://doi.org/10.3390/polym10040447 An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids] ([https://www.preprints.org/manuscript/201803.0203/v1 preprints])
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nature Nanotechnology'' '''13''', 739-745 (2018)
# E. Spruijt, S.E. Tusk and H. Bayley, ''Nat. Nanotechnol.'' '''13''', 739-745 (2018)
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
#: [http://dx.doi.org/10.1038/s41565-018-0139-6 DNA scaffolds support stable and uniform peptide nanopores]
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
# L. Coronel, A. Suma and C. Micheletti, ''Nucleic Acids Res.'' '''46''',7522–7532 (2018)
Line 209: Line 211:
# A. Bader and S.L. Cockroft, ''Chem. Commun.'' '''56''', 5135-5138 (2020)
# A. Bader and S.L. Cockroft, ''Chem. Commun.'' '''56''', 5135-5138 (2020)
#: [https://doi.org/10.1039/D0CC00882F Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices]
#: [https://doi.org/10.1039/D0CC00882F Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices]
# J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton and B.E.K. Snodin, ''Methods in Molecular Biology'', submitted.  
# 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 ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
#: [https://doi.org/10.1007/978-1-0716-3028-0_6 The oxDNA coarse-grained model as a tool to simulate DNA origami] ([http://arxiv.org/abs/2004.05052 arXiv]) ([http://dx.doi.org/10.5287/bodleian:vgqKg0rYo data])
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''', 5118–5125 (2020)
# J. Lee, J.-H. Huh, S. Lee, ''Langmuir'' '''36''', 5118–5125 (2020)
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
#: [https://doi.org/10.1021/acs.langmuir.0c00239 DNA Base Pair-Stacking Crystallization of Gold Colloids]
Line 295: Line 297:
# Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, ''J. Am. Chem. Soc.'' '''143''', 13292–13298 (2021)
# Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, and M. Famulok, ''J. Am. Chem. Soc.'' '''143''', 13292–13298 (2021)
#: [https://doi.org/10.1021/jacs.1c06226 A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy]
#: [https://doi.org/10.1021/jacs.1c06226 A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy]
# T. Lee, S. Do, J.G. Lee, D.-N. Kim and Y. Shin, ''Nanoscale'' '''13''', 17638-17647 (2021)
#: [https://doi.org/10.1039/D1NR03495B The flexibility-based modulation of DNA nanostar phase separation]
# 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)
# 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)
#: [https://doi.org/10.1093/nar/gkab656 A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules]
#: [https://doi.org/10.1093/nar/gkab656 A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules]
Line 335: Line 339:
# D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, ''Molecules'' '''27''', 63 (2022)
# D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, ''Molecules'' '''27''', 63 (2022)
#: [https://doi.org/10.3390/molecules27010063 Unified Nanotechnology Format: One Way to Store Them All]
#: [https://doi.org/10.3390/molecules27010063 Unified Nanotechnology Format: One Way to Store Them All]
# M. Centola,  E. Poppleton,  M. Centola,  J. Valero,  P. Šulc and  M. Famulok, submitted.
# 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 ([https://doi.org/10.1101/2021.12.22.473833 biorXiv])
#: [https://doi.org/10.1038/s41565-023-01516-x A rhythmically pulsing leaf-spring nanoengine that drives a passive follower] ([https://doi.org/10.1101/2021.12.22.473833 biorXiv])
# C.K. Wong and J.P.K. Doye, ''Appl. Sci.'' '''12''', 5875 (2022)
# C.K. Wong and J.P.K. Doye, ''Appl. Sci.'' '''12''', 5875 (2022)
#: [https://doi.org/10.3390/app12125875 The free-energy landscape of a mechanically bistable DNA origami] ([http://arxiv.org/abs/2201.08920 arXiv])
#: [https://doi.org/10.3390/app12125875 The free-energy landscape of a mechanically bistable DNA origami] ([http://arxiv.org/abs/2201.08920 arXiv])
Line 343: Line 347:
# 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 359:
# 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
# A. Dutta, K. Tapio, A. Suma, A. Mostafa, Y. Kanehira, V. Carnevale, G. Bussi and I. Bald, ''Nanoscale'' '''14''', 16467-16478 (2022)
#: Weak tension accelerates hybridization and dehybridization of short oligonucleotides ([https://doi.org/10.1101/2022.04.19.488836 bioRxiv])
#: [https://doi.org/10.1039/D2NR03664A Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering]
# D.J. Hart, J. Jeong, J.C. Gumbart and H.D. Kim, ''Nucleic Acids Res.'' '''51''', 3030–3040 (2023)
#: [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 363: Line 369:
# D. Luo, A. Kouyoumdjian, O. Strnad, H. Miao, I. Barišić and I. Viola, submitted (2022)
# 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 ([https://arxiv.org/abs/2205.01628 arXiv])
#: SynopSet: Multiscale visual abstraction set for explanatory analysis of DNA nanotechnology simulations ([https://arxiv.org/abs/2205.01628 arXiv])
# L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, ''Nanoscale'', accepted (2022)
# L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc and P. Sulc, ''Nanoscale'' '''14''', 14268-14275 (2022)
#: [https://doi.org/10.1039/D2NR03533B A simple solution to the problem of self-assembling cubic diamond crystals] ([https://arxiv.org/abs/2205.10680 arXIv])
#: [https://doi.org/10.1039/D2NR03533B A simple solution to the problem of self-assembling cubic diamond crystals] ([https://arxiv.org/abs/2205.10680 arXIv])
# 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, submitted (2022)
# 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 ([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])
# C. Xie, Y. Hu, Z. Chen, K. Chen and L. Pan, ''Nanotechnology'' '''33''', 405603 (2022)
# C. Xie, Y. Hu, Z. Chen, K. Chen and L. Pan, ''Nanotechnology'' '''33''', 405603 (2022)
#: [https://doi.org/10.1088/1361-6528/ac7d62 Tuning curved DNA origami structures through mechanical design and chemical adducts]
#: [https://doi.org/10.1088/1361-6528/ac7d62 Tuning curved DNA origami structures through mechanical design and chemical adducts]
# 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)
# 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)
#: Designing the self-assembly of arbitrary shapes using minimal complexity building blocks ([https://arxiv.org/abs/2207.06954 arXiv])
#: [https://doi.org/10.1016/j.aca.2022.339568 Specific and robust hybridization based on double-stranded nucleic acids with single-base resolution]
# J. Bohlin, A.J. Turberfield, A.A. Louis and P. Šulc, ''ACS Nano'' '''17''', 5387–5398 (2023)
#: [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, submitted (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'' '''16''', 16608–16616 (2022)
#: 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])
# 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)
# D. Fu, R.P. Narayanan, A. Prasad, F. Zhang, D. Williams, J.S. Schreck, H. Yan and J. Reif, ''Sci. Adv.'' '''8''', ade4455 (2022)
#: [https://doi.org/10.1126/sciadv.ade4455 Automated design of 3D DNA origami with non-rasterized 2D curvature]
# 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)
#: [https://doi.org/10.1021/jacs.2c04835 Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus]
#: [https://doi.org/10.1021/jacs.2c04835 Net-shaped DNA nanostructures designed for rapid/sensitive detection and potential inhibition of the SARS-CoV-2 virus]
# 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. 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)
Line 393: Line 403:
# E.E. Kurisinkal, V. Caroprese, M.M. Koga, D. Morzy and M.M.C. Bastings, ''Molecules'' '''27''' 4968 (2022)
# E.E. Kurisinkal, V. Caroprese, M.M. Koga, D. Morzy and M.M.C. Bastings, ''Molecules'' '''27''' 4968 (2022)
#: [https://doi.org/10.3390/molecules27154968 Selective integrin α5β1 targeting through spatially constrained multivalent DNA-based nanoparticles]
#: [https://doi.org/10.3390/molecules27154968 Selective integrin α5β1 targeting through spatially constrained multivalent DNA-based nanoparticles]
# 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'' accepted (2022)
# 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)
#: [https://doi.org/10.1021/acsnano.2c04013 Coarse-grained simulations for the characterization and optimization of hybrid protein–DNA nanostructures]
#: [https://doi.org/10.1021/acsnano.2c04013 Coarse-grained simulations for the characterization and optimization of hybrid protein–DNA nanostructures]
# 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)
# 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)
Line 403: Line 413:
# Y. Li, C. Maffeo, H. Joshi, A. Aksimentiev, B. Ménard and R. Schulman, ''Sci. Adv.'' '''8''', eabq4834 (2022)
# Y. Li, C. Maffeo, H. Joshi, A. Aksimentiev, B. Ménard and R. Schulman, ''Sci. Adv.'' '''8''', eabq4834 (2022)
#:[https://doi.org/10.1126/sciadv.abq4834 Leakless end-to-end transport of small molecules through micron-length DNA nanochannels]
#:[https://doi.org/10.1126/sciadv.abq4834 Leakless end-to-end transport of small molecules through micron-length DNA nanochannels]
# G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, ''Nano Lett.'' accepted (2022)
# G. Kloes, T.J.D. Bennett, A. Chapet-Batlle, A. Behjatian, A.J. Turberfield and M. Krishnan, ''Nano Lett.'' '''22''', 7834–7840 (2022)
#: [https://doi.org/10.1021/acs.nanolett.2c02485 Far-field electrostatic signatures of macromolecular 3D conformation]
#: [https://doi.org/10.1021/acs.nanolett.2c02485 Far-field electrostatic signatures of macromolecular 3D conformation]
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' accepted (2022)
# 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)
#: [https://doi.org/10.1002/anie.202117168 Directing multivalent aptamer-receptor binding on the cell surface with programmable atom-like nanoparticles]
# 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)
#: [https://doi.org/10.1021/jacs.2c03258 Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions]
# E. Lattuada, T. Pietrangeli and F. Sciortino, ''J. Chem. Phys.'' '''157''', 135101 (2022)
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# A. Büchl, E. Kopperger, M. Vogt, M. Langecker, F.C.Simmel and J. List, ''Biophys. J.'' '''121''', 4849-4859 (2022)
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# 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)
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# H.L. Too and Z. Wang, ''Nanoscale'' '''15''', 11915-11926 (2023)
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# J. Lee and S. Lee, ''Anal. Chem.'' '''95''', 1856–1866 (2023) 
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#: Bimodal DNA self-origami material with nucleic acid function enhancement
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# M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023)
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# K. Gallagher, J. Yu, D.A. King, R. Liu, E. Eiser, ''APL Mater.'' '''11''', 061129 (2023)
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# 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 ([https://doi.org/10.1101/2023.08.29.555281 bioRxiv])
# H. Koh, J.Y. Lee, J.G. Lee, submitted
#: Forming superhelix of double stranded DNA from local deformation ([https://doi.org/10.48550/arXiv.2307.04597 arXiv])
# N.P. Agarwal and A. Gopinath, submited
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# 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)
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# 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)
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# F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
#: nNxB: a new coarse-grained model for RNA and DNA nanotechnology ([https://doi.org/10.48550/arXiv.2311.03317 arXiv])
# E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys.'' '''160''', 115101 (2024)
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# M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, ''Nat. Commun.'' '''15''', 3015 (2024)
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# 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)
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# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024)
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# 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)
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# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''',  1408–1417 (2024)
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# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' '''19''', 1674–1685 (2024)
#: [https://doi.org/10.1038/s41565-024-01723-0 Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors]
# D. Svenšek, J. Sočan and M. Praprotnik, ''Macromol. Rapid Commun.'' accepted 2400382 (2024)
#: [https://doi.org/10.1002/marc.202400382 Density–nematic coupling in isotropic solution of DNA: Multiscale model]
# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024)
#: [https://doi.org/10.1063/5.0214313 Design and simulation of a wireframe DNA origami nanoactuator]
# S.H. Wong, S.N. Kopf, V. Caroprese, Y. Zosso, D. Morzy, M.M.C. Bastings, ''Nano Lett.'' '''24''', 11210–11216 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02564 Modulating the DNA/lipid interface through multivalent hydrophobicity]
# 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)
#: [https://doi.org/10.1093/nar/gkae576 Weak-cooperative binding of a long single-stranded DNA chain on a surface]
# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109  bioRxiv])
# 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 ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])
# A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, ''Nat. Commun.'' '''15''', 7564 (2024)
#: [https://doi.org/10.1038/s41467-024-51813-9 Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement] ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv])
# S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
#: Bending Unwinds DNA ([https://doi.org/10.1101/2024.02.14.579968 bioRxiv])
# X. Liu, F. Liu, H. Chhabra, C. Maffeo, Q. Huang, A. Aksimentiev, T. Arai, ''Nat. Commun.'' '''15''', 7210 (2024)
#: [https://doi.org/10.1038/s41467-024-51630-0 A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport] ([https://doi.org/10.21203/rs.3.rs-3878148/v1  ResearchSquare])
# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024)
#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling]
# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' accepted (2024)
#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications]
# C. Karfusehr, M. Eder, F.C. Simmel
#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])
# 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 ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv])
# 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 ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv])
# V. Bukina and A. Božič,  ''Biophys. J.'' '''123''', 3397-3407 (2024)
#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
# R. Walker-Gibbons, X. Zhu, A. Behjatian, T.J.D. Bennett and M. Krishnan, Sci. Rep. 14, 20582 (2024)
#: [https://doi.org/10.1038/s41598-024-70641-x Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations]
# 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 ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv])
# A. Suma and C. Micheletti, submitted
#: Unzipping of knotted DNA via nanopore translocation ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
# 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 ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
# 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 ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])
# 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 ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
# 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 ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv])
# 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 ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])


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].

Latest revision as of 13:12, 23 November 2024

  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)
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    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.

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