Publications

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. 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)
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, arXiv (2015)
Coarse-grained modelling of strong DNA bending II: Cyclization
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
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, 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, Nucl. 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)
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, Nucl. 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
B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucl. Acids Res. 46, 538-545 (2018)
Rolling circle amplification shows a sinusoidal template length-dependent amplification bias
D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, Nucl. Acids Res. 46, 1553-1561 (2018)
DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size
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, submitted
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, E. Carlon, submitted
Bend-induced twist waves and the structure of nucleosomal DNA (arXiv)
M.M.C. Tortora and J.P.K. Doye, Mol. Phys., 116 accepted (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, Just Accepted Manuscript (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
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, (2018)
DNA scaffolds support stable and uniform peptide nanopores
L. Coronel, A. Suma and C. Micheletti, submitted
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 http://dx.doi.org/10.1038/s41598-018-25270-6]

Publications

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