Difference between revisions of "Publications"

From OxDNA
m
Line 39: Line 39:
 
#  J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, ''arxiv'' (2014)
 
#  J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J.P.K. Doye, ''arxiv'' (2014)
 
#:[http://arxiv.org/abs/1408.4401 DNA hairpins primarily promote duplex melting rather than inhibiting hybridization]
 
#:[http://arxiv.org/abs/1408.4401 DNA hairpins primarily promote duplex melting rather than inhibiting hybridization]
#  T. E. Ouldridge, ''arxiv'' (2014)
 
#:[http://arxiv.org/abs/1411.1927 DNA nanotechnology: understanding and optimisation through simulation]
 
 
#  R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, ''Nature Comm.'' (2014)
 
#  R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, ''Nature Comm.'' (2014)
 
#:[http://www.nature.com/ncomms/2014/141110/ncomms6324/full/ncomms6324.html Programmable energy landscapes for kinetic control of DNA strand displacement]
 
#:[http://www.nature.com/ncomms/2014/141110/ncomms6324/full/ncomms6324.html 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)
 
# M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis, J. P. K. Doye, ''J. Phys. Chem. B'' '''118''', 14326-14335 (2014)
 
#:[http://arxiv.org/ct?url=http%3A%2F%2Fdx.doi.org%2F10%252E1021%2Fjp510061f&v=13bb91c1 The role of loop stacking in the dynamics of DNA hairpin formation] ([http://arxiv.org/abs/1410.1218 arXiv])
 
#:[http://arxiv.org/ct?url=http%3A%2F%2Fdx.doi.org%2F10%252E1021%2Fjp510061f&v=13bb91c1 The role of loop stacking in the dynamics of DNA hairpin formation] ([http://arxiv.org/abs/1410.1218 arXiv])
# P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis  ''arxiv'' (2014)
 
#:[http://arxiv.org/abs/1411.3239 Modelling toehold-mediated RNA strand displacement]
 
 
# P. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', (2015)
 
# P. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', (2015)
 
#:[http://dx.doi.org/10.1088/0957-4484/26/8/084001 Physical model for recognition tunneling]
 
#:[http://dx.doi.org/10.1088/0957-4484/26/8/084001 Physical model for recognition tunneling]
Line 57: Line 53:
 
# T. E. Ouldridge, ''Mol. Phys.'' '''113''', 1-15 (2015)
 
# T. E. Ouldridge, ''Mol. Phys.'' '''113''', 1-15 (2015)
 
#:[http://www.tandfonline.com/doi/abs/10.1080/00268976.2014.975293 DNA nanotechnology: understanding and optimisation through simulation] ([http://arxiv.org/abs/1411.1927 arXiv])
 
#:[http://www.tandfonline.com/doi/abs/10.1080/00268976.2014.975293 DNA nanotechnology: understanding and optimisation through simulation] ([http://arxiv.org/abs/1411.1927 arXiv])
 +
# P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis  ''Biophys. J.'' '''Vol 108, iss. 5''' (2015)
 +
#:[http://dx.doi.org/10.1016/j.bpj.2015.01.023 Modelling toehold-mediated RNA strand displacement] ([http://arxiv.org/abs/1411.3239 arXiv])

Revision as of 17:31, 10 March 2015

  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. Vol 108, iss. 5 (2015)
    Modelling toehold-mediated RNA strand displacement (arXiv)