Publications: Difference between revisions

Revision as of 12:01, 29 March 2022

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
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, Nature Nanotechnology 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, submitted.
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)
Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending (arXiv)
F. Spinozzi, M.G. Ortore, G. Nava, F. Bomboi, F. Carducci, H. Amenitsch, T. Bellini, F. Sciortino, and P. Mariani, Langmuir 36, 10387–10396 (2020)
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J. Huang A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar and A. Keller, Small Str. 1, 2000038 (2020)
Arranging small molecules with sub‐nanometer precision on DNA origami substrates for the single‐molecule investigation of protein‐ligand interactions
G. Yao, F. Zhang, F. Wang, T. Peng, H. Liu, E. Poppleton, P. Šulc, S. Jiang, L. Liu, C. Gong, X. Jing, X. Liu, L. Wang, Y. Liu, C. Fan and H. Yan, Nat. Chem. 12, 1067–1075 (2020)
Meta-DNA structures
J.F. Berengut, C.K. Wong, J.C. Berengut, J.P.K. Doye, T.E. Ouldridge and L.K. Lee, ACS Nano 14, 17428–17441 (2020)
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J. Procyk, E. Poppleton and P. Šulc, Soft Matter 17, 3586-3593 (2021).
Coarse-grained nucleic acid-protein model for hybrid nanotechnology (arXiv)
Z. Sierzega, J. Wereszczynski and C. Prior, Sci. Rep. 11, 1527 (2021)
WASP: A software package for correctly characterizing the topological development of ribbon structures (bioRXiv)
E. Skoruppa, A. Voorspoels, J. Vreede and E. Carlon, Phys. Rev. E 103, 042408 (2021)
Length scale dependent elasticity in DNA from coarse-grained and all-atom models (arXiv)
C. Bores, M. Woodson, M.C. Morais, and B. Montgomery Pettitt, J. Phys. Chem. B 124, 10337–10344 (2020)
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E. Lattuada, D. Caprara, V. Lamberti, F. Sciortino, Nanoscale 12, 23003-23012 (2020)
Hyperbranched DNA clusters (arXiv)
B.J.H.M. Rosier, A.J. Markvoort, B. Gumí Audenis, J.A.L. Roodhuizen, A. den Hamer, L. Brunsveld and T.F.A. de Greef, Nat. Catal. 3, 295–306 (2020)
Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome
R. Li, H. Chen and J.H. Choi, Angew. Chem. Int. Ed. 60, 7165-7173 (2021)
Auxetic Two‐Dimensional Nanostructures from DNA (bioRXiv)
D. Wang, L. Yu, C.-M. Huang, G. Arya, S. Chang, and Y. Ke, J. Am. Chem. Soc. 143, 2256–2263 (2021)
Programmable transformations of DNA origami made of small modular dynamic units
R. Li, H. Chen, H. Lee, J. H. Choi, Appl. Sci. 11, 2357 (2021)
Elucidating the mechanical energy for cyclization of a DNA origami tile (bioRxiv)
G. Park, M. K. Cho, and Y. Jung, J. Chem. Theory Comput., 17 1308-1317 (2021)
Sequence-dependent kink formation in short DNA loops: Theory and molecular dynamics simulations
S. Jonchhe, S. Pandey, D. Karna, P. Pokhrel, Y. Cui, S. Mishra, H. Sugiyama, M. Endo and H. Mao, J. Am. Chem. Soc 142, 10042–10049 (2020)
Duplex DNA Is Weakened in Nanoconfinement
R. Li, H. Chen and J. H. Choi, Small 17, 2007069 (2021)
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S. Naskar, P. K. Maiti, J. Mater. Chem. B 9, 5102-5113
Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA (arXiv)
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Generating DNA origami nanostructures through shape annealing
N.M. Gravina, J.C. Gumbart and H.D. Kim, J. Phys. Chem. B 125, 4016–4024 (2021)
Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding
A. Sengar, T.E. Ouldridge, O. Henrich, L. Rovigatti and P. Šulc, Front. Mol. Biosci. 8, 693710 (2021)
A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results (arXiv) (data)
E. Poppleton, R. Romero, A. Mallya, L. Rovigatti and P. Šulc, Nucl. Acids Res. 49 W491–W498 (2021)
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Y. Yamashita, K. Watanabe, S. Murata and I. Kawamata, Chem-Bio Informatics Journal 21, 28-38 (2021)
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Strategies for Constructing and Operating DNA Origami Linear Actuators
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DNA framework-engineered long-range electrostatic interactions for DNA hybridization reactions
Y. Wang, I. Baars, F. Fördös and B. Högberg, ACS Nano 15 9614–9626 (2021)
Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides
Y. Wang, E. Benson, F. Fördős, M. Lolaico, I. Baars, T. Fang, A.I. Teixeira, B. Högberg, Adv. Mater. 33, 2008457 (2021)
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Quantify the combined effects of temperature and force on the stability of DNA hairpin
J. P. Mahalik and M. Muthukumar, submitted
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A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy
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Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
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Characterizing the free-energy landscapes of DNA origamis (arXiv)
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The interplay of supercoiling and thymine dimers in DNA (bioRxiv)
W.T. Kaufhold, W. Pfeifer, C.E. Castro and L. Di Michele, submitted.
Probing the mechanical properties of DNA nanostructures with metadynamics (arXiv)
H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, J. Am. Chem. Soc. 43, 19466–19473 (2021).
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Detection of short DNA sequences with DNA nanopores (arXiv)
Y. Pan, R. Weng, L. Zhang, J. Qiu, X. Wang, G. Liao, Z. Qin, R. Liu, X. Dai, Y. Qian, X. Su, submitted.
Intramolecular Orthogonal Reporters for Dissecting Oxidative Stress and Response (Research Square)
X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, submitted.
Planar 2D wireframe DNA origami
E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, Nucleic Acids Res. 50, D246–D252 (2022)
Nanobase.org: a repository for DNA and RNA nanostructures
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J. Yoo, S. Park, C. Maffeo, T. Ha, A. Aksimentiev, Nucleic Acids Res. 49, 11459–11475 (2021).
DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles
E. Lin-Shiao, W.G. Pfeifer, B.R. Shy, M. Saffari Doost, E. Chen, V.S. Vykunta, J.R. Hamilton, E.C. Stahl, D.M. Lopez, C.R. Sandoval Espinoza, A.E. Dejanov, R.J. Lew, M.G. Poirer, A. Marson, C.E. Castro, J.A. Doudna, Nucleic Acids Res. 50, 1256–1268 (2022)
CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells (bioRxiv)
J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, to appear in Energy Landscapes of Nanoscale Systems, ed. D.J. Wales, Frontiers of Nanoscience Vol. 21 (Elsevier)
Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling (arXiv)
Y. Deng, Y. Tan, L. Zhang, C. Zhang, X. Su, submitted.
Forecasting the reaction of DNA modifying enzymes on DNA nanostructures by coarse grained model for stimuli-responsive drug delivery (Research Square)
D. Smith and G. Tikhomirov, submitted.
small: A programmatic nanostructure design and modelling environment (arXiv)
S. Assenza and R. Pérez, submitted.
Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA (biorXiv)
D. Kuťák, E. Poppleton, H. Miao, P. Šulc and I. Barišić, Molecules 27, 63 (2022)
Unified Nanotechnology Format: One Way to Store Them All
M. Centola, E. Poppleton, M. Centola, J. Valero, P. Šulc and M. Famulok, submitted.
A rhythmically pulsing leaf-spring nanoengine that drives a passive follower (biorXiv)
C.K. Wong and J.P.K. Doye, submitted
The free-energy landscape of a mechanically bistable DNA origami (arXiv)
L. Zhang, J. Chen, M. He, X. Su, Exploration 2, 20210265 (2022)
Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection
F. Mambretti, N. Pedrani, L. Casiraghi, E. M. Paraboschi, T. Bellini, S. Suweis, submitted
OxDNA to study species interactions (arXiv)
Y.A.G. Fosado, submitted
Nanostars planarity modulates the elasticity of DNA hydrogels (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)
Structure-Guided Designing Pre-Organization in Bivalent Aptamers
L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, Sci. Adv. 8, eabm9530 (2022)
A localized DNA finite-state machine with temporal resolution

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

@@ Line 345: / Line 345: @@
 # Y.A.G. Fosado, submitted
 #: 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)
+#: [https://doi.org/10.1021/jacs.1c12593 Structure-Guided Designing Pre-Organization in Bivalent Aptamers]
+# L. Liu F. Hong H. Liu X. Zhou S. Jiang P. Šulc J.-H. Jiang and H. Yan, ''Sci. Adv.'' '''8''', eabm9530 (2022)
+#: [https://doi.org/10.1126/sciadv.abm9530 A localized DNA finite-state machine with temporal resolution]
 We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Publications: Difference between revisions

Revision as of 12:01, 29 March 2022

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