Publications: Difference between revisions

From OxDNA
Jump to navigation Jump to search
No edit summary
No edit summary
Line 35: Line 35:
#  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)
#  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)
#:[http://nar.oxfordjournals.org/content/43/13/6181 DNA hairpins primarily promote duplex melting rather than inhibiting hybridization] ([http://arxiv.org/abs/1408.4401 arXiv])
#:[http://nar.oxfordjournals.org/content/43/13/6181 DNA hairpins primarily promote duplex melting rather than inhibiting hybridization] ([http://arxiv.org/abs/1408.4401 arXiv])
# R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, ''Nature Comm.'' '''5''', (2014)
# R. Machinek, T.E. Ouldridge, N.E.C. Haley, J. Bath, A. J. Turberfield, ''Nature Comm.'' '''5''', 5324 (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)
Line 43: Line 43:
# L. Rovigatti, P. Šulc, I. Reguly, F. Romano, ''J. Comput. Chem.'', '''36''', 1 (2015)
# L. Rovigatti, P. Šulc, I. Reguly, F. Romano, ''J. Comput. Chem.'', '''36''', 1 (2015)
#:[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23763/pdf A comparison between parallelization approaches in molecular dynamics simulations on GPUs] ([http://arxiv.org/abs/1401.4350 arXiv])
#:[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23763/pdf A comparison between parallelization approaches in molecular dynamics simulations on GPUs] ([http://arxiv.org/abs/1401.4350 arXiv])
# P. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', (2015)
# P. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', '''26''', 084001 (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]
# F. Romano and F. Sciortino, ''Phys. Rev. Lett.'' '''114''', 078104 (2015)
# F. Romano and F. Sciortino, ''Phys. Rev. Lett.'' '''114''', 078104 (2015)
Line 53: 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.'' '''108''', iss. 5, 1238-1247 (2015)
# P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis,  ''Biophys. J.'' '''108''', 1238-1247 (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])
#:[http://dx.doi.org/10.1016/j.bpj.2015.01.023 Modelling toehold-mediated RNA strand displacement] ([http://arxiv.org/abs/1411.3239 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)
# 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)
Line 64: Line 64:
#:[http://arxiv.org/abs/1506.09008 Coarse-grained modelling of strong DNA bending II: Cyclization]
#:[http://arxiv.org/abs/1506.09008 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)
# 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]
#:[http://dx.doi.org/10.1126/science.aab2666  Base triplet stepping by the Rad51/RecA family of recombinases
# P. Krstić, B. Ashcroft, S. Lindsay, ''Nanotechnology'' '''26''', (2015)
#:[http://iopscience.iop.org/article/10.1088/0957-4484/26/8/084001/meta  Physical model for recognition tunneling]
# B.E.K. Snodin, F. Romano, L. Rovigatti, T.E. Ouldridge, A.A. Louis, J.P.K. Doye, ''ACS Nano'' '''10''', 1724-1737 (2016)
# B.E.K. Snodin, F. Romano, L. Rovigatti, T.E. Ouldridge, A.A. Louis, J.P.K. Doye, ''ACS Nano'' '''10''', 1724-1737 (2016)
#:[http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp53545b#!divAbstract Direct Simulation of the Self-Assembly of a Small DNA Origami]
#:[http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp53545b#!divAbstract Direct Simulation of the Self-Assembly of a Small DNA Origami]

Revision as of 21:19, 13 February 2017

  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 (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
Retrieved from "https://dna.physics.ox.ac.uk/index.php?title=Publications&oldid=1039"