Publications

1. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010)

   DNA Nanotweezers Studied with a Coarse-Grained Model of DNA (arXiv)

2. T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)

   Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)

3. T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.

   Coarse-grained modelling of DNA and DNA self-assembly

4. 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)

5. 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)

6. 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)

7. 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)

8. 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)

9. 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

10. 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)

11. 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)

12. 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

13. 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)

14. L. Rovigatti, F. Bomboi, F. Sciortino, J. Chem. Phys. 140, 154903 (2014)

    Accurate phase diagram of tetravalent DNA nanostars (arXiv)

15. 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)

16. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano 8, 3567-3574 (2014)

    Gels of DNA Nanostars Never Crystallise

17. Q. Wang, B. M. Pettitt, Biophys. J. 106, 1182–1193 (2014)

    Modeling DNA Thermodynamics under Torsional Stress

18. 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)

19. 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

20. 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)

21. 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)

22. 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)

23. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, 26, 084001 (2015)

    Physical model for recognition tunneling

24. F. Romano and F. Sciortino, Phys. Rev. Lett. 114, 078104 (2015)

    Switching Bonds in a DNA Gel: An All-DNA Vitrimer

25. 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)

26. 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)

27. T. E. Ouldridge, Mol. Phys. 113, 1-15 (2015)

    DNA nanotechnology: understanding and optimisation through simulation (arXiv)

28. 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)

29. 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)

30. 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)

31. 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"

32. 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

33. 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)

    [http://dx.doi.org/10.1126/science.aab2666 Base triplet stepping by the Rad51/RecA family of recombinases

34. 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

35. 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

36. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)

    [http://dx.doi.org/10.1021/acsnano.5b07664 Characterizing DNA star-tile-based nanostructures using a coarse-grained model