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 (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. 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)

10. T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ACS Nano (2013)

    Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker

11. T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye, A. A. Louis, Nucleic Acids Res., (2013)

    DNA hybridization kinetics: zippering, internal displacement and sequence dependence (arXiv)

12. 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 (2013)

    Coarse-graining DNA for simulations of DNA nanotechnology (arXiv)

13. N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, E. Winfree, Nucleic Acids Res., (2013)

    On the biophysics and kinetics of toehold-mediated DNA strand displacement

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

    Accurate phase diagram of tetravalent DNA nanostars (arXiv)

15. L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1 (2015)

    A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)

16. 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)

17. L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ACS Nano, (2014)

    Gels of DNA Nanostars Never Crystallise

18. 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)

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

    Modeling DNA Thermodynamics under Torsional Stress

20. J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, arxiv (2014)

    DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

21. R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, Nature Comm. (2014)

    Programmable energy landscapes for kinetic control of DNA strand displacement

22. 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)

23. P. Krstić, B. Ashcroft and S. Lindsay, Nanotechnology, (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, arxiv (2014)

    Characterizing the bending and flexibility induced by bulges in DNA duplexes

26. M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge arxiv (2015)

    Force-induced rupture of a DNA duplex

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, iss. 5, 1238-1247 (2015)

    Modelling toehold-mediated RNA strand displacement (arXiv)

29. Benedict E. K. Snodin, Ferdinando Randisi, Majid Mosayebi, Petr Šulc, John S. Schreck, Flavio Romano, Thomas E. Ouldridge, Roman Tsukanov, Eyal Nir, Ard A. Louis, Jonathan P. K. Doye, arxiv (2015)

    Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)