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# L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024) | # L. Kilwing, P. Lill, B. Nathwani, R. Guerra, E. Benson, T. Liedl and W. M. Shih, ''ACS Nano'' '''18''', 885–893 (2024) | ||
#: [https://doi.org/10.1021/acsnano.3c09522 Multilayer DNA origami with terminal interfaces that are flat and wide-area] | #: [https://doi.org/10.1021/acsnano.3c09522 Multilayer DNA origami with terminal interfaces that are flat and wide-area] | ||
# N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, ''Small'', | # N. Adžić, C. Jochum, C. N. Likos, E. Stiakakis, ''Small'', '''20''', 2308763 (2024) | ||
#: [https://doi.org/10.1002/smll.202308763 Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility] | #: [https://doi.org/10.1002/smll.202308763 Engineering ultrasoft interactions in stiff all-DNA dendrimers by site-specific control of scaffold flexibility] | ||
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024) | # A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024) | ||
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# S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, ''Nanoscale'' '''16''', 4872-4879 (2024) | # S Dey, R. Rivas-Barbosa, F. Sciortino, E. Zaccarelli and P. Zijlstra, ''Nanoscale'' '''16''', 4872-4879 (2024) | ||
#: [https://doi.org/10.1039/D3NR06140J Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective] | #: [https://doi.org/10.1039/D3NR06140J Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective] | ||
# T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, ''Angew. Chem. Int. Ed'' | # T. Chen, S. Mao, J. Ma, X. Tang, R. Zhu, D. Mao, X. Zhu, Q. Pan, ''Angew. Chem. Int. Ed'' '''63''', e202319117 (2024) | ||
#: [https://doi.org/10.1002/anie.202319117 Proximity-enhanced functional imaging analysis of engineered tumors] | #: [https://doi.org/10.1002/anie.202319117 Proximity-enhanced functional imaging analysis of engineered tumors] | ||
# 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) | # 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) | ||
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# M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023) | # M. Sample, M. Matthies and P. Šulc, ''2023 Winter Simulation Conference (WSC)'', San Antonio, TX, USA, pp. 91-105 (2023) | ||
#: [https://doi.org/10.1109/WSC60868.2023.10407580 Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial] ([https://doi.org/10.48550/arXiv.2308.01455 arXiv]) | #: [https://doi.org/10.1109/WSC60868.2023.10407580 Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial] ([https://doi.org/10.48550/arXiv.2308.01455 arXiv]) | ||
# V. Caroprese, C. Tekin, V. Cencen, M. Mosayebi, T.B. Liverpool, D.N. Woolfson, G. Fantner, M.M.C. Bastings, submitted | # 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 ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv]) | #: Structural flexibility dominates over binding strength for supramolecular crystallinity ([https://doi.org/10.1101/2023.09.04.556250 bioRxiv]) | ||
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# 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 | # 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 ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv]) | #: High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv]) | ||
# 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, | # 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 ([https://doi.org/10.48550/arXiv.2310.10995 arXiv]) | #: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv]) | ||
# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, submitted | # L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, submitted | ||
#: Engineering modular and tunable single Molecule sensors by decoupling sensing from signal output ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv]) | #: Engineering modular and tunable single Molecule sensors by decoupling sensing from signal output ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv]) | ||
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#: nNxB: a new coarse-grained model for RNA and DNA nanotechnology ([https://doi.org/10.48550/arXiv.2311.03317 arXiv]) | #: 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) | # 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 ([https://doi.org/10.48550/arXiv.2311.07709 arXiv]) | #: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv]) | ||
# M. DeLuca, D. Duke, T. Ye, M. Poirier, Y. Ke, C. Castro and G. Arya, ''Nat. Commun.'' '''15''', 3015 (2024) | |||
#: [https://doi.org/10.1038/s41467-024-46998-y Mechanism of DNA origami folding elucidated by mesoscopic simulations] ([https://doi.org/10.1101/2023.06.20.545758 bioRxiv]) | |||
# 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) | |||
#: [https://doi.org/10.1021/acs.biomac.3c01435 Simulating the lyotropic phase behavior of a partially self-complementary DNA tetramer] | |||
# A. Velusamy, R. Sharma, S.A. Rashid, H. Ogasawara and K. Salaita, ''Nat. Commun.'' '''15''', 704 (2024) | |||
#: [https://doi.org/10.1038/s41467-023-44061-w DNA mechanocapsules for programmable piconewton responsive drug delivery] | |||
# 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) | |||
#: [https://doi.org/10.1021/acs.jpca.4c01772 Design principles of DNA-barcodes for nanopore-FET readout, based on molecular dynamics and TCAD simulations] | |||
# F. Tosti Guerra, E. Poppletoni, P. Šulc and L. Rovigatti, ''J. Chem. Phys.'' '''160''', 205102 (2024) | |||
#: [https://doi.org/10.1063/5.0202829 ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems] ([https://doi.org/10.48550/arXiv.2311.03317 arXiv]) | |||
# 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.'' accepted (2024) | |||
#: [https://doi.org/10.1038/s41565-024-01676-4 A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns] | |||
# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' accepted (2024) | |||
#: [https://doi.org/10.1038/s41557-024-01565-2 Encoding signal propagation on topology-programmed DNA origami] | |||
# M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, ''Nat. Chem.'' accepted (2024) | |||
#: [https://doi.org/10.1038/s41557-024-01571-4 De novo DNA-based catch bonds] | |||
# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted | # 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]) | #: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109 bioRxiv]) | ||
Line 579: | Line 593: | ||
# 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 | # 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]) | #: 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, submitted | |||
#: Context-dependent structure formation of RNA hairpin motifs ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv]) | |||
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 13:00, 13 July 2024
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We are also maintaining a list of all published papers using oxDNA at publons.