Publications: Difference between revisions

Latest revision as of 13:12, 23 November 2024

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)
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)
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)
T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
Coarse-grained modelling of DNA and DNA self-assembly
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)
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)
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)
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)
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)
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)
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
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)
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)
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
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)
L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)
Accurate phase diagram of tetravalent DNA nanostars (arXiv)
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)
L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)
Gels of DNA Nanostars Never Crystallise
Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)
Modeling DNA Thermodynamics under Torsional Stress
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)
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
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)
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
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)
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)
P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)
Physical model for recognition tunneling
F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)
Switching Bonds in a DNA Gel: An All-DNA Vitrimer
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)
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)
T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)
DNA nanotechnology: understanding and optimisation through simulation (arXiv)
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)
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)
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)
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
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"
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)
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
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)
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
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
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
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
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
Q. Wang and B.M. Pettitt, J. Phys. Chem. Lett 7, 1042–1046 (2016)
Sequence affects the cyclization of DNA minicircles
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)
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
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)
A. Suma and C. Micheletti, Proc. Natl. Acad. Sci. USA 114, E2991–E2997 (2017)
Pore translocation of knotted DNA rings
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
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
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
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
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
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
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
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
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)
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
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)
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)
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)
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
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)
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)
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)
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
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
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
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)
E. Spruijt, S.E. Tusk and H. Bayley, Nat. Nanotechnol. 13, 739-745 (2018)
DNA scaffolds support stable and uniform peptide nanopores
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)
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
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)
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
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
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)
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)
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)
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
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)
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
Y. Choi, H. Choi, A.C. Lee, S. Kwon, J. Vis. Exp., e58364 (2018)
Design and Synthesis of a Reconfigurable DNA Accordion Rack
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)
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
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
M. Coraglio, E. Skoruppa and E. Carlon, J. Chem. Phys. 150, 135101 (2019)
Overtwisting induces polygonal shapes in bent DNA (arXiv)
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
Y.A.G. Fosado, Z. Xing, E. Eiser, M. Hudek, O. Henrich, submitted
A Numerical Study of Three-Armed DNA Hydrogel Structures (arXiv)
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
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)
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)
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
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
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)
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
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)
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
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
Z. Shi and G. Arya, Nucleic Acids Research 48, 548-560 (2020)
Free energy landscape of salt-actuated reconfigurable DNA nanodevices
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)
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)
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
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)
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)
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
A. Bader and S.L. Cockroft, Chem. Commun. 56, 5135-5138 (2020)
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 2639, 93-112 (2023).
The oxDNA coarse-grained model as a tool to simulate DNA origami (arXiv) (data)
J. Lee, J.-H. Huh, S. Lee, Langmuir 36, 5118–5125 (2020)
DNA Base Pair-Stacking Crystallization of Gold Colloids
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)
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)
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)
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
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)
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)
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)
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)
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
Y.A.G. Fosado, F. Landuzzi and T. Sakaue, Soft Matter 17, 1530-1537 (2021)
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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
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
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
M.C. Engel, J.A. Smith and M.P. Brenner, Phys. Rev. X 13, 041032 (2023)
Optimal control of nonequilibrium systems through automatic differentiation
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
Y.-P. Qiao and C.-L. Ren, Langmuir 40, 109–117 (2024)
Correlated hybrid DNA structures explored by the oxDNA Model
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
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
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
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
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
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
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
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
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
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
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
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)
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)
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)
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)
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)
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)
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)
H. Koh, J.Y. Lee, J.G. Lee, submitted
Forming superhelix of double stranded DNA from local deformation (arXiv)
N.P. Agarwal and A. Gopinath, submited
DNA origami 2.0 (bioRxiv)
J.M. Weck and A. Heuer-Jungemann, submitted
Fully addressable, designer superstructures assembled from a single modular DNA origami (bioRxiv)
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)
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)
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)
F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
nNxB: a new coarse-grained model for RNA and DNA nanotechnology (arXiv)
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)
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)
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
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
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
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)
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
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
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
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
D. Svenšek, J. Sočan and M. Praprotnik, Macromol. Rapid Commun. accepted 2400382 (2024)
Density–nematic coupling in isotropic solution of DNA: Multiscale model
M. Mogheiseh and R.H. Ghasemi, J. Chem. Phys. 161, 045101 (2024)
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)
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)
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 (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 (bioRxiv)
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)
S. Chandrasekhar, T.P. Swope, F. Fadaei, D.R. Hollis, R. Bricker, D. Houser, J. Portman, T.L. Schmidt, submitted
Bending Unwinds DNA (bioRxiv)
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)
L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, Nano Lett. 24, 13481–13486 (2024)
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)
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 (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 (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 (bioRxiv)
V. Bukina and A. Božič, Biophys. J. 123, 3397-3407 (2024)
Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA (bioRxiv)
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
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)
A. Suma and C. Micheletti, submitted
Unzipping of knotted DNA via nanopore translocation (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 (arXiv)
S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
How we simulate DNA origami (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 (ResearchSquare)
R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
A Differentiable Model of Nucleic Acid Dynamics (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 (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 (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 (arXiv)

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

@@ Line 629: / Line 629: @@
 # 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, submitt
+# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
-ed
 #: 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].

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