OxDNA - User contributions [en]

Publications

2015-12-11T14:58:26Z

Romanof:

#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#:[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
#T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
#:[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 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)
#:[http://jcp.aip.org/resource/1/jcpsa6/v136/i21/p215102_s1 The effect of topology on the structure and free energy landscape of DNA kissing complexes] ([http://arxiv.org/abs/1203.3577 arXiv])
#C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, ''Soft Matter'' '''8''', 8388 (2012)
#:[http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25845e Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link] ([http://arxiv.org/abs/1204.0985 arXiv])
#C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, ''J. Phys. Chem. B'' '''116''', 1161-11625 (2012)
#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#:[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#:[http://jcp.aip.org/resource/1/jcpsa6/v138/i8/p085101_s1 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
#P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, ''Natural Computing'' '''13''', 535 (2014)
#:[http://link.springer.com/article/10.1007%2Fs11047-013-9391-8 Simulating a burnt-bridges DNA motor with a coarse-grained DNA model] ([http://arxiv.org/abs/1212.4536 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)
#:[http://pubs.acs.org/doi/abs/10.1021/nn3058483 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.'' (2013)
#:[http://nar.oxfordjournals.org/content/early/2013/08/08/nar.gkt687 DNA hybridization kinetics: zippering, internal displacement and sequence dependence] ([http://arxiv.org/abs/1303.3370 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)
#:[http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp53545b#!divAbstract Coarse-graining DNA for simulations of DNA nanotechnology] ([http://arxiv.org/abs/1308.3843 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.'', (2013)
#:[http://nar.oxfordjournals.org/content/early/2013/09/07/nar.gkt801.full?sid=762d341b-b72f-4a09-9235-20ad3ef8aeed On the biophysics and kinetics of toehold-mediated DNA strand displacement]
#L. Rovigatti, F. Bomboi, F. Sciortino, ''J. Chem. Phys.'' '''140''', 154903 (2014)
#:[http://dx.doi.org/10.1063/1.4870467 Accurate phase diagram of tetravalent DNA nanostars] ([http://arxiv.org/abs/1401.2837 arXiv])
# 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])
#P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''140''', 235102 (2014)
#:[http://scitation.aip.org/content/aip/journal/jcp/140/23/10.1063/1.4881424 A nucleotide-level coarse-grained model of RNA] ([http://arxiv.org/abs/1403.4180 arXiv])
#L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ''ACS Nano'' '''8''', 3567-3574 (2014)
#:[http://pubs.acs.org/doi/abs/10.1021/nn501138w Gels of DNA Nanostars Never Crystallise]
#C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, ''Sci. Rep.'', '''5''', 7655 (2015)
#:[http://dx.doi.org/10.1038/srep07655 Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA] ([http://arxiv.org/abs/1404.2869 arXiv])
#Q. Wang, B. M. Pettitt, ''Biophys. J.'' '''106''', 1182–1193 (2014)
#:[http://www.sciencedirect.com/science/article/pii/S0006349514000927 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)
#:[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)
#:[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)
#:[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. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', (2015)
#:[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)
#:[http://dx.doi.org/10.1103/PhysRevLett.114.078104 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)
#:[http://scitation.aip.org/content/aip/journal/jcp/142/16/10.1063/1.4917199 Characterizing the bending and flexibility induced by bulges in DNA duplexes] ([http://arxiv.org/abs/1412.6309 arXiv])
# M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ''arxiv'' (2015)
#:[http://arxiv.org/abs/1502.03623 Force-induced rupture of a DNA duplex]
# 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])
# P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, ''Biophys. J.'' '''108''', iss. 5, 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])
# 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)
#:[http://scitation.aip.org/content/aip/journal/jcp/142/23/10.1063/1.4921957 Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/1504.00821 arXiv])
# C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''143''', 243122 (2015)
#:[http://dx.doi.org/10.1063/1.4933066 Coarse-grained modelling of supercoiled RNA] ([http://arxiv.org/abs/1506.02539 arXiv])
# R. M. Harryson, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, ''arXiv'' (2015)
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
# R. M. Harryson, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, ''arXiv'' (2015)
#:[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)
#:[http://dx.doi.org/10.1126/science.aab2666 Base triplet stepping by the Rad51/RecA family of recombinases]

Publications

2015-12-11T14:51:52Z

Romanof:

#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#:[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
#T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
#:[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 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)
#:[http://jcp.aip.org/resource/1/jcpsa6/v136/i21/p215102_s1 The effect of topology on the structure and free energy landscape of DNA kissing complexes] ([http://arxiv.org/abs/1203.3577 arXiv])
#C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, ''Soft Matter'' '''8''', 8388 (2012)
#:[http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25845e Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link] ([http://arxiv.org/abs/1204.0985 arXiv])
#C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, ''J. Phys. Chem. B'' '''116''', 1161-11625 (2012)
#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#:[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#:[http://jcp.aip.org/resource/1/jcpsa6/v138/i8/p085101_s1 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
#P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, ''Natural Computing'' '''13''', 535 (2014)
#:[http://link.springer.com/article/10.1007%2Fs11047-013-9391-8 Simulating a burnt-bridges DNA motor with a coarse-grained DNA model] ([http://arxiv.org/abs/1212.4536 arXiv])
#T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ''ACS Nano'' (2013)
#:[http://pubs.acs.org/doi/abs/10.1021/nn3058483 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.'' '''7''', 2479-2490 (2013)
#:[http://nar.oxfordjournals.org/content/early/2013/08/08/nar.gkt687 DNA hybridization kinetics: zippering, internal displacement and sequence dependence] ([http://arxiv.org/abs/1303.3370 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'' (2013)
#:[http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp53545b#!divAbstract Coarse-graining DNA for simulations of DNA nanotechnology] ([http://arxiv.org/abs/1308.3843 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.'', (2013)
#:[http://nar.oxfordjournals.org/content/early/2013/09/07/nar.gkt801.full?sid=762d341b-b72f-4a09-9235-20ad3ef8aeed On the biophysics and kinetics of toehold-mediated DNA strand displacement]
#L. Rovigatti, F. Bomboi, F. Sciortino, ''J. Chem. Phys.'' '''140''', 154903 (2014)
#:[http://dx.doi.org/10.1063/1.4870467 Accurate phase diagram of tetravalent DNA nanostars] ([http://arxiv.org/abs/1401.2837 arXiv])
# 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])
#P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''140''', 235102 (2014)
#:[http://scitation.aip.org/content/aip/journal/jcp/140/23/10.1063/1.4881424 A nucleotide-level coarse-grained model of RNA] ([http://arxiv.org/abs/1403.4180 arXiv])
#L. Rovigatti, F. Smallenburg, F. Romano, F. Sciortino, ''ACS Nano'', (2014)
#:[http://pubs.acs.org/doi/abs/10.1021/nn501138w Gels of DNA Nanostars Never Crystallise]
#C. Matek, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, ''Sci. Rep.'', '''5''', 7655 (2015)
#:[http://dx.doi.org/10.1038/srep07655 Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA] ([http://arxiv.org/abs/1404.2869 arXiv])
#Q. Wang, B. M. Pettitt, ''Biophys. J.'' '''106''', 1182–1193 (2014)
#:[http://www.sciencedirect.com/science/article/pii/S0006349514000927 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)
#:[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.'' (2014)
#:[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)
#:[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. Krstić, B. Ashcroft and S. Lindsay, ''Nanotechnology'', (2015)
#:[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)
#:[http://dx.doi.org/10.1103/PhysRevLett.114.078104 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)
#:[http://scitation.aip.org/content/aip/journal/jcp/142/16/10.1063/1.4917199 Characterizing the bending and flexibility induced by bulges in DNA duplexes] ([http://arxiv.org/abs/1412.6309 arXiv])
# M. Mosayebi, A. A. Louis, J.P.K. Doye, T. E. Ouldridge ''arxiv'' (2015)
#:[http://arxiv.org/abs/1502.03623 Force-induced rupture of a DNA duplex]
# 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])
# P. Šulc, T. E. Ouldridge, F. Romano, J.P.K. Doye, A. A. Louis, ''Biophys. J.'' '''108''', iss. 5, 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])
# 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)
#:[http://scitation.aip.org/content/aip/journal/jcp/142/23/10.1063/1.4921957 Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/1504.00821 arXiv])
# C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''143''', 243122 (2015)
#:[http://dx.doi.org/10.1063/1.4933066 Coarse-grained modelling of supercoiled RNA] ([http://arxiv.org/abs/1506.02539 arXiv])
# R. M. Harryson, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, ''arXiv'' (2015)
#:[http://arxiv.org/abs/1506.09005 Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"]
# R. M. Harryson, F. Romano, T. E. Ouldridge, A. A. Louis, J.P.K. Doye, ''arXiv'' (2015)
#:[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)
#:[http://dx.doi.org/10.1126/science.aab2666 Base triplet stepping by the Rad51/RecA family of recombinases]